Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
Open accessAbstract
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.
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Many multi-omics studies co-profiling protein and mRNA rely on predetermined curated antibody panels, losing novel and unexpected proteomic information.
“Many multi-omics studies, in which protein and mRNA are co-profiled, rely on the use of predetermined, curated antibody panels to confer single-cell phenotypes, thereby losing novel and unexpected proteomic information63–66.”
From The technological landscape and applications of single-cell multi-omics (2023) · cites this paper as [65]
An integrated method combining PEA and specific target amplification detects RNAs and proteins from the same single cell in a single reaction chamber of the Fluidigm C1 platform.
“An integrated protein and RNA detection method combining PEA and specific target amplification was also developed in 2016 to detect RNAs and proteins from the same single cell in a single reaction chamber of the Fluidigm C1 platform65.”
From The technological landscape and applications of single-cell multi-omics (2023) · cites this paper as [65]
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- Authors
- Genshaft, A. S., Li, S., Gallant, C. J., Darmanis, S., Prakadan, S. M., Ziegler, C. G. K., Lundberg, M., Fredriksson, S., Hong, J., Regev, A., Livak, K. J., Landegren, U., & Shalek, A. K.
- Affiliations
- Broad Institute (US)
- Uppsala University (SE)
- Olink Bioscience (Sweden) (SE)
- Massachusetts Institute of Technology (US)
- Standard BioTools (United States) (US)
- Corresponding author
- Livak, Kenneth J.
- Shalek, Alex K.
- ORCID
- Venue
- Genome Biology
- Published
- 2016-09-19
- Volume
- 17
- Issue
- 1
- Pages
- 188-188
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC5027636
- OpenAlex
- W2522699003
- Cited by
- 175
- References
- 53
- Citations by year
- 2026: 6 · 2025: 12 · 2024: 10 · 2023: 25 · 2022: 15 · 2021: 15 · 2020: 20 · 2019: 25 · 2018: 22 · 2017: 23
- FWCI
- 12.06
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Uppsala University Publications (Uppsala University) (submittedVersion, other-oa)
- Funders
- Searle Scholars Program
- Arnold and Mabel Beckman Foundation (Beckman Young Investigator)
- National Institutes of Health (P50HG006193, T32GM007753, U24AI11862, DP2OD020839)
- Klarman Cell Observatory
- European Community (7th Framework Program)
- Howard Hughes Medical Institute
- European Community's 7th Framework Program (259796)
- European Research Council (294409)
- Vetenskapsrådet
- IngaBritt och Arne Lundbergs Forskningsstiftelse
- Svenska Sällskapet för Medicinsk Forskning
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Keywords
- single-cell proteomics, single-cell transcriptomics, proximity extension assay, reverse transcriptase, breast adenocarcinoma, chemical perturbation, single-cell RNA sequencing
- MeSH terms
- Breast Neoplasms, Female, Humans, RNA, Proteome, Gene Expression Profiling, Single-Cell Analysis, Transcriptome
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