LINCS PCCSE GCP 2020

Global Chromatin Profiling Dataset of Chemical Perturbations in Multiple Biological Backgrounds

  • Organism: Homo sapiens
  • Instrument: Q Exactive Plus
  • SpikeIn: Yes
  • Keywords: Targeted mass spectrometry, proteomics, histones, epigenetics, post-translational modification
  • Lab head: Malvina Papanastasiou
Abstract
The Library of Integrated Network-based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The goal of this project is to test the hypothesis that modulation of phosphorylation-mediated signaling events in response to perturbations can establish new cellular states by altering their epigenetic landscape. We have performed mass spectrometry (MS)-based proteomic assays that target quantitative readouts of phospho-signaling and chromatin modifications in cellular models, following perturbation by compounds with varying mechanisms of action. We have employed 128 compounds and treated 5 cancer and 2 neuronal cell lines. The resulting data collected and tools created have been contributed to the LINCS program for the purpose of making connections among disparate perturbations through phosphoproteomics and chromatin modification signatures in concert with other available data types. The data is publicly available on PanoramaPublic and can be queried using Clue (Broad Institute). Analysis of our data will inform novel therapeutic opportunities and synergies, as dysregulation of phospho-signaling and epigenetic systems are two of the most common molecular etiologies identified in a growing number of diseases.
Experiment Description
Detailed GCP protocols can be found in Creech et al., 2015, Methods and online at https://panoramaweb.org/wiki/LINCS/Overview%20Information/page.view?name=sops. Cells were washed with PBS and frozen immediately after drug treatment (24 hrs). Nuclei were extracted from cells using the classic low-detergent lysis method (0.3% NP-40). Histones were extracted from the nuclei with 0.4 N H2SO4 and solubilized histones were precipitated from solution using 20% w/v trichloroacetic acid. Following isolation, 10 μg of histone proteins were chemically propionylated with NHS-propionate, cleaned using reversed phase SPE cartridges, and digested overnight with trypsin. Peptides were then propionylated again to block nascent N-termini. Finally, a cocktail of isotopically-labeled heavy peptides were spiked into each sample to allow for quantitation and cross-sample comparisons. Samples were analyzed using liquid-chromatography mass spectrometry. Samples were injected using a targeted acquisition method to monitor for the presence of defined combinatorial forms of modified histone peptides. Results were analyzed independently using Skyline software package (MacLean et al., 2014) as described in (Creech et al. 2015).
Sample Description
Drug signatures were profiled in various cancer cell lines (A375, YAPC, A549, MCF7, and PC3) and neuronal cell models (Astrocytes & NPCs). Drugs were grouped into four tranches: epigenetically active, neuroactive, kinase inhibitors and cardiotoxic compounds. A detailed description of their mechanism of action can be found online at https://panoramaweb.org/wiki/LINCS/Overview%20Information/page.view?name=LINCS%20PCCSE%20Overview and https://clue.io/touchstone. Drug stocks were dissolved in DMSO for treatment in cell line media and cells were treated in 6 well plates for 24 hours. For cell harvesting, cells from 1-2 wells of a 6 well plate were scraped in PBS and combined per sample. All drug perturbations occurred in triplicates.
Created on 2/7/20, 1:17 PM
PlateLabelCell LineLevel 1Level 2Level 3Level 4Config
Plate67Cardiotoxic DrugsAstrocyte Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate66Kinase InhibitorsAstrocyte Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate65Neuroactive DrugsAstrocyte Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate64Epigenetic DrugsAstrocyte Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate63Cardiotoxic DrugsNPC Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate62Cardiotoxic DrugsYAPC Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate61Cardiotoxic DrugsPC3 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate60Cardiotoxic DrugsMCF7 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate59Cardiotoxic DrugsA375 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate58Cardiotoxic DrugsA549 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate34Kinase InhibitorsPC3 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate33Kinase InhibitorsA549 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate32Kinase InhibitorsYAPC Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate31Neuroactive DrugsYAPC Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate30Epigenetic DrugsYAPC Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate29Kinase InhibitorsMCF7 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate28Kinase InhibitorsA375 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate27Kinase InhibitorsNPC Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate25Neuroactive DrugsA549 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate24Neuroactive DrugsPC3 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate23Neuroactive DrugsMCF7 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate22Neuroactive DrugsA375 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate20Neuroactive DrugsNPC Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate19Epigenetic DrugsA549 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate18Epigenetic DrugsPC3 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate17Epigenetic DrugsA375 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate16Epigenetic DrugsNPC Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Plate15Epigenetic DrugsMCF7 Skyline  GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   GCT  [ View in Morpheus  ]   CFG 
Clustergrammer Heatmap
Flag FileDownloadCreatedProteinsPeptidesPrecursorsTransitionsReplicatesCalibration Curves
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LINCS_GCP_Plate61_annotated_minimized_2018-01-10_11-34-56.sky.zip2020-02-0781811627699681
LINCS_GCP_Plate60_annotated_minimized_2018-04-20_14-36-43.sky.zip2020-02-0781811628769681
LINCS_GCP_Plate32_annotated_minimized_2018-05-07_15-51-20.sky.zip2020-02-0760601205169660
LINCS_GCP_Plate27_annotated_minimized_2018-05-07_14-51-21.sky.zip2020-02-0760601204929660
LINCS_GCP_Plate23_annotated_minimized_2018-05-07_14-31-53.sky.zip2020-02-075959118502960
LINCS_GCP_Plate20_annotated_minimized_2018-05-07_15-41-44.sky.zip2020-02-076060120514960
LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.sky.zip2020-02-076060120506960
LINCS_GCP_Plate16_annotated_minimized_2018-05-09_11-16-44.sky.zip2020-02-075959118516960
LINCS_GCP_Plate22_annotated_minimized_2018-05-15_14-16-43.sky.zip2020-02-076060120506930
LINCS_GCP_Plate66_annotated_minimized_2018-09-05_11-44-04.sky.zip2020-02-0781811628489681
LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35.sky.zip2020-02-0781811628669681
LINCS_GCP_Plate58_annotated_minimized_2018-01-02_14-26-56.sky.zip2020-02-0781811628689681
LINCS_GCP_Plate31_annotated_minimized_2018-05-07_16-53-24.sky.zip2020-02-0760601205189660
LINCS_GCP_Plate67_annotated_minimized_2018-07-18_16-39-05.sky.zip2020-02-0781811629149681
LINCS_GCP_Plate33_annotated_minimized_2018-05-07_15-20-54.sky.zip2020-02-0760601205049660
LINCS_GCP_Plate15_annotated_minimized_2018-05-02_22-46-29.sky.zip2020-02-0760601205329660
LINCS_GCP_Plate65_annotated_minimized_2019-10-17_15-57-42.sky.zip2020-02-0781811628249681
LINCS_GCP_Plate63_annotated_minimized_2019-09-12_11-57-23.sky.zip2020-02-0781811628829681
LINCS_GCP_Plate17_annotated_minimized_2018-05-07_14-10-50.sky.zip2020-02-0760601205169660
LINCS_GCP_Plate30_annotated_minimized_2018-05-07_16-32-39.sky.zip2020-02-0760601205069660
LINCS_GCP_Plate29_annotated_minimized_2018-05-15_13-51-04.sky.zip2020-02-0760601205169560
LINCS_GCP_Plate28_annotated_minimized_2018-05-07_15-02-14.sky.zip2020-02-0760601205069660
LINCS_GCP_Plate25_annotated_minimized_2018-05-07_16-09-52.sky.zip2020-02-076161122528960
LINCS_GCP_Plate24_annotated_minimized_2018-05-07_16-43-23.sky.zip2020-02-075959118484930

This data is available under the CC BY 4.0 license.