title: Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells.
abstract: Significant advances have been made in methods to analyze genomes and transcriptomes of single cells, but to fully define cell states, proteins must also be accessed as central actors defining a cell's phenotype. Methods currently used to analyze endogenous protein expression in single cells are limited in specificity, throughput, or multiplex capability. Here, we present an approach to simultaneously and specifically interrogate large sets of protein and RNA targets in lysates from individual cells, enabling investigations of cell functions and responses. We applied our method to investigate the effects of BMP4, an experimental therapeutic agent, on early-passage glioblastoma cell cultures. We uncovered significant heterogeneity in responses to treatment at levels of RNA and protein, with a subset of cells reacting in a distinct manner to BMP4. Moreover, we found overall poor correlation between protein and RNA at the level of single cells, with proteins more accurately defining responses to treatment.
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden.
authors.forename: Spyros
authors.initials: S
authors.lastname: Darmanis
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden.
authors.forename: Caroline Julie
authors.initials: CJ
authors.lastname: Gallant
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden.
authors.forename: Voichita Dana
authors.initials: VD
authors.lastname: Marinescu
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden.
authors.forename: Mia
authors.initials: M
authors.lastname: Niklasson
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden.
authors.forename: Anna
authors.initials: A
authors.lastname: Segerman
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden.
authors.forename: Georgios
authors.initials: G
authors.lastname: Flamourakis
authors.affiliation: Olink Bioscience, Uppsala 75237, Sweden.
authors.forename: Simon
authors.initials: S
authors.lastname: Fredriksson
authors.affiliation: Olink Bioscience, Uppsala 75237, Sweden.
authors.forename: Erika
authors.initials: E
authors.lastname: Assarsson
authors.affiliation: Olink Bioscience, Uppsala 75237, Sweden.
authors.forename: Martin
authors.initials: M
authors.lastname: Lundberg
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden.
authors.forename: Sven
authors.initials: S
authors.lastname: Nelander
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden.
authors.forename: Bengt
authors.initials: B
authors.lastname: Westermark
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75108, Sweden; Science for Life Laboratory, Uppsala University, Uppsala 75108, Sweden. Electronic address: ulf.landegren@igp.uu.se.
authors.forename: Ulf
authors.initials: U
authors.lastname: Landegren
mesh_terms: D045744:Cell Line, Tumor; D006801:Humans; D011506:Proteins / Q000235:genetics*; D040901:Proteomics / Q000379:methods*; D012313:RNA / Q000235:genetics*
chemical_list: D011506:Proteins; D012313:RNA