Dataset Information

The immunopeptidome of HLA-DR from PBMC

ABSTRACT: Quantifiying the impact of initial cell counts on the identified HLA-DR immunopeptidome of PBMC.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Cell, Blood

DISEASE(S): Disease Free

SUBMITTER: Hesham ElAbd

LAB HEAD: Prof. Dr. Andreas Tholey

PROVIDER: PXD023032 | Pride | 2021-08-23

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	08102020_0.5_all_ids_merged_psm_perc_filtered.mzTab.gz	Mztab
	08102020_1_all_ids_merged_psm_perc_filtered.mzTab.gz	Mztab
	08102020_HLA_0_5.mzML	Mzml
	08102020_HLA_0_5.raw	Raw
	08102020_HLA_1.mzML	Mzml

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Publications

Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data.

ElAbd Hesham H Degenhardt Frauke F Koudelka Tomas T Kamps Ann-Kristin AK Tholey Andreas A Bacher Petra P Lenz Tobias L TL Franke Andre A Wendorff Mareike M

BMC bioinformatics 20210817 1

<h4>Background</h4>The human leukocyte antigen (HLA) proteins play a fundamental role in the adaptive immune system as they present peptides to T cells. Mass-spectrometry-based immunopeptidomics is a promising and powerful tool for characterizing the immunopeptidomic landscape of HLA proteins, that is the peptides presented on HLA proteins. Despite the growing interest in the technology, and the recent rise of immunopeptidomics-specific identification pipelines, there is still a gap in data-anal ...[more]

PMID: 34404349

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Project description:Corneal endothelial cells (CECs) are critical to maintaining clarity of the cornea. This study was initiated to develop peripheral blood mononuclear cells (PBMC)-originated induced pluripotent stem cells (iPSCs)-derived CECs. We isolated PBMC and programmed the mononuclear cells to generate iPSCs. Subsequently, the PBMC-originated iPSCs were differentiated to CECs. The morphology of differentiating iPSCs was examined at regular intervals by phase contrast microscopy. In parallel, the expression of pluripotent, and CECs-associated markers was investigated by quantitative real-time PCR (qRT-PCR). The molecular architecture of the iPSCs-derived CECs and human corneal endothelium (CE) were examined by mass spectrometry-based proteome sequencing. The PBMC-originated iPSCs expressed pluripotent-specific markers at levels similar to expression in H9 human embryonic stem cells (hESCs). Phase contrast microscopy illustrated that iPSCs-derived CECs are tightly adherent, exhibiting a hexagonal-like shape, one of the cardinal characteristics of CECs. The CECs-associated markers were expressed at many orders of magnitude higher in iPSCs-derived CECs at days 13, 20, and 30 compared to their respective levels in iPSCs. Importantly, only residual expression levels of pluripotency markers were detected in iPSCs-derived CECs. Mass spectrometry-based proteome profiling identified 10,575 proteins in iPSCs-derived CECs. In parallel, we completed proteome profiling of the human CE identifying 6345 proteins. Of these, 5763 proteins were identified in the iPSCs-derived CECs suggesting a 90.82% overlap between the iPSCs-derived CECs and human CE proteomes. Importantly, cryopreservation of iPSCs-derived CECs did not affect the tight adherence of CECs, and their hexagonal-like shape while expressing high levels of CECs-associated markers. We have successfully developed a personalized approach to generate CECs that closely mimic the molecular architecture of the human CE. To the best of our knowledge, this is the first report describing the development of PBMC-originated, iPSCs-derived CECs.