title: Cancer cell profiling by barcoding allows multiplexed protein analysis in fine-needle aspirates.
abstract: Immunohistochemistry-based clinical diagnoses require invasive core biopsies and use a limited number of protein stains to identify and classify cancers. We introduce a technology that allows analysis of hundreds of proteins from minimally invasive fine-needle aspirates (FNAs), which contain much smaller numbers of cells than core biopsies. The method capitalizes on DNA-barcoded antibody sensing, where barcodes can be photocleaved and digitally detected without any amplification steps. After extensive benchmarking in cell lines, this method showed high reproducibility and achieved single-cell sensitivity. We used this approach to profile ~90 proteins in cells from FNAs and subsequently map patient heterogeneity at the protein level. Additionally, we demonstrate how the method could be used as a clinical tool to identify pathway responses to molecularly targeted drugs and to predict drug response in patient samples. This technique combines specificity with ease of use to offer a new tool for understanding human cancers and designing future clinical trials.
authors.affiliation: Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN 5206, Boston, MA 02114, USA.
authors.forename: Adeeti V
authors.initials: AV
authors.lastname: Ullal
authors.forename: Vanessa
authors.initials: V
authors.lastname: Peterson
authors.forename: Sarit S
authors.initials: SS
authors.lastname: Agasti
authors.forename: Suan
authors.initials: S
authors.lastname: Tuang
authors.forename: Dejan
authors.initials: D
authors.lastname: Juric
authors.forename: Cesar M
authors.initials: CM
authors.lastname: Castro
authors.forename: Ralph
authors.initials: R
authors.lastname: Weissleder
mesh_terms: D000906:Antibodies / Q000276:immunology; D044963:Biopsy, Fine-Needle; D045744:Cell Line, Tumor; D004247:DNA / Q000378:metabolism; D006801:Humans; D009363:Neoplasm Proteins / Q000032:analysis* / Q000378:metabolism; D009369:Neoplasms / Q000378:metabolism*; D019869:Phosphatidylinositol 3-Kinases / Q000378:metabolism; D000081082:Phosphoinositide-3 Kinase Inhibitors; D040081:Protein Array Analysis / Q000379:methods*; D047428:Protein Kinase Inhibitors / Q000494:pharmacology; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000187:drug effects; D059010:Single-Cell Analysis
chemical_list: D000906:Antibodies; D004247:DNA; D009363:Neoplasm Proteins; D019869:Phosphatidylinositol 3-Kinases; D000081082:Phosphoinositide-3 Kinase Inhibitors; D047428:Protein Kinase Inhibitors