PXD037655-1

PXD037655 is an original dataset announced via ProteomeXchange.

Title	Proteogenomic analysis reveals RNA as an important source for tumor-agnostic neoantigen identification correlating with T-cell infiltration
Description	Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 patients across 25 tumor types by combining proteogenomics with phenotypic and functional analyses. By using an optimized computational approach, we discovered a large number of novel tumor-specific and tumor-associated antigens including shared common target candidates. To create a pipeline for the identification of neoantigens in our cohort, we combined deep DNA and RNA sequencing with MS-based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity. In fact, we could detect a broad variety of non-wild type HLA-binding peptides in the majority of patients and confirmed the immunogenicity of 24 neoantigens. Most interestingly, the majority of total and immunogenic neoantigens originated from variants identified in the RNA dataset, illustrating the importance of RNA as a still understudied source of cancer antigens. Moreover, the amount of these mainly RNA-based immunogenic neoantigens correlated positively with overall CD8+ tumor-infiltrating T cells. This study therefore underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates.
HostingRepository	PRIDE
AnnounceDate	2023-05-16
AnnouncementXML	Submission_2023-05-16_00:40:05.845.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	CelinaTretter
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-24 00:57:41	ID requested
⏵ 1	2023-05-16 00:40:06	announced
2	2023-11-22 02:53:22	announced	2023-11-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: proteogenomics, neoantigens, human tumor,HLA class I immunopeptidomics

AngelaKrackhardt
contact affiliation	1 German Cancer Consortium of Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany 2 IIIrd Medical Department, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany 3 Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
contact email	angela.krackhardt@tum.de
lab head
CelinaTretter
contact affiliation	German Cancer Research Center, Heidelberg, Germany 3rd Medical Department, School of Medicine, Technical University Munich, Munich, Germany
contact email	c.schwencke-westphal@tum.de
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/2023/05/PXD037655

PRIDE project URI

• PRIDE
  1. PXD037655
     1. Label: PRIDE project
     2. Name: Proteogenomic analysis reveals RNA as an important source for tumor-agnostic neoantigen identification correlating with T-cell infiltration