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idr0150-study.txt
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idr0150-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] idr0150
Study Title Cancer-associated fibroblast compositions change with breast cancer progression linking the ratio of S100A4+Êand PDPN+ÊCAFs to clinical outcome
Study Type multiplexed immunofluorescence
Study Type Term Source REF NCIT
Study Type Term Accession NCIT_C181928
Study Description Tumors are supported by cancer-associated fibroblasts (CAFs). CAFs are heterogeneous and carry out distinct cancer-associated functions. Understanding the full repertoire of CAFs and their dynamic changes as tumors evolve could improve the precision of cancer treatment. Here we comprehensively analyze CAFs using index and transcriptional single-cell sorting at several time points along breast tumor progression in mice, uncovering distinct subpopulations. Notably, the transcriptional programs of these subpopulations change over time and in metastases, transitioning from an immunoregulatory program to wound-healing and antigen-presentation programs, indicating that CAFs and their functions are dynamic. Two main CAF subpopulations are also found in human breast tumors, where their ratio is associated with disease outcome across subtypes and is particularly correlated withÊBRCAÊmutations in triple-negative breast cancer. These findings indicate that the repertoire of CAF changes over time in breast cancer progression, with direct clinical implications.
Study Key Words Breast cancer Cancer associated fibroblasts (CAFs)
Study Organism Homo sapiens
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 9606
Study Experiments Number 1
Study External URL
Study BioImage Archive Accession
Study Public Release Date 2023-10-09
# Study Publication
Study PubMed ID 35122040
Study Publication Title Cancer-associated fibroblast compositions change with breast cancer progression linking the ratio of S100A4+Êand PDPN+ÊCAFs to clinical outcome
Study Author List Friedman G, Levi-Galibov O, David E, Bornstein C, Giladi A, Dadiani M, Mayo A, Halperin C, Pevsner-Fischer M, Lavon H, Mayer S, Nevo R, Stein Y, Balint-Lahat N, Barshack I, Ali HR, Caldas C, Nili-Gal-Yam E, Alon U, Amit I, Scherz-Shouval R
Study PMC ID
Study DOI https://doi.org/10.1038/s43018-020-0082-y
# Study Contacts
Study Person Last Name Scherz-Shouval
Study Person First Name Ruth
Study Person Email [email protected]
Study Person Address Weizmann Institute of Science; Herzl 234 Rehovot' Israel 7610001
Study Person ORCID 0000-0002-4570-121X
Study Person Roles submitter
# Study License and Data DOI
Study License CC BY 4.0
Study License URL https://creativecommons.org/licenses/by/4.0/
Study Copyright Scherz-Shouval et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000193
Term Source Name NCBITaxon
Term Source URI http://purl.obolibrary.org/obo/ http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/cmpo/ http://purl.obolibrary.org/obo/
# EXPERIMENT SECTION
# Experiment Section containing all information relative to each experiment in the study including materials used, protocols names and description, phenotype names and description. For multiple experiments this section should be repeated. Copy and paste the whole section below and fill out for the next experiment
Experiment Number 1
Comment[IDR Experiment Name] idr0150-friedman-cafs/experimentA
Experiment Sample Type tissue
Experiment Description Immunofluorescent staining performed on FFPE sections from a cohort of triple-negative breast cancer patients and a cohort of breast cancer patients.
Experiment Size 3D Images: Average Image Dimension (XYC): Total Tb:
Experiment Example Images TNBC, Patient_51_core_1
Experiment Imaging Method fluorescence microscopy
Experiment Imaging Method Term Source REF Fbbi
Experiment Imaging Method Term Accession FBbi_00000246
Experiment Comments Wide field microscopy
# assay files
Experiment Assay File idr0150-experimentA-annotation
Experiment Assay File Format tab-delimited text
Assay Experimental Conditions
Assay Experimental Conditions Term Source REF
Assay Experimental Conditions Term Accession
Quality Control Description
# Protocols
Protocol Name growth protocol treatment protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type growth protocol treatment protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type Term Source REF EFO EFO
Protocol Type Term Accession EFO_0003789 EFO_0003969
Protocol Description Sample Description: Formalin-fixed paraffin-embedded tissues represented in tissue arrays. Processed data were obtained using Fiji and the 'rolling ball' method.
Quantification Process: Quantification of TMA staining was performed using the Fiji image processing platform. ROIs were manually depicted to include all intact tissue areas and exclude regions of adipose tissue (due to nonspecific staining). H&Es from the TNBC TMA were used to assist in training and optimizing this step. Following background subtraction using a rolling ball with a radius of 200 pixels, the CK, S100A4 and PDPN channels were thresholded using Otsu method. All pixels above the threshold were counted as 1, and their sum was divided by the ROI. Channel/ROI scores of all replicate cores from the same patient (typically three) were averaged and the average score was used for statistical analysis. Ratios between different stains were calculated for each core and averaged for each patient.
# Phenotypes
Phenotype Name
Phenotype Description
Phenotype Score Type
Phenotype Term Source REF CMPO
Phenotype Term Name
Phenotype Term Accession
# Feature Level Data Files (give individual file details unless there is one file per well)
Feature Level Data File Name
Feature Level Data File Format
Feature Level Data File Description
Feature Level Data Column Name
Feature Level Data Column Description
# 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 Assay File