PXD028107 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Defining the Tumor Microenvironment by Integration of Im-munohistochemistry and Extracellular Matrix Targeted Imaging Mass Spectrometry |
Description | Breast stroma plays a significant role in breast cancer risk and progression yet remains poorly understood. In breast stroma, collagen is the most abundantly expressed protein and its increased deposition and alignment contributes to progression and poor prognosis. Collagen post-translation modifications such as hydroxylated-proline (HYP) control deposition and stromal organization. The clinical relevance of collagen HYP site modifications in cancer processes remains undefined due to technical issues accessing collagen from formalin-fixed, paraffin-embedded (FFPE) tissues. We previously developed a targeted approach for investigating collagen and other extracellular matrix proteins from FFPE tissue. Here, we hypothesized that immunohistochem-istry staining for fibroblastic markers would not interfere with targeted detection of collagen stroma peptides and could reveal peptide regulation influenced by specific cell types. Our initial work demonstrated that stromal peptide peak intensities when using MALD-IMS following IHC staining (αSMA, FAP, P4HA3 and PTEN) were comparable to serial sections of non-stained tissue. Analysis of histology-directed IMS using PTEN on breast tissues and TMAs revealed heteroge-neous PTEN staining patterns and suggestive roles in stromal protein regulation. This study sets the foundation for investigations of target cell types and their unique contribution to collagen regulation within extracellular matrix niches. |
HostingRepository | PRIDE |
AnnounceDate | 2022-02-15 |
AnnouncementXML | Submission_2022-02-15_09:12:24.708.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Jennifer Bethard |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; deamidated residue |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-08-25 03:54:21 | ID requested | |
⏵ 1 | 2022-02-15 09:12:27 | announced | |
Publication List
Rujchanarong D, Lefler J, Saunders JE, Pippin S, Spruill L, Bethard JR, Ball LE, Mehta AS, Drake RR, Ostrowski MC, Angel PM, Defining the Tumor Microenvironment by Integration of Immunohistochemistry and Extracellular Matrix Targeted Imaging Mass Spectrometry. Cancers (Basel), 13(17):(2021) [pubmed] |
Keyword List
submitter keyword: imaging mass spectrometry (IMS) |
immunohistochemistry (IHC) |
PTEN |
stroma |
ECM |
tumor microenvironment |
breast cancer |
Contact List
Peggi M. Angel |
contact affiliation | Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston SC USA |
contact email | angelp@musc.edu |
lab head | |
Jennifer Bethard |
contact affiliation | Medical University of SC |
contact email | bethard@musc.edu |
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/2022/02/PXD028107 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD028107
- Label: PRIDE project
- Name: Defining the Tumor Microenvironment by Integration of Im-munohistochemistry and Extracellular Matrix Targeted Imaging Mass Spectrometry