<<< Full experiment listing


PXD041625 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleTranscriptomics and proteomics reveal distinct biology for lymph node metastases and tumor deposits in colorectal cancer
DescriptionObjective: Both lymph node metastases (LNMs) and tumor deposits (TDs) are included in colorectal cancer (CRC) staging, although knowledge regarding their biological background is lacking. This study aims to compare the biology of these prognostic features, which is essential for a better understanding of their role in CRC spread. Design: Spatially resolved transcriptomic analysis using Digital Spatial Profiling was performed on TDs and LNMs from 10 CRC patients using 1,388 RNA targets, for the tumor cells and tumor microenvironment (TME). Shotgun proteomics identified 5,578 proteins in 12 different patients. Differences in RNA and protein expression were analyzed, and spatial deconvolution was performed. Image-based CMS (imCMS) analysis was performed on all TDs and LNMs included in the study. Results: Transcriptome and proteome profiles identified distinct clusters for TDs and LNMs in both the tumor and TME segment, with upregulation of matrix remodeling, cell adhesion/motility and epithelial mesenchymal transition (EMT) in TDs (all p<0.05). Spatial deconvolution showed a significantly increased number of fibroblasts, macrophages, and regulatory T cells (p<0.05) in TDs. In consistency with a higher fibroblast and EMT component, imCMS classified 62% of TDs as poor prognosis subtype CMS4 compared to 36% of LNMs (p<0.05). Conclusion: Compared to LNMs, TDs have a more invasive state; involving a distinct TME and upregulation of EMT, which are reflected in a more frequent histological classification of TDs as CMS4. These results emphasize the heterogeneity of locoregional spread the fact that TDs should merit more attention both in future research and during staging.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListamidated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-04-18 08:41:46ID requested
12023-09-19 02:59:46announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: imCMS, proteomics, Lymph node metastases, Tumor deposits,Colorectal cancer, digital spatial profiling, transcriptomics
Contact List
contact affiliationDepartment of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
contact emailmichiel.vermeulen@science.ru.nl
lab head
contact affiliationRadboud University
contact emailp.jansen@science.ru.nl
dataset submitter
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/09/PXD041625
PRIDE project URI
Repository Record List
[ + ]