Quantifying tumor specificity using Bayesian probabilistic modeling for drug and immunotherapeutic target discovery

In diseases such as cancer, the design of new therapeutic strategies requires extensive, costly, and unfortunately sometimes deadly testing to reveal life threatening off-target effects. We hypothesized that the disease specificity of targets can be systematically learned for all genes by jointly evaluating complementary molecular measurements of healthy tissues using a hierarchical Bayesian modeling approach. Our method, BayesTS, integrates protein and gene expression evidence and includes tunable parameters to moderate tissue essentiality. Applied to all protein coding genes, BayesTS outperforms alternative strategies to define therapeutic targets and nominates previously unknown targets while allowing for incorporation of new types of modalities. To expand target repertoires, we show that extension of BayesTS to splicing antigens and combinatorial target pairs results in more specific targets for therapy. We expect that BayesTS will facilitate improved target prioritization for oncology drug development, ultimately leading to the discovery of more effective and safer treatments.