PXD035340

PXD035340 is an original dataset announced via ProteomeXchange.

Title	Spatially variant immune infiltration scoring in human cancer tissues
Description	The Immunoscore is a method to quantify the immune cell infiltration within cancers to predict the disease prognosis. Previous immune profiling approaches relied on limited immune markers to establish patients’ tumor immunity. However, immune cells exhibit a higher-level complexity that is typically not obtained by the conventional immunohistochemistry methods. Herein, we present a spatially variant immune infiltration score, termed as SpatialVizScore, to quantify immune cells infiltration within lung tumor samples using multiplex protein imaging data. Imaging mass cytometry (IMC) was used to target 26 markers in tumors to identify stromal, immune, and cancer cell states within 26 human tissues from lung cancer patients. Unsupervised clustering methods dissected the spatial infiltration of cells in tissue using the high-dimensional analysis of 16 immune markers and other cancer and stroma enriched labels to profile alterations in the tumors’ immune infiltration patterns. Spatially resolved maps of distinct tumors determined the spatial proximity and neighborhoods of immune-cancer cell pairs. These SpatialVizScore maps provided a ranking of patients’ tumors consisting of immune inflamed, immune suppressed, and immune cold states, demonstrating the tumor’s immune continuum assigned to three distinct infiltration score ranges. Several inflammatory and suppressive immune markers were used to establish the cell-based scoring schemes at the single-cell and pixel-level, depicting the cellular spectra in diverse lung tissues. Thus, SpatialVizScore is an emerging quantitative method to deeply study tumor immunology in cancer tissues.
HostingRepository	PRIDE
AnnounceDate	2024-10-08
AnnouncementXML	Submission_2024-10-08_11:18:16.630.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	THOMAS HU
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	mass spectrometry imaging

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-14 07:19:26	ID requested
⏵ 1	2024-10-08 11:18:21	announced

10.1038/s41698-022-00305-4;

Allam M, Hu T, Lee J, Aldrich J, Badve SS, G, ö, kmen-Polar Y, Bhave M, Ramalingam SS, Schneider F, Coskun AF, Spatially variant immune infiltration scoring in human cancer tissues. NPJ Precis Oncol, 6(1):60(2022) [pubmed]

submitter keyword: Lung Cancer IMC

Ahmet F. Coskun
contact affiliation	Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of 6 Technology and Emory University, Atlanta, GA, USA
contact email	ahmet.coskun@bme.gatech.edu
lab head
THOMAS HU
contact affiliation	Georgia Institute of Technology
contact email	thu71@gatech.edu
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/PXD035340

PRIDE project URI

• PRIDE
  1. PXD035340
     1. Label: PRIDE project
     2. Name: Spatially variant immune infiltration scoring in human cancer tissues