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Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution

Author

Listed:
  • Ana Martinez-Val

    (University of Copenhagen)

  • Dorte B. Bekker-Jensen

    (University of Copenhagen
    Evosep Systems)

  • Sophia Steigerwald

    (University of Copenhagen
    Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction)

  • Claire Koenig

    (University of Copenhagen)

  • Ole Østergaard

    (University of Copenhagen)

  • Adi Mehta

    (Oslo University Hospital, Rikshospitalet)

  • Trung Tran

    (Oslo University Hospital, Rikshospitalet)

  • Krzysztof Sikorski

    (Oslo University Hospital, Rikshospitalet)

  • Estefanía Torres-Vega

    (University of Copenhagen)

  • Ewa Kwasniewicz

    (University of Copenhagen)

  • Sólveig Hlín Brynjólfsdóttir

    (Danish Cancer Society)

  • Lisa B. Frankel

    (Danish Cancer Society
    Danish Cancer Society Research Center
    University of Copenhagen)

  • Rasmus Kjøbsted

    (University of Copenhagen)

  • Nicolai Krogh

    (University of Copenhagen)

  • Alicia Lundby

    (University of Copenhagen
    University of Copenhagen)

  • Simon Bekker-Jensen

    (University of Copenhagen)

  • Fridtjof Lund-Johansen

    (Oslo University Hospital, Rikshospitalet)

  • Jesper V. Olsen

    (University of Copenhagen)

Abstract

Dynamic change in subcellular localization of signaling proteins is a general concept that eukaryotic cells evolved for eliciting a coordinated response to stimuli. Mass spectrometry-based proteomics in combination with subcellular fractionation can provide comprehensive maps of spatio-temporal regulation of protein networks in cells, but involves laborious workflows that does not cover the phospho-proteome level. Here we present a high-throughput workflow based on sequential cell fractionation to profile the global proteome and phospho-proteome dynamics across six distinct subcellular fractions. We benchmark the workflow by studying spatio-temporal EGFR phospho-signaling dynamics in vitro in HeLa cells and in vivo in mouse tissues. Finally, we investigate the spatio-temporal stress signaling, revealing cellular relocation of ribosomal proteins in response to hypertonicity and muscle contraction. Proteomics data generated in this study can be explored through https://SpatialProteoDynamics.github.io .

Suggested Citation

  • Ana Martinez-Val & Dorte B. Bekker-Jensen & Sophia Steigerwald & Claire Koenig & Ole Østergaard & Adi Mehta & Trung Tran & Krzysztof Sikorski & Estefanía Torres-Vega & Ewa Kwasniewicz & Sólveig Hlín B, 2021. "Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-27398-y
    DOI: 10.1038/s41467-021-27398-y
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    References listed on IDEAS

    as
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    Cited by:

    1. Henrik M. Hammarén & Eva-Maria Geissen & Clement M. Potel & Martin Beck & Mikhail M. Savitski, 2022. "Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Julia P. Schessner & Vincent Albrecht & Alexandra K. Davies & Pavel Sinitcyn & Georg H. H. Borner, 2023. "Deep and fast label-free Dynamic Organellar Mapping," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    3. Tanveer Singh Batth & Marie Locard-Paulet & Nadezhda T. Doncheva & Blanca Lopez Mendez & Lars Juhl Jensen & Jesper Velgaard Olsen, 2024. "Streamlined analysis of drug targets by proteome integral solubility alteration indicates organ-specific engagement," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. Joanne Watson & Harriet R. Ferguson & Rosie M. Brady & Jennifer Ferguson & Paul Fullwood & Hanyi Mo & Katherine H. Bexley & David Knight & Gareth Howell & Jean-Marc Schwartz & Michael P. Smith & Chiar, 2022. "Spatially resolved phosphoproteomics reveals fibroblast growth factor receptor recycling-driven regulation of autophagy and survival," Nature Communications, Nature, vol. 13(1), pages 1-22, December.

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