PXD034772-1

PXD034772 is an original dataset announced via ProteomeXchange.

Title	The immunopeptidome landscape associated with T cell infiltration, inflammation and immune-editing in lung cancer
Description	One key barrier to improving efficacy of personalized cancer immunotherapies that are dependent on the tumor antigenic landscape remains patient stratification. While patients with CD3+CD8+ T cell inflamed tumors typically show better response to immune checkpoint inhibitors, it is still unknown if the repertoire of HLA bound peptides presented in highly inflamed and non-inflamed tumors is substantially different. We surveyed 61 tumor regions and adjacent non-malignant lung tissues from eight lung cancer patients and performed deep antigen discovery combining immunopeptidomics, genomics, bulk and spatial transcriptomics and explored the heterogeneous expression and presentation of tumor (neo)antigens. Here we associated diverse immune cell populations with the immunopeptidome in CD3+CD8+ T cell excluded, infiltrated, highly- and lowly-inflamed tumors. We found evidence for lower immune-editing and higher presentation efficiency of tumor-associated antigens in lowly-inflamed and CD3+CD8+ T cell excluded tumors. This could have implications for the choice of combination therapies tailored to the patient’s mutanome and microenvironment.
HostingRepository	PRIDE
AnnounceDate	2023-03-21
AnnouncementXML	Submission_2023-03-21_16:13:29.083.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	MichalBassani-Sternberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-21 01:52:11	ID requested
⏵ 1	2023-03-21 16:13:29	announced

Dataset with its publication pending

submitter keyword: Immunopeptidomics, proteogenomics, neoantigens, lung cancer

MichalBassani-Sternberg
contact affiliation	Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Office B25A/04/94 Rue du Bugnon 25a, CH-1005 Lausanne
contact email	michal.bassani@chuv.ch
lab head
MichalBassani-Sternberg
contact affiliation	UNIL/CHUV
contact email	michal.bassani@chuv.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD034772
     1. Label: PRIDE project
     2. Name: The immunopeptidome landscape associated with T cell infiltration, inflammation and immune-editing in lung cancer