Abstract 4936: An ultrahigh-throughput synergy screening platform enables discovery of novel drug combinations

Abstract

Abstract The battle against many cancers and infectious diseases has long been hindered due to the complexity of finding potent and effective drug combinations. With each new drug considered, the number of combinations to potentially test increases exponentially, posing substantial challenges in screening throughput. These challenges further intensify when accounting for the number of doses of each drug that need to be tested in a drug combination matrix (known as matrix density). There is a pressing need to screen large amounts of combinations at sufficient density to discover new therapies for diseases like cancer, but this has traditionally been out of reach. However, the recent widespread adoption of acoustic liquid handling robots has shown promise to overcome these obstacles by allowing for intricate drug screening template designs which were previously not possible to make. Despite these advances, the throughput achieved by these technologies has been limited due to lack of broadly accessible protocols and analytical tools for drug combination screening. We present Combocat, an end-to-end platform that allows for substantial increases in throughput of drug combination screens by combining experimental protocols that can be deployed for acoustic liquid handlers, machine learning algorithms for data imputation, and software that allows for in-depth analysis of results. We first generated a reference dataset of over 250,000 unique drug combination measurements in multiple cancer cell lines. The combination data were collected in a dense format (10×10 combination matrices) using a novel drug-drug template and achieved a dramatic increase in throughput compared to conventional methods. We then used this dataset to build a computational model which allowed us to accurately estimate drug combination effects using sparse measurements and imputing non-measured values with machine learning. The sparse measurements are collected in 1536-well microplates and substantially boost the throughput capabilities of drug-drug screens. As proof-of-concept, we used our method to screen a preclinical model of neuroblastoma with 9,045 drug combinations. This represents 10% the scale of the largest drug combination studies ever reported, achieved using a fraction of the resources, and in dense formats. We validated our findings by re-screening top hits using the fully-measured, non-imputed method and demonstrate the accuracy of our platform. The Combocat platform’s documentation and codebase is open-source, and we also make a GUI available for interactive exploration of screening results. By integrating advanced experimental and computational methods, we provide a generalizable pipeline that will expedite synergy screens and the drug combination discovery process for many diseases. Citation Format: William C. Wright, Paul Geeleher. An ultrahigh-throughput synergy screening platform enables discovery of novel drug combinations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4936.