Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

Alex S Genshaft; Shuqiang Li; Caroline J Gallant; Spyros Darmanis; Sanjay M Prakadan; Carly G K Ziegler; Martin Lundberg; Simon Fredriksson; Joyce Hong; Aviv Regev; Kenneth J Livak; Ulf Landegren; Alex K Shalek

doi:10.1186/s13059-016-1045-6

Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

Genome Biol. 2016 Sep 19;17(1):188. doi: 10.1186/s13059-016-1045-6.

Authors

Alex S Genshaft^{1

2

3

4}, Shuqiang Li³, Caroline J Gallant⁵, Spyros Darmanis^{5

6}, Sanjay M Prakadan^{1

2

3

4}, Carly G K Ziegler^{1

3

4

7}, Martin Lundberg⁸, Simon Fredriksson⁸, Joyce Hong⁹, Aviv Regev^{3

10

11}, Kenneth J Livak¹², Ulf Landegren⁵, Alex K Shalek^{13

14

15

16

17}

Affiliations

¹ Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
² Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
³ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁴ Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA.
⁵ Department of Immunology, Genetics & Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
⁶ Departments of Bioengineering and Applied Physics, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA.
⁷ Division of Health Sciences & Technology, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA.
⁸ Olink Proteomics, Uppsala, Sweden.
⁹ Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁰ Department of Biology and Koch Institute, MIT, Boston, MA, 02142, USA.
¹¹ Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
¹² Fluidigm Corporation, South San Francisco, CA, USA. ken.livak@fluidigm.com.
¹³ Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA. shalek@mit.edu.
¹⁴ Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. shalek@mit.edu.
¹⁵ Broad Institute of MIT and Harvard, Cambridge, MA, USA. shalek@mit.edu.
¹⁶ Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA. shalek@mit.edu.
¹⁷ Division of Health Sciences & Technology, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA. shalek@mit.edu.

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.

Keywords: Metadata; Proximity extension assay; Single-cell multi-omics; Single-cell proteomics; Single-cell transcriptomics.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Breast Neoplasms / genetics*
Breast Neoplasms / pathology
Female
Gene Expression Profiling
Humans
Proteome / genetics*
RNA / biosynthesis
RNA / genetics*
Single-Cell Analysis
Transcriptome / genetics*

Substances

Proteome
RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding