Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells
Open accessAbstract
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.
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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 [64]
A method using PEA interrogated ~100 protein targets in single-cell lysates and simultaneously co-detected RNA by real-time PCR.
“Another method used a homogeneous affinity-based proximity extension assay (PEA) to interrogate ~100 protein targets in single-cell lysates by linking matched pairs of oligonucleotide–antibody conjugates to target antigens and simultaneously co-detecting RNA by real-time PCR64.”
From The technological landscape and applications of single-cell multi-omics (2023) · cites this paper as [64]
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- Authors
- Darmanis, S., Gallant, C. J., Marinescu, V. D., Niklasson, M., Segerman, A., Flamourakis, G., Fredriksson, S., Assarsson, E., Lundberg, M., Nelander, S., Westermark, B., & Landegren, U.
- Affiliations
- Uppsala University (SE)
- Olink Bioscience (Sweden) (SE)
- Corresponding author
- Landegren, Ulf
- ORCID
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2016-01
- Volume
- 14
- Issue
- 2
- Pages
- 380-389
- ISSN
- 2211-1247 (ISSN-L)
- PMC
- PMC4713867
- OpenAlex
- W2211104821
- Cited by
- 219
- References
- 33
- Citations by year
- 2026: 9 · 2025: 6 · 2024: 10 · 2023: 16 · 2022: 23 · 2021: 37 · 2020: 16 · 2019: 25 · 2018: 34 · 2017: 25 · 2016: 17
- FWCI
- 11.01
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- KTH Publication Database DiVA (KTH Royal Institute of Technology) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Svenska Sällskapet för Medicinsk Forskning
- Vetenskapsrådet
- IngaBritt och Arne Lundbergs Forskningsstiftelse
- Seventh Framework Programme (259796, FP/2007-2013)
- Knut och Alice Wallenbergs Stiftelse
- Cancerfonden
- European Research Council (294409)
- 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 › Molecular Biology Techniques and Applications
- Keywords
- endogenous protein expression, cellular heterogeneity, BMP4, glioblastoma, treatment response, cell states
- MeSH terms
- Humans, Proteins, RNA, Proteomics, Cell Line, Tumor
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