Analysis code for "A compendium of Amplification-Related Gain Of Sensitivity (ARGOS) genes in human cancer"

Chromosomal gains are among the most frequent somatic genetic alterations occurring in cancer. While the effect of sustained oncogene expression has been characterized, the impact of copy-number gains affecting collaterally-amplified “bystander” genes on cellular fitness remains less understood. To investigate this, we built a comprehensive map of dosage compensations across human cancers by integrating expression and copy number profiles from over 8,000 TCGA tumors and CCLE cell lines. Further, we analyzed the effect of gene overexpression across 17 human cancer ORF screens to provide an overview of genes that prove toxic to cancer cells when overexpressed. Combining these two independent approaches we propose a class of ‘Amplification-Related Gain Of Sensitivity’ (ARGOS) genes. These genes are located in commonly amplified regions of the genome, have lower expression levels than expected by their copy-number status, and are toxic to cancer cells when overexpressed. We experimentally validated CDKN1A and RBM14 as high-confidence pan-cancer ARGOS genes in lung and breast cancer cell line models. We additionally suggest that RBM14’s mechanism of toxicity involves altered DNA damage response and innate immune signaling processes following gene overexpression. Finally, we provide a comprehensive catalog of compensated, toxic, and ARGOS genes as a community resource.

Analysis directories

The main Analysis steps are performed in the following directories:

• data - Creating the analytical data sets
• model_compensation - The compensation analysis
• model_orf - The ORF toxicity analysis
• misc - Specific questions and reviewer requests
• report - The scripts to create all figures in the manuscript

Those can be run via the snakemake workflow manager once all dependencies are met.

All other directories contain analyses that are not part of the publication.

Dependencies

• All required R packages and their versions are listed in renv.lock.
• The ebits toolkit and setup according to the project README
• The ORF and TCGA data sets from their respective publications