Highly multiplexed and quantitative cell-surface protein profiling using genetically barcoded antibodies

Proceedings of the National Academy of Sciences of the United States of America
Samuel B PollockJames A Wells

Abstract

Human cells express thousands of different surface proteins that can be used for cell classification, or to distinguish healthy and disease conditions. A method capable of profiling a substantial fraction of the surface proteome simultaneously and inexpensively would enable more accurate and complete classification of cell states. We present a highly multiplexed and quantitative surface proteomic method using genetically barcoded antibodies called phage-antibody next-generation sequencing (PhaNGS). Using 144 preselected antibodies displayed on filamentous phage (Fab-phage) against 44 receptor targets, we assess changes in B cell surface proteins after the development of drug resistance in a patient with acute lymphoblastic leukemia (ALL) and in adaptation to oncogene expression in a Myc-inducible Burkitt lymphoma model. We further show PhaNGS can be applied at the single-cell level. Our results reveal that a common set of proteins including FLT3, NCR3LG1, and ROR1 dominate the response to similar oncogenic perturbations in B cells. Linking high-affinity, selective, genetically encoded binders to NGS enables direct and highly multiplexed protein detection, comparable to RNA-sequencing for mRNA. PhaNGS has the potential to profil...Continue Reading

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Citations

Sep 26, 2020·Proceedings of the National Academy of Sciences of the United States of America·Jie ZhouJames A Wells
Oct 31, 2018·Proceedings of the National Academy of Sciences of the United States of America·Damaris Bausch-FluckBernd Wollscheid
Feb 2, 2019·SLAS Technology·Loïc BinanSantiago Costantino
Mar 9, 2019·Current Opinion in Biotechnology·Koli BasuCharles S Craik
May 27, 2021·Scientific Reports·Cyrille L Delley, Adam R Abate
Jul 2, 2021·Expert Review of Proteomics·Jarne Pauwels, Kris Gevaert
Jul 23, 2020·Journal of Proteome Research·Matthew Waas, Thomas Kislinger
Oct 15, 2021·Nature Communications·Mary S MorrisonDavid R Liu
Sep 8, 2021·Journal of Proteome Research·Longxiang WangAntoine Dufour

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Datasets Mentioned

BETA
GSE102712
GSE102301

Methods Mentioned

BETA
phage display
PCR
xenografts
RNAseq
Flow Cytometry

Software Mentioned

Excel
STDEV

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