title: Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells.
abstract: Immunophenotyping by flow cytometry or immunohistochemistry is a clinical standard procedure for diagnosis, classification, and monitoring of hematologic malignancies. Antibody-based cell surface phenotyping is commonly limited to cell surface proteins for which specific antibodies are available and the number of parallel measurements is limited. The resulting limited knowledge about cell surface protein markers hampers early clinical diagnosis and subclassification of hematologic malignancies. Here, we describe the mass spectrometry based phenotyping of 2 all-trans retinoic acid treated acute myeloid leukemia model systems at an unprecedented level to a depth of more than 500 membrane proteins, including 137 bona fide cell surface exposed CD proteins. This extensive view of the leukemia surface proteome was achieved by developing and applying new implementations of the Cell Surface Capturing (CSC) technology. Bioinformatic and hierarchical cluster analysis showed that the applied strategy reliably revealed known differentiation-induced abundance changes of cell surface proteins in HL60 and NB4 cells and it also identified cell surface proteins with very little prior information. The extensive and quantitative analysis of the cell surface protein landscape from a systems biology perspective will be most useful in the clinic for the improved subclassification of hematologic malignancies and the identification of new drug targets.
authors.affiliation: Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
authors.forename: Andreas
authors.initials: A
authors.lastname: Hofmann
authors.forename: Bertran
authors.initials: B
authors.lastname: Gerrits
authors.forename: Alexander
authors.initials: A
authors.lastname: Schmidt
authors.forename: Thomas
authors.initials: T
authors.lastname: Bock
authors.forename: Damaris
authors.initials: D
authors.lastname: Bausch-Fluck
authors.forename: Rudolf
authors.initials: R
authors.lastname: Aebersold
authors.forename: Bernd
authors.initials: B
authors.lastname: Wollscheid
mesh_terms: D015703:Antigens, CD / Q000378:metabolism; D000970:Antineoplastic Agents / Q000494:pharmacology; D002454:Cell Differentiation / Q000187:drug effects; D045744:Cell Line, Tumor; D005434:Flow Cytometry; D018922:HL-60 Cells; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000188:drug therapy / Q000378:metabolism* / Q000473:pathology; D008565:Membrane Proteins / Q000378:metabolism; D009363:Neoplasm Proteins / Q000378:metabolism; D010641:Phenotype; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry; D014212:Tretinoin / Q000494:pharmacology
chemical_list: D015703:Antigens, CD; D000970:Antineoplastic Agents; D008565:Membrane Proteins; D009363:Neoplasm Proteins; D020543:Proteome; D014212:Tretinoin