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Cited by 4Protein Kinase Regulation and GTPase SignalingGene Regulatory Network AnalysisPI3K/AKT/mTOR signaling in cancer

Computational modeling implicates protein scaffolding in p38 regulation of Akt

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Kinnunen, Patrick C., Luker, Gary D., Luker, Kathryn E., Linderman, Jennifer J.·2022·Journal of Theoretical Biology
DOI 10.1016/j.jtbi.2022.111294PMC PMC10394737
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Abstract

Cells process environmental cues by activating intracellular signaling pathways with numerous interconnections and opportunities for cross-regulation. We employed a systems biology approach to investigate intersections of kinase p38, a context-dependent tumor suppressor or promoter, with Akt and ERK, two kinases known to promote cell survival, proliferation, and drug resistance in cancer. Using live, single cell microscopy, multiplexed fluorescent reporters of p38, Akt, and ERK activities, and a custom automated image-processing pipeline, we detected marked heterogeneity of signaling outputs in breast cancer cells stimulated with chemokine CXCL12 or epidermal growth factor (EGF). Basal activity of p38 correlated inversely with amplitude of Akt and ERK activation in response to either ligand. Remarkably, small molecule inhibitors of p38 immediately decreased basal activities of Akt and ERK but increased the proportion of cells with high amplitude ligand-induced activation of Akt signaling. To identify mechanisms underlying cross-talk of p38 with Akt signaling, we developed a computational model incorporating subcellular compartmentalization of signaling molecules by scaffold proteins. Dynamics of this model revealed that subcellular scaffolding of Akt accounted for observed regulation by p38. The model also predicted that differences in the amount of scaffold protein in a subcellular compartment captured the observed single cell heterogeneity in signaling. Finally, our model predicted that reduction in kinase signaling can be accomplished by both scaffolding and direct kinase inhibition. However, scaffolding inhibition can potentiate future kinase activity by redistribution of pathway components, potentially amplifying oncogenic signaling. These studies reveal how computational modeling can decipher mechanisms of cross-talk between the p38 and Akt signaling pathways and point to scaffold proteins as central regulators of signaling dynamics and amplitude.

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References 50 · Cited by 4

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  1. [1]Miura H, Kondo Y, Matsuda M & Aoki K Cell-to-Cell Heterogeneity in p38-Mediated Cross-Inhibition of JNK Causes Stochastic Cell Death. Cell Rep 24, 2658– 2668 (2018). 30184500
  2. [3]Tomida T, Takekawa M & Saito H Oscillation of p38 activity controls efficient pro-inflammatory gene expression. Nat. Commun 6, (2015). PMC4598561 26399197
  3. [4]Yao J, Pilko A & Wollman R Distinct cellular states determine calcium signaling response. Mol. Syst. Biol 12, 894 (2016). 27979909 PMC5199124
  4. [5]Iwamoto K, Shindo Y & Takahashi K Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway. PLOS Comput. Biol 12, e1005222 (2016). 27902699 PMC5130170
  5. [6]Kim E, Kim J-Y, Smith MA, Haura EB & Anderson ARA Cell signaling heterogeneity is modulated by both cell-intrinsic and -extrinsic mechanisms: An integrated approach to understanding targeted therapy. PLOS Biol 16, e2002930 (2018). 29522507 PMC5844524
  6. [7]Gerosa L Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells. Cell Syst 11, 478– 494. e9 (2020). 33113355 PMC8009031
  7. [8]Comandante-Lou N, Khaliq M, Venkat D, Manikkam M & Fallahi-Sichani M Phenotype-based probabilistic analysis of heterogeneous responses to cancer drugs and their combination efficacy. PLOS Comput. Biol 16, e1007688 (2020). 32084135 PMC7055924
  8. [9]Canovas B & Nebreda AR Diversity and versatility of p38 kinase signalling in health and disease. Nat. Rev. Mol. Cell Biol 1– 21 (2021) doi: 10.1038/s41580-020-00322-w. 33504982 PMC7838852 · DOI · Paper page
  9. [10]Zhang Y PP2AC Level Determines Differential Programming of p38-TSC-mTOR Signaling and Therapeutic Response to p38-Targeted Therapy in Colorectal Cancer. EBioMedicine 2, 1944– 1956 (2015). 26844273 PMC4703732
  10. [11]Chen L Inhibition of the p38 Kinase Suppresses the Proliferation of Human ER-Negative Breast Cancer Cells. Cancer Res 69, 8853– 8861 (2009). 19920204 PMC2830975
  11. [12]Fey D, Croucher DR, Kolch W & Kholodenko BN Crosstalk and Signaling Switches in Mitogen-Activated Protein Kinase Cascades. Front. Physiol 3, (2012). PMC3449335 23060802
  12. [13]Westermarck J, Li S-P, Kallunki T, Han J & Kähäri V-M p38 Mitogen-Activated Protein Kinase-Dependent Activation of Protein Phosphatases 1 and 2A Inhibits MEK1 and MEK2 Activity and Collagenase 1 (MMP-1) Gene Expression. Mol. Cell. Biol 21, 2373– 2383 (2001). 11259586 PMC86870
  13. [14]Saini KS Targeting the PI3K/AKT/mTOR and Raf/MEK/ERK pathways in the treatment of breast cancer. Cancer Treat. Rev 39, 935– 946 (2013). 23643661
  14. [16]Braun C p38 regulates the tumor suppressor PDCD4 via the TSC-mTORC1 pathway. Cell Stress 5, 176– 182 (2021). 34917890 PMC8645265
  15. [17]Wu R Hsp27 Regulates Akt Activation and Polymorphonuclear Leukocyte Apoptosis by Scaffolding MK2 to Akt Signal Complex*. J. Biol. Chem 282, 21598– 21608 (2007). 17510053
  16. [18]Kim J, Kang D, Sun BK, Kim J-H & Song JJ TRAIL/MEKK4/p38/HSP27/Akt survival network is biphasically modulated by the Src/CIN85/c-Cbl complex. Cell. Signal 25, 372– 379 (2013). 23085457
  17. [19]Nazarewicz RR Early Endosomal Antigen 1 (EEA1) Is an Obligate Scaffold for Angiotensin II-induced, PKC-α-dependent Akt Activation in Endosomes. J. Biol. Chem 286, 2886– 2895 (2011). 21097843 PMC3024784
  18. [20]Levchenko A, Bruck J & Sternberg PW Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc. Natl. Acad. Sci 97, 5818– 5823 (2000). 10823939 PMC18517
  19. [21]Locasale JW, Shaw AS & Chakraborty AK Scaffold proteins confer diverse regulatory properties to protein kinase cascades 6. PMC1948937 17686969
  20. [22]Kudo T Live-cell measurements of kinase activity in single cells using translocation reporters. Nat. Protoc 13, 155– 169 (2017). 29266096
  21. [23]Regot S, Hughey JJ, Bajar BT, Carrasco S & Covert MW High-Sensitivity Measurements of Multiple Kinase Activities in Live Single Cells. Cell 157, 1724– 1734 (2014). 24949979 PMC4097317
  22. [24]Bagley MC, Davis T, Murziani PGS, Widdowson CS & Kipling D Use of p38 MAPK Inhibitors for the Treatment of Werner Syndrome. Pharmaceuticals 3, 1842– 1872 (2010). 27713332 PMC4033955
  23. [25]Perdiguero E Genetic analysis of p38 MAP kinases in myogenesis: fundamental role of p38α in abrogating myoblast proliferation. EMBO J 26, 1245– 1256 (2007). 17304211 PMC1817635
  24. [26]Sugiyama MG, Fairn GD & Antonescu CN Akt-ing Up Just About Everywhere: Compartment-Specific Akt Activation and Function in Receptor Tyrosine Kinase Signaling. Front. Cell Dev. Biol 7, (2019). PMC6509475 31131274
  25. [27]Mendoza MC, Er EE & Blenis J The Ras-ERK and PI3K-mTOR pathways: cross-talk and compensation. Trends Biochem. Sci 36, 320– 328 (2011). 21531565 PMC3112285
  26. [28]Liang Y & Sheikh F Scaffold Proteins Regulating Extracellular Regulated Kinase Function in Cardiac Hypertrophy and Disease. Front. Pharmacol 7, (2016). PMC4770026 26973524
  27. [29]Good MC, Zalatan JG & Lim WA Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information. Science 332, 680– 686 (2011). 21551057 PMC3117218
  28. [30]Gonzalez E & McGraw TE Insulin-modulated Akt subcellular localization determines Akt isoform-specific signaling. Proc. Natl. Acad. Sci 106, 7004– 7009 (2009). 19372382 PMC2678468
  29. [31]Banani SF, Lee HO, Hyman AA & Rosen MK Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol 18, 285– 298 (2017). 28225081 PMC7434221
  30. [32]Su X Phase separation of signaling molecules promotes T cell receptor signal transduction. Science 352, 595– 599 (2016). 27056844 PMC4892427
  31. [33]Zou X & Blank M Targeting p38 MAP kinase signaling in cancer through post-translational modifications. Cancer Lett 384, 19– 26 (2017). 27725227
  32. [34]Bao F Akt scaffold proteins: the key to controlling specificity of Akt signaling. Am. J. Physiol.-Cell Physiol 321, C429– C442 (2021). 34161152
  33. [35]Locasale JW & Chakraborty AK Regulation of Signal Duration and the Statistical Dynamics of Kinase Activation by Scaffold Proteins. PLoS Comput. Biol 4, e1000099 (2008). 18584022 PMC2427176
  34. [36]Su Z, Dhusia K & Wu Y Understand the Functions of Scaffold Proteins in Cell Signaling by a Mesoscopic Simulation Method. Biophys. J 119, 2116– 2126 (2020). 33113350 PMC7732726
  35. [37]Martínez-Limón A, Joaquin M, Caballero M, Posas F & de Nadal E The p38 Pathway: From Biology to Cancer Therapy. Int. J. Mol. Sci 21, 1913 (2020). 32168915 PMC7139330
  36. [38]Domanska UM A review on CXCR4/CXCL12 axis in oncology: No place to hide. Eur. J. Cancer 49, 219– 230 (2013). 22683307
  37. [39]Normanno N Epidermal growth factor receptor (EGFR) signaling in cancer. Gene 366, 2– 16 (2006). 16377102
  38. [40]Betz C mTOR complex 2-Akt signaling at mitochondria-associated endoplasmic reticulum membranes (MAM) regulates mitochondrial physiology. Proc. Natl. Acad. Sci 110, 12526– 12534 (2013). 23852728 PMC3732980
  39. [41]Mazumder S Indomethacin impairs mitochondrial dynamics by activating the PKCζ–p38–DRP1 pathway and inducing apoptosis in gastric cancer and normal mucosal cells. J. Biol. Chem 294, 8238– 8258 (2019). 30940726 PMC6527165
  40. [42]Debattisti V, Gerencser AA, Saotome M, Das S & Hajnóczky G ROS Control Mitochondrial Motility through p38 and the Motor Adaptor Miro/Trak. Cell Rep 21, 1667– 1680 (2017). 29117569 PMC5710826
  41. [43]Yang J-M Integrating chemical and mechanical signals through dynamic coupling between cellular protrusions and pulsed ERK activation. Nat. Commun 9, 4673 (2018). 30405112 PMC6220176
  42. [44]Colquhoun D, Dowsland KA, Beato M & Plested AJR How to Impose Microscopic Reversibility in Complex Reaction Mechanisms. Biophys. J 86, 3510– 3518 (2004). 15189850 PMC1304255
  43. [45]Kinzer-Ursem TL & Linderman JJ Both Ligand- and Cell-Specific Parameters Control Ligand Agonism in a Kinetic Model of G Protein–Coupled Receptor Signaling. PLoS Comput. Biol 3, e6 (2007). 17222056 PMC1769407
  44. [46]Marino S, Hogue IB, Ray CJ & Kirschner DE A methodology for performing global uncertainty and sensitivity analysis in systems biology. J. Theor. Biol 254, 178– 196 (2008). 18572196 PMC2570191

Authors
Kinnunen, P. C., Luker, G. D., Luker, K. E., & Linderman, J. J.
Affiliations
University of Michigan (US)
Corresponding author
Linderman, Jennifer J.
ORCID
Venue
Journal of Theoretical Biology
Publisher
Elsevier BV
Published
2022-12
Volume
555
Pages
111294
ISSN
0022-5193 (ISSN-L)
DOI
10.1016/j.jtbi.2022.111294
PMC
PMC10394737
OpenAlex
W4298137241
Cited by
4
References
50
Citations by year
2025: 1 · 2024: 2 · 2023: 1
FWCI
0.33
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Theoretical Biology (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • W. M. Keck Foundation
  • National Institutes of Health
  • Michigan Institute for Data Science, University of Michigan
  • National Cancer Institute (R33CA225549, U24CA237683, U01CA210152, R01CA238042, R01CA238023, R50CA221807, R37CA222563)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › PI3K/AKT/mTOR signaling in cancer
Keywords
p38 MAPK, Akt signaling, ERK signaling, protein scaffolding, breast cancer, CXCL12, epidermal growth factor, p38 inhibitor, subcellular compartmentalization, computational modeling of signaling
MeSH terms
Computer Simulation, Epidermal Growth Factor, Ligands, MAP Kinase Signaling System, Proto-Oncogene Proteins c-akt, Chemokine CXCL12

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