Cited by 129Single-cell and spatial transcriptomicsRNA Research and SplicingGene Regulatory Network Analysis

A combined approach for single-cell mRNA and intracellular protein expression analysis

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Reimegård, Johan, Tarbier, Marcel, Danielsson, Marcus, Schuster, Jens, Baskaran, Sathishkumar, Panagiotou, Styliani, Dahl, Niklas, Friedländer, Marc R. +1 more·2021·Communications Biology

Abstract

Combined measurements of mRNA and protein expression in single cells enable in-depth analysis of cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells. We show that mRNA expression fails to accurately reflect protein abundance at the time of measurement, although the direction of changes is in agreement during neuronal differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do their corresponding transcripts. Finally, we highlight that protein expression variation is overall lower than mRNA variation, but relative protein variation does not reflect the mRNA level. Our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. SPARC presents a state-of-the-art co-profiling method that overcomes current limitations in throughput and protein localization, including removing the need for cell fixation.

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  • mRNA abundance from transcriptomics alone is insufficient to infer protein abundance.

    “For example, mRNA abundance from transcriptomics alone is insufficient to infer protein abundance [Chen et al., 2020; Reimegård et al., 2021]”

    From Cell signaling pathways discovery from multi-modal data (2025) · cites this paper as Reimegård et al., 2021

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Authors
Reimegård, J., Tarbier, M., Danielsson, M., Schuster, J., Baskaran, S., Panagiotou, S., Dahl, N., Friedländer, M. R., & Gallant, C. J.
Affiliations
  • Uppsala University (SE)
  • Stockholm University (SE)
Corresponding author
Gallant, Caroline J.
Venue
Communications Biology
Published
2021-05-25
Volume
4
Issue
1
Pages
624-624
ISSN
2399-3642 (ISSN-L)
OpenAlex
W3164706810
Cited by
129
References
39
Citations by year
2026: 25 · 2025: 26 · 2024: 22 · 2023: 23 · 2022: 28 · 2021: 5
FWCI
6.12
Type
journal article
Language
en
Open access
Locations
  • Communications Biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Uppsala University Publications (Uppsala University) (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
Vetenskapsrådet (2017-05229)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Keywords
single-cell transcriptomics, single-cell proteomics, proximity extension assay, SPARC, intracellular protein expression, neuronal differentiation, transcription factor activity, mRNA-protein correlation, protein localization
MeSH terms
Humans, Proteins, RNA, Messenger, Transcription, Genetic, Sequence Analysis, RNA, Gene Expression Profiling, Proteomics, Single-Cell Analysis

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