Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution

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 Brynjólfsdóttir, Lisa B. Frankel, Rasmus Kjøbsted, Nicolai Krogh, Alicia Lundby, Simon Bekker-Jensen, Fridtjof Lund-Johansen () and Jesper V. Olsen ()
Additional contact information
Ana Martinez-Val: University of Copenhagen
Dorte B. Bekker-Jensen: University of Copenhagen
Sophia Steigerwald: University of Copenhagen
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
Rasmus Kjøbsted: University of Copenhagen
Nicolai Krogh: University of Copenhagen
Alicia Lundby: University of Copenhagen
Simon Bekker-Jensen: University of Copenhagen
Fridtjof Lund-Johansen: Oslo University Hospital, Rikshospitalet
Jesper V. Olsen: University of Copenhagen

Nature Communications, 2021, vol. 12, issue 1, 1-17

Abstract: 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 .

Date: 2021
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DOI: 10.1038/s41467-021-27398-y

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