Dataset Information

Characterizing T-cell immunopeptidomes

ABSTRACT: Imunopeptidomes promise novel surface markers as ideal targets for immunotherapies, but their characterization by mass spectrometry (MS) remains challenging. Until recently, cell numbers exceeding 1.0xE9 were needed for reasonably deep immunopeptidome surveys of at least 1,000 HLA ligands. Such limitation in analytical sensitivity necessarily constrains the types of clinical specimens that can evaluated. To evaluate the feasibility of immunopeptidome profiling from limiting cell amounts, primary purified human regulatory (Treg) and conventional T cells (Tconv) were compared, evaluating the relative immunopeptide recovery from T cells isolated from individual healthy donors (N=5) versus pools (N=2 pools from 13 donors). Two donors’ Tconv were subsequently stimulated with CD3/CD28 and IL-2 and compared to resting Tconv. The combined T-cell immunopeptide dataset reported here contains over 13,000 unique peptides derived from over 5,000 proteins. In comparison to protein expression, T cell immunopeptidomes revealed complementary aspects of T cell biology, while pointing to HLA ligands specific for distinct T cell subsets (e.g., FOXP3, CD5 and WNK1). Taken together, these findings have implications for understanding conditions required to induce therapeutic immune responses and may open up new avenues for tuning Treg suppressive functions to treat cancer.

INSTRUMENT(S): Orbitrap Fusion Lumos, LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): T Cell, Blood

SUBMITTER: Niclas Olsson

LAB HEAD: Joshua E Elias

PROVIDER: PXD007860 | Pride | 2018-03-08

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	20170728_swissprot_reviewed_with_contam.fasta	Fasta
	Donor_5_Expanded_CD4p_CD25neg_MHC1_Fusion_PSMs.txt	Txt
	Donor_6_expanded_CD4p_CD25neg_MHC1_Fusion_PSMs.txt	Txt
	FL0012779.raw	Raw
	FL0012783.raw	Raw

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Publications

T-Cell Immunopeptidomes Reveal Cell Subtype Surface Markers Derived From Intracellular Proteins.

Olsson Niclas N Schultz Liora M LM Zhang Lichao L Khodadoust Michael S MS Narayan Rupa R Czerwinski Debra K DK Levy Ronald R Elias Joshua E JE

Proteomics 20180418 12

Immunopeptidomes promise novel surface markers as ideal immunotherapy targets, but their characterization by mass spectrometry (MS) remains challenging. Until recently, cell numbers exceeding 10<sup>9</sup> were needed to survey thousands of HLA ligands. Such limited analytical sensitivity has historically constrained the types of clinical specimens that can be evaluated to cell cultures or bulk tissues. Measuring immunopeptidomes from purified cell subpopulations would be preferable for many ap ...[more]

PMID: 29493099

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