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Mol Cell Proteomics. 2019 Jan 10. pii: mcp.RA118.001141. doi: 10.1074/mcp.RA118.001141. [Epub ahead of print]

Proteome analysis of human neutrophil granulocytes from patients with monogenic disease using data-independent acquisition.

Author information

1
TU Berlin, Germany.
2
Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, 80337 Munich, Germany, Germany.
3
Children's Hospital, Hematology-Oncology, Technical University Munich, 80804 Munich, Germany, Germany.
4
Acquired Immunodeficiency Research Center, Isfahan University of Medical Sciences, Isfahan, Iran, Iran (Islamic Republic of).
5
Schneider Children's Medical Center of Israel, Petah Tikva, Sackler School of Medicine Tel Aviv University, Israel, Israel.
6
Department of Pediatrics, Division of Pediatric Hematology & Oncology, Erciyes University, Kayseri, Turkey, Turkey.
7
Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel, Israel.
8
Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany, Germany.
9
Department of Pediatric Hematology Oncology, UZ Brussel, Brussels, Belgium, Belgium.
10
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Germany juri.rappsilber@ed.ac.uk.

Abstract

Neutrophil granulocytes are critical mediators of innate immunity and tissue regeneration. Rare diseases of neutrophil granulocytes may affect their differentiation and/or functions. However, there are very few validated diagnostic tests assessing the functions of neutrophil granulocytes in these diseases. Here, we set out to probe omics analysis as a novel diagnostic platform for patients with defective differentiation and function of neutrophil granulocytes. We analyzed highly purified neutrophil granulocytes from 68 healthy individuals and 16 patients with rare monogenic diseases. Cells were isolated from fresh venous blood (purity >99%) and used to create a spectral library covering almost 8000 proteins using strong cation exchange fractionation. Patient neutrophil samples were then analyzed by data-independent acquisition proteomics, quantifying 4154 proteins in each sample. Neutrophils with mutations in the neutrophil elastase gene ELANE, showed large proteome changes that suggest these mutations may affect maturation of neutrophil granulocytes and initiate misfolded protein response and cellular stress mechanisms. In contrast, only few proteins changed in patients with leukocyte adhesion deficiency (LAD) and chronic granulomatous disease (CGD). Strikingly, neutrophil transcriptome analysis showed no correlation with its proteome. In case of two patients with undetermined genetic causes, proteome analysis guided the targeted genetic diagnostics and uncovered the underlying genomic mutations. Data-independent acquisition proteomics may help to define novel pathomechanisms in neutrophil diseases and provide a clinically useful diagnostic dimension.

KEYWORDS:

Diagnostic; Immunology*; Omics; Personalized medicine; Proteogenomics; data-independent acquisition; neutrophil granulocyte; primary immunodeficiency diseases; systems medicine; whole exome sequencing

PMID:
30630937
DOI:
10.1074/mcp.RA118.001141
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