Implementation of the NCI-60 Human Tumor Cell Line Panel to Screen 2260 Cancer Drug Combinations to Generate >3 Million Data Points Used to Populate a Large Matrix of Anti-Neoplastic Agent Combinations (ALMANAC) Database

Abstract

Animal and clinical studies demonstrate that cancer drug combinations (DCs) are more effective than single agents. However, it is difficult to predict which DCs will be more efficacious than individual drugs. Systematic DC high-throughput screening (HTS) of 100 approved drugs in the National Cancer Institute's panel of 60 cancer cell lines (NCI-60) produced data to help select DCs for further consideration. We miniaturized growth inhibition assays into 384-well format, increased the fetal bovine serum amount to 10%, lengthened compound exposure to 72 h, and used a homogeneous detection reagent. We determined the growth inhibition 50% values of individual drugs across 60 cell lines, selected drug concentrations for 4 × 4 DC matrices (DCMs), created DCM master and replica daughter plate sets, implemented the HTS, quality control reviewed the data, and analyzed the results. A total of 2620 DCMs were screened in 60 cancer cell lines to generate 3.04 million data points for the NCI ALMANAC (A Large Matrix of Anti-Neoplastic Agent Combinations) database. We confirmed in vitro a synergistic drug interaction flagged in the DC HTS between the vinca-alkaloid microtubule assembly inhibitor vinorelbine (Navelbine) tartrate and the epidermal growth factor-receptor tyrosine kinase inhibitor gefitinib (Iressa) in the SK-MEL-5 melanoma cell line. Seventy-five percent of the DCs examined in the screen are not currently in the clinical trials database. Selected synergistic drug interactions flagged in the DC HTS described herein were subsequently confirmed by the NCI in vitro, evaluated mechanistically, and were shown to have greater than single-agent efficacy in mouse xenograft human cancer models. Enrollment is open for two clinical trials for DCs that were identified in the DC HTS. The NCI ALMANAC database therefore constitutes a valuable resource for selecting promising DCs for confirmation, mechanistic studies, and clinical translation.

Cancer Cell Lines Are Useful Model Systems for Medical Research

“…The operation of this screen utilizes 60 different human tumor cell lines representing leukemia, melanoma, and cancers of the lung, colon, brain, ovary, breast, and prostate [35]. It is designed to screen up to 3000 small molecules (synthetic or purified natural products) per year for potential anticancer activity [36,37]. Over time, the NCI-60 project has served the global cancer research community and allowed for the identification of new important anticancer drugs, including paclitaxel, cisplatin, fludarabine, and others [38].…”

Drug synergy scoring using minimal dose response matrices

“…In support of the utility of minimal drug matrices, we recently used this approach in testing drug combinations in a panel of AML cell lines to identify a biomarker for drug synergy, which we confirmed in ex vivo experiments in patient-derived AML blasts (11). Furthermore, a pseudo-5×5 matrix (monotherapy dose-responses performed separately to a 4×4 combination matrix) has been successfully deployed in a large-scale drug combination screen in cancer cell lines (17), and the NCI-ALMANAC study also contains 4×4 drug matrices (18,19).…”

Maximizing the Value of Cancer Drug Screening in Multicellular Tumor Spheroid Cultures: A Case Study in Five Head and Neck Squamous Cell Carcinoma Cell Lines

“…Nineteen FDA-approved cancer drugs were obtained from commercial sources and shipped to the University of Pittsburgh by the National Cancer Institute (NCI) Developmental Therapeutics Program (DTP). 37,38 Supplemental Table S1 lists the 19 drugs, their mechanisms of action, and the cancers for they have been either approved or under evaluation in clinical trials. Five of the drugs are approved for HNC among other cancers.…”