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idr0158-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] idr0158
Study Title Multi-omic profiling of follicular lymphoma tumors reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients
Study Type multiplexed immunofluorescence
Study Type Term Source REF NCIT
Study Type Term Accession NCIT_C181928
Study Description Reference atlases, molecular and spatial maps of mammalian tissues, are critical resources for discovery efforts and translational research. Their utility is dependent on operationalizing the resulting data by identifying cell types, histological patterns, and predictive biomarkers underlying health and disease. The human lymph node (LN) offers a compelling use case because of its importance in immunity, structural and cellular diversity, and neoplastic involvement. One hematological malignancy, follicular lymphoma (FL), evolves from developmentally blocked germinal center B cells residing in and trafficking through these tissues. To promote survival and immune escape, tumor B cells undergo significant genetic changes and extensively remodel the lymphoid microenvironment. Here, we present an integrated portrait of healthy and FL LNs using multiple genomic and advanced imaging technologies. By leveraging the strengths of each platform, we identify several tumor-specific features and microenvironmental patterns enriched in individuals who experience early relapse, the most high-risk of FL patients.
Study Key Words Follicular lymphoma 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 https://www.nature.com/articles/s41592-023-01846-7
Study BioImage Archive Accession
Study Public Release Date 2024-10-08
# Study Publication
Study PubMed ID 38428410
Study Publication Title Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients
Study Author List Radtke AJ, Postovalova E, Varlamova A, Bagaev A, Sorokina M, Kudryashova O, Meerson M, Polyakova M, Galkin I, Svekolkin V, Isaev S, Wiebe D, Sharun A, Sarachakov A, Perelman G, Lozinsky Y, Yaniv Z, Lowekamp BC, Speranza E, Yao L, Pittaluga S, Shaffer AL, Jonigk D, Phelan JD, Davies-Hill T, Huang DW, Ovcharov P, Nomie K, Nuzhdina E, Kotlov N, Ataullakhanov R, Fowler N, Kelly M, Muppidi J, Davis JL, Hernandez JM, Wilson WH, Jaffe ES, Staudt LM, Roschewski M, Germain RN
Study PMC ID PMC10966827
Study DOI https://doi.org/10.1016/j.ccell.2024.02.001
# Study Contacts
Study Person Last Name Radtke
Study Person First Name Andrea
Study Person Email [email protected]
Study Person Address Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, 20892, USA
Study Person ORCID 0000-0003-4379-8967
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 Radtke et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000199
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] idr0158-radtke-lymphoma/experimentA
Experiment Sample Type tissue
Experiment Description 40-plex iterative bleaching extends multiplexity (IBEX) imaging was performed on fixed frozen tissues from normal human lymph nodes and follicular lymphoma lymph nodes. Multiplexed immunofluorescence (MxIF) imaging was performed on serial FFPE tissue sections from follicular lymphoma lymph nodes. Four distinct antibody panels were applied to each tissue section referred to as MxIF Panel 1 (MxIF_P1), MxIF Panel 2 (MxIF_P2), MxIF Panel 3 (MxIF_P3), and MxIF Panel 4 (MxIF_P4). Multiplexed imaging was performed on serial FFPE tissue sections from normal and follicular lymphoma lymph nodes using the Cell DIVE imager and IBEX dye inactivation protocol (Cell DIVE-IBEX). Two panels of antibodies, immune (CellDIVE_IBEX_Immune) or stromal (CellDIVE_IBEX_Stromal), were applied to serial sections. IBEX and MxIF imaging were performed on a discovery cohort of 10 samples. Key spatial findings were extended to a larger validation cohort of 29 samples using the Cell DIVE-IBEX method.
Experiment Example Images
Experiment Imaging Method confocal microscopy
Experiment Imaging Method Term Source REF Fbbi
Experiment Imaging Method Term Accession FBbi_00000251
Experiment Comments See Cell DIVE-IBEX images for higher quality imaging data with several of the same markers present in MxIF_P1, MxIF_P2, MxIF_P3, and MxIF_P4 images.
# assay files
Experiment Assay File idr158-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 IBEX, MxIF, Cell DIVE-IBEX
Protocol Type
Protocol Type Term Source REF EFO EFO
Protocol Type Term Accession
Protocol Description Sample Description: For IBEX images: Fixed frozen tissues were prepared from excisional lymph node biopsies. Images were acquired using the IBEX method and a panel of antibodies directed against 39 protein targets and the nuclear dye (Hoechst). For MxIF images: FFPE tissues were prepared from excisional lymph node biopsies. Prior to antibody labeling, antigen retrieval was performed using the AR6 (pH 6) buffer and a water bath. Four panels of antibodies (2-4 protein targets per panel) and the nuclear dye (Hoechst) were visualized in each tissue section. For Cell DIVE-IBEX images: FFPE tissues were prepared from excisional lymph node biopsies. Prior to antibody labeling, antigen retrieval was performed using the ER1 and ER2 buffers and the Leica Bond. Two antibody panels, termed immune or stromal, were applied to serial sections using cyclic imaging with the Cell DIVE and dye inactivation using the IBEX protocol. Images were aligned using the Hoechst channel as a fiducial. Additional details on antibodies, image alignment, and related protocols can be found on the IBEX Imaging Community website: https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/ Quantification Process: Details on the advanced image analyses performed on these samples are included in the accompanying manuscript.
# 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 idr0158-experimentA-processed
Processed Data File Format xlsx
Processed Data File Description excel workbook (multiple tabs)
Processed Data Column Name
Processed Data Column Type
Processed Data Column Annotation Level
Processed Data Column Description
Processed Data Column Link To Assay File