PXD037655

PXD037655 is an original dataset announced via ProteomeXchange.

Title	Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification
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 for proteogenomic-based discovery of neoantigens. By using an optimized computational approach, we discover a large number of tumor-specific and tumor-associated antigens. To create a pipeline for the identification of neoantigens in our cohort, we combine DNA and RNA sequencing with MS-based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity and an in-depth validation process. We detect a broad variety of non-canonical HLA-binding peptides in the majority of patients demonstrating partially immunogenicity. Our validation process allows for the selection of 32 potential neoantigen candidates. The majority of neoantigen candidates originates from variants identified in the RNA data set, illustrating the relevance of RNA as a still understudied source of cancer antigens. This study underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates.
HostingRepository	PRIDE
AnnounceDate	2023-11-22
AnnouncementXML	Submission_2023-11-22_02:53:21.921.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Celina Tretter
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.

Tretter C, de Andrade Kr, ä, tzig N, Pecoraro M, Lange S, Seifert P, von Frankenberg C, Untch J, Zuleger G, Wilhelm M, Zolg DP, Dreyer FS, Br, ä, unlein E, Engleitner T, Uhrig S, Boxberg M, Steiger K, Slotta-Huspenina J, Ochsenreither S, von Bubnoff N, Bauer S, Boerries M, Jost PJ, Schenck K, Dresing I, Bassermann F, Friess H, Reim D, Gr, ü, tzmann K, Pf, ü, tze K, Klink B, Schr, ö, ck E, Haller B, Kuster B, Mann M, Weichert W, Fr, ö, hling S, Rad R, Hiltensperger M, Krackhardt AM, Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nat Commun, 14(1):4632(2023) [pubmed]

10.1038/s41467-023-39570-7;

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

Angela Krackhardt
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
Celina Tretter
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 a source for tumor-agnostic neoantigen identification