A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations

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 B.; Gould, Joshua; Ko, Tak; Johnson, Sarah A.; Lahr, David L.; Lam, Daniel D.; Liu, Zihan; Lyons, Nicholas; Lü, Xiaodong; MacLean, Brendan; Mungenast, Alison E.; Officer, Adam; Natoli, Ted; Papanastasiou, Malvina; Patel, Jayvadan; 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.

doi:10.1016/j.cels.2018.03.012

Cited by 74 publications

(75 citation statements)

References 72 publications

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“…Data for the P100 assay were acquired in PRM or in DIA mode and analyzed using Skyline (23). A more detailed description of the different data processing steps, including the analysis of DIA data, are described in (24). We first normalized P100 probes to the DMSO control experiment, which was present in each 96 well plate, by subtracting the average log2 DMSO ratio followed by Z-score transformation (per sample column).…”

Section: Methodsmentioning

confidence: 99%

A Curated Resource for Phosphosite-specific Signature Analysis

Krug

Mertins

Zhang

et al. 2019

Molecular & Cellular Proteomics

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In BriefPathway analysis of PTM data sets is typically performed at a gene-centric level because of the lack of appropriately curated PTM signature databases. We have developed a PTM signatures database (PTMsigDB) providing curated phosphorylation signatures of kinases, perturbations and signaling pathways to enable site-specific PTM signature enrichment analysis (PTM-SEA). Application of PTM-SEA to phosphoproteomes of several cell lines perturbed with growth factors, cell cycle inhibitors, or a specific PI3K inhibitor demonstrated the potential of our site centric approach to study dysregulated pathways in cancers. Graphical Abstract Highlights• Database of PTM site-specific phosphorylation signatures of kinases, perturbations and signaling pathways (PTMsigDB).• PTM signature enrichment analysis (PTM-SEA) outperformed gene-centric analysis in detection of EGF induced phospho signaling events.• PI3K perturbation signatures were readily detected in PI3Ka inhibited human breast cancer cells.• PTMsigDB and PTM-SEA can be freely accessed at https://github.com/broadinstitute/ssGSEA2.0.

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Section: Methodsmentioning

confidence: 99%

A Curated Resource for Phosphosite-specific Signature Analysis

Krug

Mertins

Zhang

et al. 2019

Molecular & Cellular Proteomics

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236

320

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“…In particular: achieving sufficient sensitivity to identify high coverage of key phosphorylation sites from the minimal amounts of protein material that can be retrieved from tumor biopsies; the throughput to process large numbers of patient samples; and the reproducibility to measure phosphorylation with high quantitative precision. Although several phosphoproteomics studies have demonstrated exquisite sensitivity (181) and the ability to measure hundreds of phosphosites in hundreds of samples (182), existing global phosphoproteomics workflows have not been sufficiently streamlined or robust to enable measurement of phosphoproteomes across very large numbers of samples at sufficient depth to cover key pathways and sites. To address this, we developed a phosphoproteomics workflow called "EasyPhos," which simplifies sample preparation to such an extent that it enables the measurement of hundreds of phosphoproteomes in cells and tissues, and with very high reproducibility such that metabolic or chemical labeling is often not required (183).…”

Section: The Druggable Phosphoproteomementioning

confidence: 99%

Illuminating the dark phosphoproteome

et al. 2019

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Protein phosphorylation is a major regulator of protein function and biological outcomes. This was first recognized through functional biochemical experiments, and in the past decade, major technological advances in mass spectrometry have enabled the study of protein phosphorylation on a global scale. This rapidly growing field of phosphoproteomics has revealed that more than 100,000 distinct phosphorylation events occur in human cells, which likely affect the function of every protein. Phosphoproteomics has improved the understanding of the function of even the most well-characterized protein kinases by revealing new downstream substrates and biology. However, current biochemical and bioinformatic approaches have only identified kinases for less than 5% of the phosphoproteome, and functional assignments of phosphosites are almost negligible. Notably, our understanding of the relationship between kinases and their substrates follows a power law distribution, with almost 90% of phosphorylation sites currently assigned to the top 20% of kinases. In addition, more than 150 kinases do not have a single known substrate. Despite a small group of kinases dominating biomedical research, the number of substrates assigned to a kinase does not correlate with disease relevance as determined by pathogenic human mutation prevalence and mouse model phenotypes. Improving our understanding of the substrates targeted by all kinases and functionally annotating the phosphoproteome will be broadly beneficial. Advances in phosphoproteomics technologies, combined with functional screening approaches, should make it feasible to illuminate the connectivity and functionality of the entire phosphoproteome, providing enormous opportunities for discovering new biology, therapeutic targets, and possibly diagnostics.

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“…Since proteins are the targets of most drugs, proteome responses can be more specific to drug action. One recent effort has focused on building a connectivity map based on phosphoproteomic and chromatin signatures, measuring the abundances of 100 phosphopeptides and 59 histone modifications for treatments with 90 drugs (4).…”

Section: Introductionmentioning

confidence: 99%

ProTargetMiner: A proteome signature library of anticancer molecules for functional discovery

Saei

Chernobrovkin

Sabatier

et al. 2018

Preprint

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We present a publicly available, expandable proteome signature library of anticancer molecules in A549 adenocarcinoma cells. Based on 287 proteomes affected by 56 drugs, the main dataset contains 7,328 proteins and 1,307,859 refined protein-drug pairs. By employing the specificity concept in partial least square modeling, deconvolution of drug targets and mechanistic proteins is achieved for most compounds, including some kinase inhibitors. We built the first protein co-regulation database that takes into account both protein expression and degradation. A surprising number of strong anti-correlations is found, underscoring the importance of protein repression in cell regulation. Our analysis uncovered a group of proteins with extremely steady expression which are likely essential for core cellular functions. These findings bring about deeper understanding of cell mechanics. Extension of the dataset to novel compounds will facilitate drug design. The introduced specificity concept and modeling scheme are beneficial in other analysis types as well.Statement of SignificanceProTargetMiner is the first of its kind library of proteome responses of human cancer cells to anticancer molecules. This expandable resource facilitates the deconvolution of drug targets, action mechanisms, and cellular effects. It reveals death modalities, uncovers protein co-regulation and anti-correlation networks and defines the “untouchable” proteome essential for core cellular functionalities.

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A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations

Cited by 74 publications

References 72 publications

A Curated Resource for Phosphosite-specific Signature Analysis

A Curated Resource for Phosphosite-specific Signature Analysis

Illuminating the dark phosphoproteome

ProTargetMiner: A proteome signature library of anticancer molecules for functional discovery

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