In this analysis mutation is defined as either the presence of a specific gene fusion, a sequence change or a copy number change across 84 cancer genes. Cell Culture Neuroblastoma cell lines were maintained in DMEM (Cellgro, Manassas, VA, USA) supplemented with UNC0321 10% fetal bovine serum (Sigma-Aldrich, St. in patients with neuroblastoma. and in mouse models (7C12). While disease-specific indications for drugs modifying epigenetic regulators have been uncovered, precise genomic biomarkers predictive of treatment response remain elusive. To date, the best validated genetic predictor of response to BET inhibitors is in a rare genetically-defined subset of poorly differentiated squamous cell carcinomas (NUT midline carcinoma), where the presence of recurrent t(15;19) chromosomal translocation results in the expression of the twin N-terminal bromodomains of BRD4 as an in-frame fusion with the NUT protein (13). High-throughput pharmacogenomic profiling offers the opportunity to reveal new insights into selective responses to drugs in defined cancer genotypes. Initial efforts to connect drug response with genotype in the NCI60 cell line panel have since been expanded to screening campaigns in large panels of genetically characterized cancer cell lines (14C17). These efforts have revealed both expected and unexpected connections. For example, the anticipated response to UNC0321 ALK inhibitors in tumors with aberrant ALK activation, such as lymphoma, non-small cell lung cancer, and neuroblastoma, was demonstrated in a screen of over 600 tumor cell lines (15). More recently, the unexpected connections between response to poly (ADP-ribose) polymerase (PARP) inhibitors and expression of the EWS/FLI fusion protein in Ewing sarcoma was elucidated in a screen of 130 drugs in over 600 cancer cell lines (16). In an independent study of 24 anti-cancer drugs in 479 human cancer cell lines, new connections were also observed between small-molecule sensitivities and cell lineage, gene expression, and genotype (17). We performed a high-throughput pharmacogenomic screen to identify biomarkers of response to BET bromodomain inhibitors. The prototype ligand JQ1, a novel thieno-triazolo-1,4-diazepine, which displaces BET bromodomains from chromatin by competitively binding to the acetyl lysine recognition pocket, has been validated in numerous models, nominating it as an excellent chemical probe for UNC0321 high-throughput screening (7C10). In this study, we therefore queried a large compendium of genetically characterized tumor cell lines to identify predictors of sensitivity to JQ1. We identified amplification Acvrl1 as a top predictive marker of response to JQ1 treatment and characterized the mechanistic and translational significance of this finding in neuroblastoma, the most common extra-cranial solid tumor diagnosed in children, and a cancer notable for frequent amplification in patients with high-risk disease. Results High-throughput Pharmacogenomic Profiling Reveals Amplification as a Predictor of Response to Bromodomain Inhibitors We first conducted an unbiased screen of a collection of 673 genetically characterized tumor derived cell lines (16) to understand response and resistance to BET bromodomain inhibition, so as to discover new opportunities for therapeutic development. Cell lines with response to JQ1 yielding IC50 1 M and Emax 70 %70 % were designated as sensitive and all other were designated as resistant in a stringent classification schema. Cell lines arising from the pediatric solid tumor of neural crest origin, neuroblastoma, were identified as among the most JQ1-sensitive and UNC0321 amplification as the most predictive marker of sensitivity; four cell lines out of the 99 sensitive cell lines are amplified and zero lines out of the 237 resistant cell lines are amplified. The two-tailed Fisher exact test returns a P value of 0.007 (Fig. 1ACB and Supplementary Table S1). We next determined expression level of in the neuroblastoma cell lines from the primary screen (Supplementary Fig. S1A) and evaluated the correlation of MYCN protein levels with JQ1 response. MYCN protein level is also substantially correlated with response to JQ1 treatment (Fig. 1C). Open in a separate window Figure 1 amplification based UNC0321 on SNP 6.0 arrays and/or high levels of protein expression. Black dots indicate neuroblastoma cell lines wildtype for and poor MYCN expression. Drug response is presented as the natural log of the half-maximal effective concentration [Ln(IC50)], plotted against the maximum effect corresponding to the minimum measured viability (Emax). (B) Distribution of Emax and Ln(IC50) for wildtype versus amplified cancer cell lines based on SNP 6.0 copy number analysis. P.