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Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets, and small-molecule and biological therapeutics and to identify new marker-driven cancer dependencies. To improve our understanding of the molecular features that contribute to cancer phenotypes, including drug responses, here we have expanded the characterizations of cancer cell lines to include genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cell lines from individuals of various lineages and ethnicities. Integration of these data with functional characterizations such as drug-sensitivity, short hairpin RNA knockdown and CRISPR–Cas9 knockout data reveals potential targets for cancer drugs and associated biomarkers. Together, this dataset and an accompanying public data portal provide a resource for the acceleration of cancer research using model cancer cell lines. The original Cancer Cell Line Encyclopedia (CCLE) is expanded with deeper characterization of over 1,000 cell lines, including genomic, transcriptomic, and proteomic data, and integration with drug-sensitivity and gene-dependency data.

Though the added value of proteomic measurements to gene expression profiling has been demonstrated, profiling of gene expression on its own remains the dominant means of understanding cellular responses to perturbation. Direct protein measurements are typically limited due to issues of cost and scale; however, the recent development of high-throughput, targeted sentinel mass spectrometry assays provides an opportunity for proteomics to contribute at a meaningful scale in high-value areas for drug development. To demonstrate the feasibility of a systematic and comprehensive library of perturbational proteomic signatures, we profiled 90 drugs (in triplicate) in six cell lines using two different proteomic assays -- one measuring global changes of epigenetic marks on histone proteins and another measuring a set of peptides reporting on the phosphoproteome -- for a total of more than 3,400 samples. This effort represents a first-of-its-kind resource for proteomics. The majority of tested drugs generated reproducible responses in both phosphosignaling and chromatin states, but we observed differences in the responses that were cell line- and assay-specific. We formalized the process of comparing response signatures within the data using a concept called connectivity, which enabled us to integrate data across cell types and assays. Furthermore, it facilitated incorporation of transcriptional signatures. Consistent connectivity among cell types revealed cellular responses that transcended cell-specific effects, while consistent connectivity among assays revealed unexpected associations between drugs that were confirmed by experimental follow-up. We further demonstrated how the resource could be leveraged against public domain external datasets to recognize therapeutic hypotheses that are consistent with ongoing clinical trials for the treatment of multiple myeloma and acute lymphocytic leukemia (ALL). These data are available for download via the Gene Expression Omnibus (accession GSE101406), and web apps for interacting with this resource are available at https://clue.io/proteomics.

Background. Metamodels can simplify complex health policy models and yield instantaneous results to inform policy decisions. We investigated the predictive validity of linear regression metamodels used to support a real-time decision-making tool that compares infant HIV testing/screening strategies. Methods. We developed linear regression metamodels of the Cost-Effectiveness of Preventing AIDS Complications Pediatric (CEPAC-P) microsimulation model used to predict life expectancy and lifetime HIV-related costs/person of two infant HIV testing/screening programs in South Africa. Metamodel performance was assessed with cross-validation and Bland-Altman plots, showing between-method differences in predicted outcomes against their means. Predictive validity was determined by the percentage of simulations in which the metamodels accurately predicted the strategy with the greatest net health benefit (NHB) as projected by the CEPAC-P model. We introduced a zone of indifference and investigated the width needed to produce between-method agreement in 95% of the simulations. We also calculated NHB losses from “wrong” decisions by the metamodel. Results. In cross-validation, linear regression metamodels accurately approximated CEPAC-P-projected outcomes. For life expectancy, Bland-Altman plots showed good agreement between CEPAC-P and the metamodel (within 1.1 life-months difference). For costs, 95% of between-method differences were within $65/person. The metamodels predicted the same optimal strategy as the CEPAC-P model in 87.7% of simulations, increasing to 95% with a zone of indifference of 0.24 life-months ( ∼ 7 days). The losses in health benefits due to “wrong” choices by the metamodel were modest (range: 0.0002–1.1 life-months). Conclusions. For this policy question, linear regression metamodels offered sufficient predictive validity for the optimal testing strategy as compared with the CEPAC-P model. Metamodels can simulate different scenarios in real time, based on sets of input parameters that can be depicted in a widely accessible decision-support tool.