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idr0119-study.txt
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# FILL IN AS MUCH INFORMATION AS YOU CAN. HINTS HAVE BEEN PUT IN SOME FIELDS AFTER THE HASH # SYMBOL. REPLACE THE HINT WITH TEXT WHERE APPROPRIATE.
# STUDY DESCRIPTION SECTION
# Section with generic information about the study including title, description, publication details (if applicable) and contact details
Comment[IDR Study Accession] idr0119
Study Title Analysis and modeling of cancer drug responses using cell cycle phase-specific rate effects
Study Type high content screen
Study Type Term Source REF EFO
Study Type Term Accession EFO_0007550
Study Description Identifying effective therapeutic treatment strategies is a major challenge to improving outcomes for patients with breast cancer. To gain a comprehensive understanding of how clinically relevant anti-cancer agents modulate cell cycle progression, we genetically-engineered breast cancer cell lines express a fluorescently-labelled cell cycle reporter. We then used these cell lines to track drug-induced changes in cell number and cell cycle phase, which revealed drug-specific cell cycle effects that vary across time. We developed a linear chain trick (LCT) computational model, where the cell cycle is partitioned into subphases that can faithfully capture drug-induced dynamic responses. The model correctly infers drug effects and also localizes them to specific cell cycle phases. We used our LCT model to predict the effect of unseen drug combinations and experimentally confirmed the effectiveness of predicted combination treatment strategies. Our integrated experimental and modeling approach opens avenues to assess drug responses, predict effective drug combinations, and identify optimal drug sequencing strategies.
Study Key Words cell cycle live-cell imaging dose response drug combinations dynamical model cancer
Study Organism Homo sapiens
Study Organism Term Source REF EFO
Study Organism Term Accession 9606
Study Screens Number 1
Study External URL
Study BioImage Archive Accession
Study Public Release Date 2023-07-17
# Study Publication
Study PubMed ID 37301933
Study Publication Title Analysis and modeling of cancer drug responses using cell cycle phase-specific rate effects
Study Author List Gross SM, Mohammadi F, Sanchez-Aguila C, Zhan PJ, Liby TA, Dane MA, Meyer AS, Heiser LM
Study PMC ID PMC10257663
Study DOI https://doi.org/10.1038/s41467-023-39122-z
# Study Contacts
Study Person Last Name Heiser
Study Person First Name Laura M.
Study Person Email [email protected]
Study Person Address Department of Biomedical Engineering, 2730 S. Moody Ave. CL3G, Portland, OR 97201
Study Person ORCID 0000-0003-3330-0950
Study Person Roles corresponding author
# Study License and Data DOI
Study License CC BY 4.0
Study License URL https://creativecommons.org/licenses/by/4.0/
Study Copyright Gross et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000189
Term Source Name NCBITaxon EFO CMPO Fbbi
Term Source File http://purl.obolibrary.org/obo/ http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/cmpo/ http://purl.obolibrary.org/obo/
# SCREEN SECTION
# Screen Section containing all information relative to each screen in the study including materials used, protocols names and description, phenotype names and description.
Screen Number 1
Comment[IDR Screen Name] idr0119-gross-cellresponse/screenA
Screen Sample Type cell
Screen Description Time series phase and fluorescent microscopy of AU565, HCC1143, 21MT1 and MDAMB157 breast cancer cells response to single drugs and AU565 breast cancer cells response to drug combinations. Fluorescent reporters show nuclei and cell cycle state.
Screen Size Plates: 34 5D Images: Planes: Average Image Dimension (XYZCT): Total Tb:
Screen Example Images
Screen Imaging Method phase contrast microscopy fluorescence microscopy
Screen Imaging Method Term Source REF FBbi FBbi
Screen Imaging Method Term Accession FBbi_00000247 FBbi_00000246
Screen Technology Type compound screen
Screen Technology Type Term Source REF EFO
Screen Technology Type Term Accession EFO_0007553
Screen Type primary screen
Screen Type Term Source REF EFO
Screen Type Term Accession EFO_0007556
Screen Organism
Screen Organism Term Source REF NCBITaxon
Screen Organism Term Accession
Screen Comments
# Library section. The library file should be supplied separately and it should contain the reagents description including, at the absolute minimum: reagent ID, sequences and position in the layout (= plate + position in the plate)
Library File Name idr0119-screenA-annotation
Library File Format tab-delimited text
Library Type compound library
Library Type Term Source REF EFO
Library Type Term Accession EFO_0007569
Library Manufacturer
Library Version
Library Experimental Conditions
Library Experimental Conditions Term Source REF EFO
Library Experimental Conditions Term Accession
Quality Control Description A vehicle well in each plate is imaged and analyzed in the same fashion as the drug wells.
# Protocols
Protocol Name growth protocol treatment protocol HCS library protocol HCS image acquisition and feature extraction protocol HCS data analysis protocol
Protocol Type growth protocol treatment protocol HCS library protocol HCS image acquisition and feature extraction protocol HCS data analysis protocol
Protocol Type Term Source REF EFO EFO EFO EFO EFO
Protocol Type Term Accession EFO_0003789 EFO_0003969 EFO_0007571 EFO_0007572 EFO_0007573
Protocol Description
Creation of Stable Cell Lines
AU565 (ATCC CRL 2351) and MDAMB157 (ATCC HTB 24) cells were grown in DMEM supplemented with 10% FBS, HCC1143 (ATCC CRL 2321) cells were grown in RPMI supplemented with 10% FBS, and 21MT1 (generous gift from Kornelia Polyak) cells were grown in DMEM/F12 supplemented with 5% horse serum, 20 ng/ml rhEGF, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, and 10 µg/ml insulin. The coding fragment for clover-HDHB was cloned in frame into a transposase expression plasmid modified to also express a nuclear localized mCherry and stable cell lines were created as previously described (Gross, Cell Systems 2019). In brief, the clover-HDHB-NLSmCherry expression plasmid was co-transfected 24-48 hours with the pSB100X transposase plasmid (Addgene 34879) at a ratio of 4:1 using Lipofectamine 3000 (AU565, HCC1143, 21MT1) or LTX (MDAMB157) and selected for 3-7 days with 0. 5-2 µg/ml puromycin. To ensure uniform fluorescence across the transfected population, HCC1143 and 21MT1 cells were sorted at OHSU’s Flow Cytometry Core and cells with a medium intensity clover-HDHB signal and a high intensity NLS-mCherry signal were selected for drug dose response experiments. In all cases, cells were validated by STR profiling (LabCorp) and tested negative for mycoplasma. Stable cell lines were then subjected to drug treatment using protocols described below.
Drug dose response protocol
AU565 cells were plated at a density of 25,000 cells per well into 24-well Falcon plates (Corning #353047). 24H after plating the media was exchanged with Fluorobrite media supplemented with 10% FBS, glutamine, and penicillin-streptomycin. Cells were then treated with dose-escalation: lapatinib (Selleckchem #S1028), gemcitabine (#S1149), paclitaxel (#S1150), doxorubicin (#S1208), palbociclib (#S1116), BEZ235 (#S1009), and trametinib (#S2673). After drug addition, plates were imaged every 30 minutes for 96H using phase, GFP, and RFP imaging channels with an IncuCyte S3. For single drug treatments of AU565 cells only, at 48H the media was replaced in all wells including the control wells, and fresh media and drug were added. Four equally-spaced image locations per well and three biological replicates were collected.
MDAMB157, HCC1143, and 21MT1 cell lines were transferred to and maintained in a base of either Fluorobrite media and 1x GlutaMAX or mixed Fluorobrite/F12 media and 0.5x GlutaMAX along with their corresponding supplements for no less than one week before performing the drug dose response protocol. MDAMB157 and HCC1143 cells were plated at a density of 25,000 cells per well, while the larger 21MT1 cells were plated at a density of 5,000 cells per well into 24-well Falcon plates (Corning #353047). 24H after plating the media was exchanged with fresh Fluorobrite media as indicated per cell line. Cells were then treated with dose-escalation: BEZ235, gemcitabine, paclitaxel, doxorubicin, palbociclib, and trametinib. After drug addition, plates were imaged every 2 hours for 96H using phase, GFP, and RFP imaging channels with the IncuCyte S3. Four equally-spaced image locations per well and three biological replicates were collected.
# Phenotypes
Phenotype Name
Phenotype Description
Phenotype Score Type
Phenotype Term Source REF CMPO
Phenotype Term Name
Phenotype Term Accession
# Raw Data Files
Raw Image Data Format Images are single-channel tiff files with one phase contrast, one green channel and one red channel image at each location and timepoint.
Raw Image Organization There is a directory for each plate which contain subdirectories for each well that have subdirectories for each field. The field subdirectories each have 193 sets of 3 files which are the phase contrast, green and red channels images taken every 30 minutes for 48 hours.
# Feature Level Data Files
Feature Level Data File Name AU00601_features.csv, AU00602_features.csv, AU00701_features.csv, AU00702_features.csv, AU00801_features.csv, AU00802_features.csv, AU00901_features.csv, AU00902_features.csv, AU01001_features.csv, AU01002_features.csv, AU01101_features.csv, AU01102_features.csv
Feature Level Data File Description The feature files contain cell counts for each image and the number and percent of cells classified as G1 vs S/G2.
Feature Level Data File Format csv formatted files
Feature Level Data Column Name Classify_Math_NCRATIO_Bin_1_NumObjectsPerBin Classify_Math_NCRATIO_Bin_1_PctObjectsPerBin Classify_Math_NCRATIO_Bin_2_NumObjectsPerBin Classify_Math_NCRATIO_Bin_2_PctObjectsPerBin Count_Nuclei ImageNumber Field Well
Feature Level Data Column Description Number of cells in S/G2 Percent of cells in S/G2 Number of cells in G1 Percent of cells in G1 Number of cells in the image Image index Field index Well in plate
# Processed Data Files
Processed Data File Name
Processed Data File Format tab-delimited text
Processed Data File Description
Processed Data Column Name
Processed Data Column Type
Processed Data Column Annotation Level
Processed Data Column Description
Processed Data Column Link To Library File