title: Technical and biological issues relevant to cell typing with aptamers.
abstract: A number of aptamers have been selected against cell surface biomarkers or against eukaryotic tissue culture cells themselves. To determine the general utility of aptamers for assessing the cell surface proteome, we developed a standardized flow cytometry assay and carried out a comprehensive study with 7 different aptamers and 14 different cell lines. By examining how aptamers performed with a variety of cell lines, we identified difficulties in using aptamers for cell typing. While there are some aptamers that show excellent correlation between cell surface binding and the expression of a biomarker on the cell surface, other aptamers showed nonspecific binding by flow cytometry. For example, it has recently been claimed that an anti-PTK7 (protein tyrosine kinase 7) aptamer identified a new biomarker for leukemia cells, but data with the additional cell lines shows that it is possible that the aptamer instead identifies a propensity for adherence. Better understanding and controlling for the role of background and nonspecific binding to cells should open the way to using arrays of aptamers for describing and quantifying the cell surface proteome.
authors.affiliation: Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.
authors.forename: Na
authors.initials: N
authors.lastname: Li
authors.forename: Jessica N
authors.initials: JN
authors.lastname: Ebright
authors.forename: Gwendolyn M
authors.initials: GM
authors.lastname: Stovall
authors.forename: Xi
authors.initials: X
authors.lastname: Chen
authors.forename: Hong Hanh
authors.initials: HH
authors.lastname: Nguyen
authors.forename: Amrita
authors.initials: A
authors.lastname: Singh
authors.forename: Angel
authors.initials: A
authors.lastname: Syrett
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Ellington
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D015153:Blotting, Western; D015815:Cell Adhesion Molecules / Q000235:genetics / Q000378:metabolism; D045744:Cell Line, Tumor; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D005434:Flow Cytometry; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism*; D018613:Microscopy, Confocal; D008954:Models, Biological; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D040901:Proteomics / Q000379:methods*; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D015815:Cell Adhesion Molecules; D004277:DNA, Single-Stranded; D008565:Membrane Proteins; C096905:PTK7 protein, human; D020794:Receptor Protein-Tyrosine Kinases