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PXD035340-1

PXD035340 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSpatially variant immune infiltration scoring in human cancer tissues
DescriptionThe 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-08
AnnouncementXMLSubmission_2024-10-08_11:18:16.630.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterTHOMAS HU
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
Instrumentmass spectrometry imaging
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-07-14 07:19:26ID requested
12024-10-08 11:18:21announced
Publication List
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]
Keyword List
submitter keyword: Lung Cancer IMC
Contact List
Ahmet F. Coskun
contact affiliationWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of 6 Technology and Emory University, Atlanta, GA, USA
contact emailahmet.coskun@bme.gatech.edu
lab head
THOMAS HU
contact affiliationGeorgia Institute of Technology
contact emailthu71@gatech.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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