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Front Genet. 2014 Sep 25;5:331. doi: 10.3389/fgene.2014.00331. eCollection 2014.

Characterizing the human hematopoietic CDome.

Author information

1
Department of Clinical Immunology, Odense University Hospital, University of Southern Denmark Odense, Denmark.
2
Disease Systems Biology, Novo Nordisk Center for Protein Research, University of Copenhagen Copenhagen, Denmark ; Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark Lyngby, Denmark.
3
Department of Biology, Bioinformatics Centre, University of Copenhagen Copenhagen, Denmark.

Abstract

In this study, we performed extensive semi-automated data collection from the primary and secondary literature in an effort to characterize the expression of all membrane proteins within the CD scheme on hematopoietic cells. Utilizing over 6000 data points across 305 CD molecules on 206 cell types, we seek to give a preliminary characterization of the "human hematopoietic CDome." We encountered severe gaps in the knowledge of CD protein expression, mostly resulting from incomplete and unstructured data generation, which we argue inhibit both basic research as well as therapies seeking to target membrane proteins. We detail these shortcomings and propose strategies to overcome these issues. Analyzing the available data, we explore the functional characteristics of the CD molecules both individually and across the groups of hematopoietic cells on which they are expressed. We compare protein and mRNA data for a subset of CD molecules, and explore cell functions in the context of CD protein expression. We find that the presence and function of CD molecules serve as good indicators for the overall function of the cells that express them, suggesting that increasing our knowledge about the cellular CDome may serve to stratify cells on a more functional level.

KEYWORDS:

CD molecules; flow cytometry; immunophenotyping; immunotherapy; membrane proteins; proteomics

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