Cell surface proteins are a rich source for druggable targets of immune and targeted therapy. By systematically integrating multidenominational studies on the genome, functionome and druggome, we comprehensively annotated and characterized the genes encoding cell surface proteins (GESPs) across cancers for expression, recurrent genomic alteration, growth dependency, receptor-ligand interactions, and therapeutic potential. We found that mRNA expression of GESPs is highly cancer type specific and positively correlated with protein expression. Large percentage of GESPs exhibit recurrent genomic alterations, serving as targetable cancer drivers. Certain subgroups of GESPs function as common or selective essential genes for in vitro tumor cell growth. We predicted 1,278 receptor-ligand interactions, many of them are remarkably dysregulated in cancer. Using systems biology approaches, GESPs with therapeutic potential were identified for each cancer type, including 409 cancer specific GESPs. We have made this resource available in the Cancer Surfaceome Atlas (TCSA) through the Functional Cancer Genome data portal.
This repository contains analysis code for the following paper: Hu and Yuan, et al. (2021) Systematic characterization of the surfaceome across human cancers. Nature Cancer.
Figure1_GESPscore.xlsx reproduces high confidence surfaceome candidates from nine complementary surfaceome resources.
Figure2.R reproduces the core analysis in Figure 2.
Figure3.R reproduces the core analysis in Figure 3.
Figure4.R reproduces the core analysis in Figure 4.
Figure5.R reproduces the core analysis in Figure 5.
Figure6_logFDR.xlsx reproduces the correlations of expressions between lighand-receptor pairs.
Figure7.R reproduces the core analysis in Figure 7.
Figure8.R reproduces the core analysis in Figure 8.