PXD049438

PXD049438 is an original dataset announced via ProteomeXchange.

Title	Impaired T cell and neoantigen retention in time serial analysis of lung cancer patients treated with TIL cell therapy
Description	Cell therapy with tumor-infiltrating lymphocytes (TIL) has yielded durable responses for multiple cancer types, but the causes of therapeutic resistance remain largely unknown. Here multi-dimensional analysis was performed on time serial tumor and blood in a lung cancer TIL therapy trial. Using T-cell receptor sequencing on both functionally expanded T cells and neoantigen-loaded tetramer-sorted T cells, we identified neoantigen specific TCRs. We then mapped clones into individual transcriptomes and found that neoantigen-reactive clonotypes expressed a dysfunctional program and lacked stem-like features among patients who lacked clinical benefit. Tracking neoantigen-reactive clonotypes over time, decay of antigen-reactive peripheral T-cell clonotypes was associated with the emergence of progressive disease. Further, subclonal neoantigens previously targeted by infused T cells were subsequently absent within tumors at progression, suggesting potential adaptive resistance. Our findings suggest that targeting clonal antigens and circumventing dysfunctional states may be important for conferring clinical responses to TIL therapy.
HostingRepository	PRIDE
AnnounceDate	2024-12-30
AnnouncementXML	Submission_2024-12-30_03:36:01.010.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD049438
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	John Koomen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-16 20:03:23	ID requested
⏵ 1	2024-12-30 03:36:01	announced

10.6019/PXD049438;

submitter keyword: Tumor Infiltrating Lymphocytes,Lung Cancer, Expression Proteomics, Immunotherapy

Ben Creelan
contact affiliation	Thoracic Oncology Moffitt Cancer Center Tampa, FL, USA
contact email	ben.creelan@moffitt.org
lab head
John Koomen
contact affiliation	Moffitt Cancer Center
contact email	john.koomen@moffitt.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD049438
     1. Label: PRIDE project
     2. Name: Impaired T cell and neoantigen retention in time serial analysis of lung cancer patients treated with TIL cell therapy