PXD014293

PXD014293 is an original dataset announced via ProteomeXchange.

Title	Defining HLA-II ligand processing and binding rules with mass spectrometry enhances cancer epitope prediction
Description	Increasing evidence indicates CD4+ T cells can recognize cancer-specific antigens and control tumor growth. However, it remains difficult to predict the antigens that will be presented by human leukocyte antigen class II molecules (HLA-II) - hindering efforts to optimally target them therapeutically. Obstacles include inaccurate peptide-binding prediction and unsolved complexities of the HLA-II pathway. To address these challenges, we introduce an improved technology for discovering HLA-II binding motifs and conduct a comprehensive analysis of tumor-ligandomes to learn processing rules relevant in the tumor microenvironment (TME). We profiled HLA-II alleles and showed that binding motifs are highly sensitive to HLA-DM, a peptide loading chaperone. We also revealed that intratumoral HLA-II presentation is dominated by professional antigen presenting cells (APCs), rather than cancer cells. Integrating these observations, we developed algorithms that accurately predict APC ligandomes, including peptides from phagocytosed cancer cells. These tools and biological insights will enhance HLA-II directed cancer therapies.
HostingRepository	MassIVE
AnnounceDate	2019-09-12
AnnouncementXML	Submission_2019-09-12_13:07:36.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jennifer Abelin
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Cysteinyl; Oxidation; Gln->pyro-Glu; Carbamidomethyl
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-18 07:21:21	ID requested
⏵ 1	2019-09-12 13:07:38	announced

Abelin JG, Harjanto D, Malloy M, Suri P, Colson T, Goulding SP, Creech AL, Serrano LR, Nasir G, Nasrullah Y, McGann CD, Velez D, Ting YS, Poran A, Rothenberg DA, Chhangawala S, Rubinsteyn A, Hammerbacher J, Gaynor RB, Fritsch EF, Greshock J, Oslund RC, Barthelme D, Addona TA, Arieta CM, Rooney MS, Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction. Immunity, 51(4):766-779.e17(2019) [pubmed]

submitter keyword: hla, epitope, prediction, classii, neoantigen

Jennifer Abelin
contact affiliation	Neon Therapeutics
contact email	jabelin@neontherapeutics.com
lab head
Jennifer Abelin
contact affiliation	Neon Therapeutics
contact email	jabelin@neontherapeutics.com
dataset submitter

MassIVE dataset URI

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