title: Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction.
abstract: We present a scalable, integrated strategy for coupled protein and RNA detection from single cells. Our approach leverages the DNA polymerase activity of reverse transcriptase to simultaneously perform proximity extension assays and complementary DNA synthesis in the same reaction. Using the Fluidigm C1™ system, we profile the transcriptomic and proteomic response of a human breast adenocarcinoma cell line to a chemical perturbation, benchmarking against in situ hybridizations and immunofluorescence staining, as well as recombinant proteins, ERCC Spike-Ins, and population lysate dilutions. Through supervised and unsupervised analyses, we demonstrate synergies enabled by simultaneous measurement of single-cell protein and RNA abundances. Collectively, our generalizable approach highlights the potential for molecular metadata to inform highly-multiplexed single-cell analyses.
authors.affiliation: Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.|Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.|Broad Institute of MIT and Harvard, Cambridge, MA, USA.|Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA.
authors.forename: Alex S
authors.initials: AS
authors.lastname: Genshaft
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, USA.
authors.forename: Shuqiang
authors.initials: S
authors.lastname: Li
authors.affiliation: Department of Immunology, Genetics & Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Caroline J
authors.initials: CJ
authors.lastname: Gallant
authors.affiliation: Department of Immunology, Genetics & Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.|Departments of Bioengineering and Applied Physics, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA.
authors.forename: Spyros
authors.initials: S
authors.lastname: Darmanis
authors.affiliation: Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.|Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.|Broad Institute of MIT and Harvard, Cambridge, MA, USA.|Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA.
authors.forename: Sanjay M
authors.initials: SM
authors.lastname: Prakadan
authors.affiliation: Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.|Broad Institute of MIT and Harvard, Cambridge, MA, USA.|Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA.|Division of Health Sciences & Technology, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA.
authors.forename: Carly G K
authors.initials: CG
authors.lastname: Ziegler
authors.affiliation: Olink Proteomics, Uppsala, Sweden.
authors.forename: Martin
authors.initials: M
authors.lastname: Lundberg
authors.affiliation: Olink Proteomics, Uppsala, Sweden.
authors.forename: Simon
authors.initials: S
authors.lastname: Fredriksson
authors.affiliation: Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
authors.forename: Joyce
authors.initials: J
authors.lastname: Hong
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, USA.|Department of Biology and Koch Institute, MIT, Boston, MA, 02142, USA.|Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.affiliation: Fluidigm Corporation, South San Francisco, CA, USA. ken.livak@fluidigm.com.
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Livak
authors.affiliation: Department of Immunology, Genetics & Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Ulf
authors.initials: U
authors.lastname: Landegren
authors.affiliation: Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA. shalek@mit.edu.|Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. shalek@mit.edu.|Broad Institute of MIT and Harvard, Cambridge, MA, USA. shalek@mit.edu.|Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA. shalek@mit.edu.|Division of Health Sciences & Technology, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA. shalek@mit.edu.
authors.forename: Alex K
authors.initials: AK
authors.lastname: Shalek
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D020543:Proteome / Q000235:genetics*; D012313:RNA / Q000096:biosynthesis / Q000235:genetics*; D059010:Single-Cell Analysis; D059467:Transcriptome / Q000235:genetics*
chemical_list: D020543:Proteome; D012313:RNA
keywords: Metadata; Proximity extension assay; Single-cell multi-omics; Single-cell proteomics; Single-cell transcriptomics