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DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2017-03-27
  • AnnouncementXML: Submission_2017-03-27_00:54:51.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Niclas Olsson
  • Title: Antigen Presentation Profiling Reveals T-cell Recognition of Lymphoma Immunoglobulin Neoantigens
  • Description: Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. Such neoantigens have been implicated in response to immunotherapies including immune checkpoint blockade, yet their identification and validation remains challenging. Here we discover neoantigens in human mantle cell lymphomas using an integrated strategy for genomic and proteomic tumor antigen discovery that interrogates peptides presented within the tumor major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically identify neoantigen peptides in diagnostic tumor specimens from 17 patients and several cell lines. Remarkably, the discovered neoantigenic peptides were invariably derived from the lymphoma immunoglobulin (Ig) heavy or light chain variable regions. Although we could identify MHC presentation of private germline polymorphic alleles, no mutated peptides were recovered from non-Ig somatically mutated genes. The immunoglobulin variable region somatic mutations were almost exclusively presented by MHC-II. We found T-cells specific for an immunoglobulin-derived neoantigen in the blood of a patient using MHC-II tetramers, and these T-cell clones expanded in frequency following tumor vaccination. These results demonstrate that an integrative approach combining MHC isolation, peptide identification and exome sequencing is an effective platform to uncover tumor neoantigens. Application of this strategy to human lymphoma implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.
  • SpeciesList: scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
  • ModificationList: phosphorylated residue; monohydroxylated residue; deamidated residue
  • Instrument: LTQ Orbitrap Elite

Dataset History

VersionDatetimeStatusChangeLog Entry
02017-01-15 09:29:50ID requested
12017-03-27 00:54:52announced

Publication List

  1. Khodadoust MS, Olsson N, Wagar LE, Haabeth OA, Chen B, Swaminathan K, Rawson K, Liu CL, Steiner D, Lund P, Rao S, Zhang L, Marceau C, Stehr H, Newman AM, Czerwinski DK, Carlton VE, Moorhead M, Faham M, Kohrt HE, Carette J, Green MR, Davis MM, Levy R, Elias JE, Alizadeh AA, Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens. Nature, 543(7647):723-727(2017) [pubmed]

Keyword List

  1. curator keyword: Biological, Biomedical
  2. submitter keyword: Human, LTQ Orbitrap Elite, antigen presentation, MHC class I

Contact List

    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: Stanford University
    • contact email: nolsson@stanford.edu
    • dataset submitter:

Full Dataset Link List

  1. Dataset FTP location
  2. PRIDE project URI
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