Abstract A1-45: In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals novel targeting opportunities
Authors: Rubio-Perez Carlota , Tamborero David , Schroeder Michael P. , Antolín Albert A. , Deu-Pons Jordi , Perez-Llamas Christian , Mestres Jordi , Gonzalez-Perez Abel , Lopez-Bigas Nuria 
Published: November 2015

The development of targeted therapies against altered driver proteins holds the promise of selectively and efficiently eliminating cancer cells. However, high intertumor heterogeneity is a major obstacle to develop and apply therapeutic targeted agents to treat most cancer patients. Here, we present the first large-scale therapeutic landscape of cancer as it stands today in a 6.792 sample cohort covering 28 tumor types.

To pursue this goal, we developed a three-step in silico drug prescription strategy. 1) To discover actionable driver events, we first comprehensively identified mutational cancer driver genes by detecting complementary signals of positive selection in the pattern of their mutations across the tumor cohorts. We also identified actionable copy number alteration (CNA) and fusion cancer driver genes. Second, we detected which of these driver genes would have an oncogenic role in the tumor and which ones would lose their function. With these two steps we generated the Drivers Database. 2) Next, we systematically gathered all information available on therapeutic agents; FDA approved and in clinical or pre-clinical stages. We considered three different types of targeting strategies for the cancer driver genes: direct targeting, indirect targeting and gene therapies in clinical trials. Moreover, we designed a set of rules for assigning therapeutic agents to specific genomic alterations beard for the driver genes. By doing this last step, we generated the Drivers Actionability Database. 3) Finally, by combining data of Drivers Database, Drivers Actionability Database and sample data, we developed in silico drug prescription, a novel approach to determine which of the drugs could benefit each of the tumor individuals.

In all, in the Driver Database we identified 460 mutational cancer driver genes acting in one or more of the tumor types along with 39 driver genes acting via CNAs or fusions. Fifty of these cancer driver genes are targeted by FDA approved agents, 63 by molecules currently in clinical trials and 74 are bound by pre-clinical ligands. We also identified 81 therapeutically unexploited targetable cancer genes. Lastly, by applying in silico drug prescription we found that only 6.7% of the patients could be treated following clinical guidelines, and were concentrated in only 6 tumor types. Moreover, considering repurposing strategies the fraction of patients that could benefit from FDA approved drugs would increase up to 40%, increasing remarkably the fraction of targetable patients in some tumor types like glioblastoma and thyroid cancer, and up to 72% if considering targeted therapies in clinical trials.

In summary, the in silico drug prescription based on Drivers and Drivers Actionability Databases was tested on one of the largest cohorts of tumor samples currently collected for research. The main result highlights the current scope of targeted anti-cancer therapies and its prospects for growth in view of the drugs that are currently in clinical trials or at pre-clinical stages. Additionally, another important output of this work is a ranked list of novel target opportunities for anticancer drug development. Continuous update of drug-target interactions information, and the application of the strategy to larger cohorts, will improve the in silico prescription rules contained within the two databases, thus enhancing its usefulness within personalized cancer medicine.

Citation Format: Carlota Rubio-Perez, David Tamborero, Michael P. Schroeder, Albert A. Antolín, Jordi Deu-Pons, Christian Perez-Llamas, Jordi Mestres, Abel Gonzalez-Perez, Nuria Lopez-Bigas. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals novel targeting opportunities. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-45.