A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations
Authors: Litichevskiy Lev , Peckner Ryan , Abelin Jennifer G. , Asiedu Jacob K. , Creech Amanda L. , Davis John F. , Davison Desiree , Dunning Caitlin M. , Egertson Jarrett D. , Egri Shawn , Gould Joshua , Ko Tak , Johnson Sarah A. , Lahr David L. , Lam Daniel , Liu Zihan , Lyons Nicholas J. , Lu Xiaodong , MacLean Brendan X. , Mungenast Alison E. , Officer Adam , Natoli Ted E. , Papanastasiou Malvina , Patel Jinal , Sharma Vagisha , Toder Courtney , Tubelli Andrew A. , Young Jennie Z. , Carr Steven A. , Golub Todd R. , Subramanian Aravind , MacCoss Michael J. , Tsai Li-Huei , Jaffe Jacob D. 
Published: September 2017

SummaryThough 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 athttps://clue.io/proteomics.HighlightsFirst-of-its-kind public resource of proteomic responses to systematically administered perturbagensDirect proteomic profiling of phosphosignaling and chromatin states in cells for 90 drugs in six different cell linesExtends Connectivity Map concept to proteomic data for integration with transcriptional dataEnables recognition of unexpected, cell type-specific activities and potential translational therapeutic opportunities