PXD012083

PXD012083 is an original dataset announced via ProteomeXchange.

Title	AML HLA Ligandome reveals mutated NPM1 as a recurrent neoantigen
Description	Somatic mutations in cancer are a potential source of cancer specific neoantigens. Acute myeloid leukemia (AML) has common recurrent mutations shared between patients in addition to private mutations specific to individuals. We hypothesized that neoantigens derived from recurrent shared mutations would be attractive targets for future immunotherapy and sought to study the Class I and II HLA ligandomes of thirteen primary AML tumor samples and two AML cell lines (OCI-AML3 and MV4-11) using mass spectrometry. We identified two endogenous, mutation-bearing HLA Class I ligands from NPM1, which are predicted to bind the common HLA haplotypes, HLA-A*03:01 and HLA-A*02:01 respectively. We further derived CD8+ T cells from healthy donor peripheral blood samples which bound mutant-peptide loaded A*03:01 and A*02:01 tetramers, suggesting a new source of NPM1 mutation-specific T cell receptors (TCRs) for future evaluation. Since NPM1 is mutated in approximately one-third of patients with AML, the finding of endogenous NPM1 neoantigens supports future studies evaluating immunotherapeutic approaches against this target, for this subset of patients with AML.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:00:10.604.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Niclas Olsson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	cysteinylation (disulfide with free L-cysteine); phosphorylated residue; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Fusion Lumos; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-17 07:12:37	ID requested
1	2019-07-16 23:55:47	announced
⏵ 2	2024-10-22 04:00:11	announced	2024-10-22: Updated project metadata.

10.1371/journal.pone.0219547;

Narayan R, Olsson N, Wagar LE, Medeiros BC, Meyer E, Czerwinski D, Khodadoust MS, Zhang L, Schultz L, Davis MM, Elias JE, Levy R, Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin. PLoS One, 14(7):e0219547(2019) [pubmed]

submitter keyword: Homo Sapiens, HLA, Acute myeloid leukemia, neoantigen

Joshua E Elias
contact affiliation	Department of Chemical & Systems Biology Stanford University USA
contact email	josh.elias@stanford.edu
lab head
Niclas Olsson
contact affiliation	Calico Life Sciences
contact email	nic.e.olsson@gmail.com
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/2019/07/PXD012083

PRIDE project URI

• PRIDE
  1. PXD012083
     1. Label: PRIDE project
     2. Name: AML HLA Ligandome reveals mutated NPM1 as a recurrent neoantigen