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Analysis of context-specific KRAS-effector (sub)complexes in Caco-2 cells
Univ Coll Dublin, Sch Med, Syst Biol Ireland, Dublin, Ireland.;Univ Coll Dublin, UCD Charles Inst Dermatol, Sch Med, Dublin, Ireland..
Univ Coll Dublin, Sch Med, Syst Biol Ireland, Dublin, Ireland.;Univ Coll Dublin, UCD Charles Inst Dermatol, Sch Med, Dublin, Ireland..ORCID iD: 0000-0002-5228-3896
Univ Coll Dublin, Sch Med, Syst Biol Ireland, Dublin, Ireland.;Univ Coll Dublin, UCD Charles Inst Dermatol, Sch Med, Dublin, Ireland..ORCID iD: 0000-0003-2596-6998
Univ Coll Dublin, Sch Med, Syst Biol Ireland, Dublin, Ireland.;Univ Coll Dublin, UCD Charles Inst Dermatol, Sch Med, Dublin, Ireland..
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2023 (English)In: Life Science Alliance, E-ISSN 2575-1077, Vol. 6, no 5, article id e202201670Article in journal (Refereed) Published
Abstract [en]

Ras is a key switch controlling cell behavior. In the GTP-bound form, Ras interacts with numerous effectors in a mutually ex-clusive manner, where individual Ras-effectors are likely part of larger cellular (sub)complexes. The molecular details of these (sub)complexes and their alteration in specific contexts are not understood. Focusing on KRAS, we performed affinity puri-fication (AP)-mass spectrometry (MS) experiments of exoge-nously expressed FLAG-KRAS WT and three oncogenic mutants ("genetic contexts") in the human Caco-2 cell line, each exposed to 11 different culture media ("culture contexts") that mimic conditions relevant in the colon and colorectal cancer. We identified four effectors present in complex with KRAS in all genetic and growth contexts ("context-general effectors"). Seven effectors are found in KRAS complexes in only some contexts ("context-specific effectors"). Analyzing all interactors in complex with KRAS per condition, we find that the culture contexts had a larger impact on interaction rewiring than genetic contexts. We investigated how changes in the interactome impact functional outcomes and created a Shiny app for interactive visualization. We validated some of the functional differences in metabolism and proliferation. Finally, we used networks to evaluate how KRAS-effectors are involved in the modulation of functions by random walk analyses of effector-mediated (sub)complexes. Altogether, our work shows the impact of environmental contexts on network rewiring, which provides insights into tissue-specific signaling mechanisms. This may also explain why KRAS oncogenic mutants may be causing cancer only in specific tissues despite KRAS being expressed in most cells and tissues.

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Life Science Alliance, LLC , 2023. Vol. 6, no 5, article id e202201670
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Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Cell and Molecular Biology
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URN: urn:nbn:se:uu:diva-500330DOI: 10.26508/lsa.202201670ISI: 000952783000001PubMedID: 36894174OAI: oai:DiVA.org:uu-500330DiVA, id: diva2:1750825
Available from: 2023-04-14 Created: 2023-04-14 Last updated: 2023-04-14Bibliographically approved

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Wåhlén, ErikHeldin, Johan

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