PXD034958

PXD034958 is an original dataset announced via ProteomeXchange.

Title	Prognostic value of molecular intratumor heterogeneity in primary oral cancer and its lymph node metastases assessed by mass spectrometry imaging
Description	Different aspects of intra-tumor heterogeneity (ITH), which are associated with development of cancer and its response to treatment, have postulated prognostic value. Here we searched for the potential association between phenotypic ITH analyzed by mass spectrometry imaging (MSI) and the prognosis of head and neck cancer. The study involved tissue specimens resected from 77 patients with locally advanced oral squamous cell carcinoma, including 37 patients where matched samples of primary tumor and synchronous lymph node metastases were analyzed. A 3-year follow-up was available for all patients that enabled their separation into two groups: with no evidence of disease (NED, n=41) and with progressive disease (PD, n=36). After the on-tissue trypsin digestion, peptide maps of all cancer regions were segmented using an unsupervised approach to reveal their intrinsic heterogeneity. We found that intra-tumor similarity of spectra was higher in the PD group and diversity of clusters identified during image segmentation was higher in the NED group, which indicated a higher level of ITH in patients with more favorable outcomes. Furthermore, signature of molecular components that correlated with long-term outcomes could be associated with proteins involved in the immune functions. Hence, we proposed that a higher level of ITH revealed by MSI in cancers with a better prognosis could reflect the presence of heterotypic components of tumor microenvironment such as infiltrating immune cells enhancing the response to the treatment. LC-MALDI-MS/MS data deposited in this repository originate from protein lysates obtained from FFPE sections consecutive to sections dedicated to MSI measurements. The hypothetical identity of the MSI components was established by assignment of a component location on the m/z scale for the measured masses of tryptic peptides identified by LC-MALDI-MS/MS allowing ±0.05% mass tolerance.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:11:33.675.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Monika Pietrowska
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	ultraflex

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-29 15:02:46	ID requested
1	2022-10-13 08:54:23	announced
⏵ 2	2023-11-14 08:11:34	announced	2023-11-14: Updated project metadata.

Kurczyk A, Gawin M, Paul P, Chmielik E, Rutkowski T, Pietrowska M, Wid, ł, ak P, Prognostic Value of Molecular Intratumor Heterogeneity in Primary Oral Cancer and Its Lymph Node Metastases Assessed by Mass Spectrometry Imaging. Molecules, 27(17):(2022) [pubmed]

submitter keyword: cancer prognosis

head and neck squamous cell carcinoma

intratumor heterogeneity

long-term outcome

mass spectrometry imaging

tumor microenvironment

Piotr Widlak
contact affiliation	Maria Sklodowska-Curie National Research Institute of Oncology
contact email	piotr.widlak@io.gliwice.pl
lab head
Monika Pietrowska
contact affiliation	Maria Sklodowska-Curie National Research Institute of Oncology
contact email	monika.pietrowska@io.gliwice.pl
dataset submitter

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/2022/10/PXD034958

PRIDE project URI

• PRIDE
  1. PXD034958
     1. Label: PRIDE project
     2. Name: Prognostic value of molecular intratumor heterogeneity in primary oral cancer and its lymph node metastases assessed by mass spectrometry imaging