1
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Imoto H, Rauch N, Neve AJ, Khorsand F, Kreileder M, Alexopoulos LG, Rauch J, Okada M, Kholodenko BN, Rukhlenko OS. A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression. Biomolecules 2023; 13:1212. [PMID: 37627277 PMCID: PMC10452107 DOI: 10.3390/biom13081212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer cells often adapt to targeted therapies, yet the molecular mechanisms underlying adaptive resistance remain only partially understood. Here, we explore a mechanism of RAS/RAF/MEK/ERK (MAPK) pathway reactivation through the upregulation of RAF isoform (RAFs) abundance. Using computational modeling and in vitro experiments, we show that the upregulation of RAFs changes the concentration range of paradoxical pathway activation upon treatment with conformation-specific RAF inhibitors. Additionally, our data indicate that the signaling output upon loss or downregulation of one RAF isoform can be compensated by overexpression of other RAF isoforms. We furthermore demonstrate that, while single RAF inhibitors cannot efficiently inhibit ERK reactivation caused by RAF overexpression, a combination of two structurally distinct RAF inhibitors synergizes to robustly suppress pathway reactivation.
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Affiliation(s)
- Hiroaki Imoto
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Nora Rauch
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Ashish J. Neve
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Fahimeh Khorsand
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Martina Kreileder
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Leonidas G. Alexopoulos
- Protavio Ltd., Demokritos Science Park, 153 43 Athens, Greece
- Department of Mechanical Engineering, National Technical University of Athens, 106 82 Athens, Greece
| | - Jens Rauch
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Biomolecular and Biomedical Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Mariko Okada
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Osaka 565-0871, Japan
| | - Boris N. Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Oleksii S. Rukhlenko
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
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2
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Liu Z, Krstic A, Neve A, Casalou C, Rauch N, Wynne K, Cassidy H, McCann A, Kavanagh E, McCann B, Blanco A, Rauch J, Kolch W. Kinase Suppressor of RAS 1 (KSR1) Maintains the Transformed Phenotype of BRAFV600E Mutant Human Melanoma Cells. Int J Mol Sci 2023; 24:11821. [PMID: 37511580 PMCID: PMC10380721 DOI: 10.3390/ijms241411821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Kinase Suppressor of RAS 1 (KSR1) is a scaffolding protein for the RAS-RAF-MEK-ERK pathway, which is one of the most frequently altered pathways in human cancers. Previous results have shown that KSR1 has a critical role in mutant RAS-mediated transformation. Here, we examined the role of KSR1 in mutant BRAF transformation. We used CRISPR/Cas9 to knock out KSR1 in a BRAFV600E-transformed melanoma cell line. KSR1 loss produced a complex phenotype characterised by impaired proliferation, cell cycle defects, decreased transformation, decreased invasive migration, increased cellular senescence, and increased apoptosis. To decipher this phenotype, we used a combination of proteomic ERK substrate profiling, global protein expression profiling, and biochemical validation assays. The results suggest that KSR1 directs ERK to phosphorylate substrates that have a critical role in ensuring cell survival. The results further indicate that KSR1 loss induces the activation of p38 Mitogen-Activated Protein Kinase (MAPK) and subsequent cell cycle aberrations and senescence. In summary, KSR1 function plays a key role in oncogenic BRAF transformation.
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Affiliation(s)
- Zhi Liu
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Aleksandar Krstic
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Ashish Neve
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Cristina Casalou
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Nora Rauch
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Kieran Wynne
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Hilary Cassidy
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Biomolecular & Biomedical Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Amanda McCann
- School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Emma Kavanagh
- School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Brendan McCann
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Alfonso Blanco
- Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Jens Rauch
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Biomolecular & Biomedical Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
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3
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Iglesias-Martinez LF, Rauch N, Wynne K, McCann B, Kolch W, Rauch J. Interactome dynamics of RAF1-BRAF kinase monomers and dimers. Sci Data 2023; 10:203. [PMID: 37045861 PMCID: PMC10097620 DOI: 10.1038/s41597-023-02115-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
RAF kinases play major roles in cancer. BRAFV600E mutants drive ~6% of human cancers. Potent kinase inhibitors exist but show variable effects in different cancer types, sometimes even inducing paradoxical RAF kinase activation. Both paradoxical activation and drug resistance are frequently due to enhanced dimerization between RAF1 and BRAF, which maintains or restores the activity of the downstream MEK-ERK pathway. Here, using quantitative proteomics we mapped the interactomes of RAF1 monomers, RAF1-BRAF and RAF1-BRAFV600E dimers identifying and quantifying >1,000 proteins. In addition, we examined the effects of vemurafenib and sorafenib, two different types of clinically used RAF inhibitors. Using regression analysis to compare different conditions we found a large overlapping core interactome but also distinct condition specific differences. Given that RAF proteins have kinase independent functions such dynamic interactome changes could contribute to their functional diversification. Analysing this dataset may provide a deeper understanding of RAF signalling and mechanisms of resistance to RAF inhibitors.
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Affiliation(s)
| | - Nora Rauch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Brendan McCann
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
- Voscuris Ltd., Jefferson House 42 Queen Street, Belfast, BT1 6HL, United Kingdom
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
| | - Jens Rauch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
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4
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Rukhlenko OS, Halasz M, Rauch N, Zhernovkov V, Prince T, Wynne K, Maher S, Kashdan E, MacLeod K, Carragher NO, Kolch W, Kholodenko BN. Control of cell state transitions. Nature 2022; 609:975-985. [PMID: 36104561 PMCID: PMC9644236 DOI: 10.1038/s41586-022-05194-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Understanding cell state transitions and purposefully controlling them is a longstanding challenge in biology. Here we present cell state transition assessment and regulation (cSTAR), an approach for mapping cell states, modelling transitions between them and predicting targeted interventions to convert cell fate decisions. cSTAR uses omics data as input, classifies cell states, and develops a workflow that transforms the input data into mechanistic models that identify a core signalling network, which controls cell fate transitions by influencing whole-cell networks. By integrating signalling and phenotypic data, cSTAR models how cells manoeuvre in Waddington's landscape1 and make decisions about which cell fate to adopt. Notably, cSTAR devises interventions to control the movement of cells in Waddington's landscape. Testing cSTAR in a cellular model of differentiation and proliferation shows a high correlation between quantitative predictions and experimental data. Applying cSTAR to different types of perturbation and omics datasets, including single-cell data, demonstrates its flexibility and scalability and provides new biological insights. The ability of cSTAR to identify targeted perturbations that interconvert cell fates will enable designer approaches for manipulating cellular development pathways and mechanistically underpinned therapeutic interventions.
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Affiliation(s)
- Oleksii S Rukhlenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Melinda Halasz
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Nora Rauch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Vadim Zhernovkov
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Thomas Prince
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Stephanie Maher
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Eugene Kashdan
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth MacLeod
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Boris N Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
- Department of Pharmacology, Yale University School of Medicine, New Haven, USA.
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5
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Kholodenko BN, Rauch N, Kolch W, Rukhlenko OS. A systematic analysis of signaling reactivation and drug resistance. Cell Rep 2021; 35:109157. [PMID: 34038718 PMCID: PMC8202068 DOI: 10.1016/j.celrep.2021.109157] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/24/2021] [Accepted: 04/29/2021] [Indexed: 01/07/2023] Open
Abstract
Increasing evidence suggests that the reactivation of initially inhibited signaling pathways causes drug resistance. Here, we analyze how network topologies affect signaling responses to drug treatment. Network-dependent drug resistance is commonly attributed to negative and positive feedback loops. However, feedback loops by themselves cannot completely reactivate steady-state signaling. Newly synthesized negative feedback regulators can induce a transient overshoot but cannot fully restore output signaling. Complete signaling reactivation can only occur when at least two routes, an activating and inhibitory, connect an inhibited upstream protein to a downstream output. Irrespective of the network topology, drug-induced overexpression or increase in target dimerization can restore or even paradoxically increase downstream pathway activity. Kinase dimerization cooperates with inhibitor-mediated alleviation of negative feedback. Our findings inform drug development by considering network context and optimizing the design drug combinations. As an example, we predict and experimentally confirm specific combinations of RAF inhibitors that block mutant NRAS signaling. Kholodenko et al. uncover signaling network circuitries and molecular mechanisms necessary and sufficient for complete reactivation or overshoot of steady-state signaling after kinase inhibitor treatment. The two means to revive signaling output fully are through network topology or reactivation of the kinase activity of the primary drug target. Blocking RAF dimer activity by a combination of type I½ and type II RAF inhibitors efficiently blocks mutant NRAS-driven ERK signaling.
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Affiliation(s)
- Boris N Kholodenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland; Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
| | - Nora Rauch
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Oleksii S Rukhlenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
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6
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Kennedy SA, Jarboui MA, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, Stagljar I, LeBihan T, Imrie L, Pillai P, Lynn MA, Fasterius E, Al-Khalili Szigyarto C, Breen J, Kiel C, Serrano L, Rauch N, Rukhlenko O, Kholodenko BN, Iglesias-Martinez LF, Ryan CJ, Pilkington R, Cammareri P, Sansom O, Shave S, Auer M, Horn N, Klose F, Ueffing M, Boldt K, Lynn DJ, Kolch W. Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS G13D. Nat Commun 2020; 11:499. [PMID: 31980649 PMCID: PMC6981206 DOI: 10.1038/s41467-019-14224-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.
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Affiliation(s)
- Susan A Kennedy
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Mohamed-Ali Jarboui
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
- Werner Siemens Imaging Center, University of Tübingen, Tübingen, Germany
| | - Sriganesh Srihari
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
- QIMR-Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Cinzia Raso
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Kenneth Bryan
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Layal Dernayka
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Theodosia Charitou
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Manuel Bernal-Llinares
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | | | | | - David Matallanas
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Jasna Curak
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Thierry LeBihan
- Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Lisa Imrie
- Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Priyanka Pillai
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Miriam A Lynn
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Erik Fasterius
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cristina Al-Khalili Szigyarto
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - James Breen
- School of Biological Sciences, University of Adelaide Bioinformatics Hub, Adelaide, SA, Australia
- Computational & Systems Biology Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Christina Kiel
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Conway Institute, University College Dublin, Dublin, Ireland
| | - Luis Serrano
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nora Rauch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | - Boris N Kholodenko
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- School of Computer Science, University College Dublin, Dublin, Ireland
| | - Ruth Pilkington
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | - Owen Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Studies, Glasgow University, Glasgow, UK
| | - Steven Shave
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Manfred Auer
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Nicola Horn
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Franziska Klose
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.
| | - David J Lynn
- EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland.
- Conway Institute, University College Dublin, Dublin, Ireland.
- School of Medicine, University College Dublin, Dublin, Ireland.
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Rodriguez J, Herrero A, Li S, Rauch N, Quintanilla A, Wynne K, Krstic A, Acosta JC, Taylor C, Schlisio S, von Kriegsheim A. PHD3 Regulates p53 Protein Stability by Hydroxylating Proline 359. Cell Rep 2018; 24:1316-1329. [PMID: 30067985 PMCID: PMC6088137 DOI: 10.1016/j.celrep.2018.06.108] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 03/30/2018] [Accepted: 06/27/2018] [Indexed: 01/05/2023] Open
Abstract
Cellular p53 protein levels are regulated by a ubiquitination/de-ubiquitination cycle that can target the protein for proteasomal destruction. The ubiquitination reaction is catalyzed by a multitude of ligases, whereas the removal of ubiquitin chains is mediated by two deubiquitinating enzymes (DUBs), USP7 (HAUSP) and USP10. Here, we show that PHD3 hydroxylates p53 at proline 359, a residue that is in the p53-DUB binding domain. Hydroxylation of p53 upon proline 359 regulates its interaction with USP7 and USP10, and its inhibition decreases the association of p53 with USP7/USP10, increases p53 ubiquitination, and rapidly reduces p53 protein levels independently of mRNA expression. Our results show that p53 is a PHD3 substrate and that hydroxylation by PHD3 regulates p53 protein stability through modulation of ubiquitination.
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Affiliation(s)
- Javier Rodriguez
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland; Cancer Research UK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Ana Herrero
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Shuijie Li
- Ludwig Institute for Cancer Research Ltd., SE-17177 Stockholm, Sweden; Department of Microbiology and Tumor and Cell Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Nora Rauch
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Andrea Quintanilla
- Cancer Research UK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Kieran Wynne
- Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Aleksandar Krstic
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Juan Carlos Acosta
- Cancer Research UK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Cormac Taylor
- Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Susanne Schlisio
- Ludwig Institute for Cancer Research Ltd., SE-17177 Stockholm, Sweden; Department of Microbiology and Tumor and Cell Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Alex von Kriegsheim
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland; Cancer Research UK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh EH4 2XR, UK.
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8
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Verlande A, Krafčíková M, Potěšil D, Trantírek L, Zdráhal Z, Elkalaf M, Trnka J, Souček K, Rauch N, Rauch J, Kolch W, Uldrijan S. Metabolic stress regulates ERK activity by controlling KSR-RAF heterodimerization. EMBO Rep 2018; 19:320-336. [PMID: 29263201 PMCID: PMC5797961 DOI: 10.15252/embr.201744524] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/15/2017] [Accepted: 11/24/2017] [Indexed: 12/24/2022] Open
Abstract
Altered cell metabolism is a hallmark of cancer, and targeting specific metabolic nodes is considered an attractive strategy for cancer therapy. In this study, we evaluate the effects of metabolic stressors on the deregulated ERK pathway in melanoma cells bearing activating mutations of the NRAS or BRAF oncogenes. We report that metabolic stressors promote the dimerization of KSR proteins with CRAF in NRAS-mutant cells, and with oncogenic BRAF in BRAFV600E-mutant cells, thereby enhancing ERK pathway activation. Despite this similarity, the two genomic subtypes react differently when a higher level of metabolic stress is induced. In NRAS-mutant cells, the ERK pathway is even more stimulated, while it is strongly downregulated in BRAFV600E-mutant cells. We demonstrate that this is caused by the dissociation of mutant BRAF from KSR and is mediated by activated AMPK. Both types of ERK regulation nevertheless lead to cell cycle arrest. Besides studying the effects of the metabolic stressors on ERK pathway activity, we also present data suggesting that for efficient therapies of both genomic melanoma subtypes, specific metabolic targeting is necessary.
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Affiliation(s)
- Amandine Verlande
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michaela Krafčíková
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Moustafa Elkalaf
- Laboratory for Metabolism and Bioenergetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Trnka
- Laboratory for Metabolism and Bioenergetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Karel Souček
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Laboratory of Cytokinetics, Institute of Biophysics, Academy of Sciences, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Nora Rauch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Jens Rauch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Stjepan Uldrijan
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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9
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Fasterius E, Raso C, Kennedy S, Rauch N, Lundin P, Kolch W, Uhlén M, Al-Khalili Szigyarto C. A novel RNA sequencing data analysis method for cell line authentication. PLoS One 2017; 12:e0171435. [PMID: 28192450 PMCID: PMC5305277 DOI: 10.1371/journal.pone.0171435] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/20/2017] [Indexed: 11/19/2022] Open
Abstract
We have developed a novel analysis method that can interrogate the authenticity of biological samples used for generation of transcriptome profiles in public data repositories. The method uses RNA sequencing information to reveal mutations in expressed transcripts and subsequently confirms the identity of analysed cells by comparison with publicly available cell-specific mutational profiles. Cell lines constitute key model systems widely used within cancer research, but their identity needs to be confirmed in order to minimise the influence of cell contaminations and genetic drift on the analysis. Using both public and novel data, we demonstrate the use of RNA-sequencing data analysis for cell line authentication by examining the validity of COLO205, DLD1, HCT15, HCT116, HKE3, HT29 and RKO colorectal cancer cell lines. We successfully authenticate the studied cell lines and validate previous reports indicating that DLD1 and HCT15 are synonymous. We also show that the analysed HKE3 cells harbour an unexpected KRAS-G13D mutation and confirm that this cell line is a genuine KRAS dosage mutant, rather than a true isogenic derivative of HCT116 expressing only the wild type KRAS. This authentication method could be used to revisit the numerous cell line based RNA sequencing experiments available in public data repositories, analyse new experiments where whole genome sequencing is not available, as well as facilitate comparisons of data from different experiments, platforms and laboratories.
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Affiliation(s)
- Erik Fasterius
- School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Cinzia Raso
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Susan Kennedy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nora Rauch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Pär Lundin
- Science for Life Laboratory, Dept of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mathias Uhlén
- School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
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Baljuls A, Dobrzyński M, Rauch J, Rauch N, Kolch W. Stabilization of C-RAF:KSR1 complex by DiRas3 reduces availability of C-RAF for dimerization with B-RAF. Cell Signal 2016; 28:1451-62. [DOI: 10.1016/j.cellsig.2016.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 06/18/2016] [Accepted: 06/27/2016] [Indexed: 12/19/2022]
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Rauch N, Rukhlenko OS, Kolch W, Kholodenko BN. MAPK kinase signalling dynamics regulate cell fate decisions and drug resistance. Curr Opin Struct Biol 2016; 41:151-158. [PMID: 27521656 DOI: 10.1016/j.sbi.2016.07.019] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/29/2016] [Indexed: 01/21/2023]
Abstract
The RAS/RAF/MEK/MAPK kinase pathway has been extensively studied for more than 25 years, yet we continue to be puzzled by its intricate dynamic control and plasticity. Different spatiotemporal MAPK dynamics bring about distinct cell fate decisions in normal vs cancer cells and developing organisms. Recent modelling and experimental studies provided novel insights in the versatile MAPK dynamics concerted by a plethora of feedforward/feedback regulations and crosstalk on multiple timescales. Multiple cancer types and various developmental disorders arise from persistent alterations of the MAPK dynamics caused by RAS/RAF/MEK mutations. While a key role of the MAPK pathway in multiple diseases made the development of novel RAF/MEK inhibitors a hot topic of drug development, these drugs have unexpected side-effects and resistance inevitably occurs. We review how RAF dimerization conveys drug resistance and recent breakthroughs to overcome this resistance.
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Affiliation(s)
- Nora Rauch
- Systems Biology Ireland, University College Dublin, Ireland
| | | | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Ireland; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Boris N Kholodenko
- Systems Biology Ireland, University College Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Ireland; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.
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12
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Dernayka L, Rauch N, Jarboui MA, Zebisch A, Texier Y, Horn N, Romano D, Gloeckner CJ, Kriegsheim AV, Ueffing M, Kolch W, Boldt K. Autophosphorylation on S614 inhibits the activity and the transforming potential of BRAF. Cell Signal 2016; 28:1432-1439. [PMID: 27345148 DOI: 10.1016/j.cellsig.2016.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 06/09/2016] [Accepted: 06/18/2016] [Indexed: 12/25/2022]
Abstract
The BRAF proto-oncogene serine/threonine-protein kinase, known as BRAF, belongs to the RAF kinase family. It regulates the MAPK/ERK signalling pathway affecting several cellular processes such as growth, survival, differentiation, and cellular transformation. BRAF is mutated in ~8% of all human cancers with the V600E mutation constituting ~90% of mutations. Here, we have used quantitative mass spectrometry to map and compare phosphorylation site patterns between BRAF and BRAF V600E. We identified sites that are shared as well as several quantitative differences in phosphorylation abundance. The highest difference is phosphorylation of S614 in the activation loop which is ~5fold enhanced in BRAF V600E. Mutation of S614 increases the kinase activity of both BRAF and BRAF V600E and the transforming ability of BRAF V600E. The phosphorylation of S614 is mitogen inducible and the result of autophosphorylation. These data suggest that phosphorylation at this site is inhibitory, and part of the physiological shut-down mechanism of BRAF signalling.
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Affiliation(s)
- Layal Dernayka
- Medical Proteome Center, Division for Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Nora Rauch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mohamed-Ali Jarboui
- Medical Proteome Center, Division for Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Armin Zebisch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Yves Texier
- Medical Proteome Center, Division for Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Nicola Horn
- Medical Proteome Center, Division for Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - David Romano
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Christian Johannes Gloeckner
- Medical Proteome Center, Division for Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen e. V., Otfried-Müller Strasse 23, 72076 Tübingen, Germany
| | - Alex von Kriegsheim
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Marius Ueffing
- Medical Proteome Center, Division for Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Karsten Boldt
- Medical Proteome Center, Division for Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany.
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Rodriguez J, Pilkington R, Garcia Munoz A, Nguyen LK, Rauch N, Kennedy S, Monsefi N, Herrero A, Taylor CT, von Kriegsheim A. Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signaling Pathways. Cell Rep 2016; 14:2745-60. [PMID: 26972000 PMCID: PMC4805855 DOI: 10.1016/j.celrep.2016.02.043] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 09/28/2015] [Accepted: 02/04/2016] [Indexed: 12/20/2022] Open
Abstract
Amino acid hydroxylation is a post-translational modification that regulates intra- and inter-molecular protein-protein interactions. The modifications are regulated by a family of 2-oxoglutarate- (2OG) dependent enzymes and, although the biochemistry is well understood, until now only a few substrates have been described for these enzymes. Using quantitative interaction proteomics, we screened for substrates of the proline hydroxylase PHD3 and the asparagine hydroxylase FIH, which regulate the HIF-mediated hypoxic response. We were able to identify hundreds of potential substrates. Enrichment analysis revealed that the potential substrates of both hydroxylases cluster in the same pathways but frequently modify different nodes of signaling networks. We confirm that two proteins identified in our screen, MAPK6 (Erk3) and RIPK4, are indeed hydroxylated in a FIH- or PHD3-dependent mechanism. We further determined that FIH-dependent hydroxylation regulates RIPK4-dependent Wnt signaling, and that PHD3-dependent hydroxylation of MAPK6 protects the protein from proteasomal degradation.
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Affiliation(s)
- Javier Rodriguez
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland; Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Ruth Pilkington
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | | | - Lan K Nguyen
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Nora Rauch
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Susan Kennedy
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Naser Monsefi
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Ana Herrero
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Cormac T Taylor
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland; Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Alex von Kriegsheim
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland; Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh EH4 2XR, UK.
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Jambrina PG, Rauch N, Pilkington R, Rybakova K, Nguyen LK, Kholodenko BN, Buchete NV, Kolch W, Rosta E. Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Nora Rauch
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Ruth Pilkington
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Katja Rybakova
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Lan K. Nguyen
- Systems Biology Ireland; University College Dublin, Belfield; Dublin 4 Ireland
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute; Monash University; Melbourne Victoria 3800 Australia
| | - Boris N. Kholodenko
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptative Systems Laboratory; University College Dublin, Belfield; Dublin 4 Ireland
| | - Walter Kolch
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
- School of Medicine & Medical Sciences; University College Dublin, Belfield; Dublin 4 Ireland
| | - Edina Rosta
- Department of Chemistry; King's College London; London SE1 1DB UK
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Fey D, Halasz M, Dreidax D, Kennedy SP, Hastings JF, Rauch N, Munoz AG, Pilkington R, Fischer M, Westermann F, Kolch W, Kholodenko BN, Croucher DR. Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients. Sci Signal 2015; 8:ra130. [DOI: 10.1126/scisignal.aab0990] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Jambrina PG, Rauch N, Pilkington R, Rybakova K, Nguyen LK, Kholodenko BN, Buchete NV, Kolch W, Rosta E. Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation. Angew Chem Int Ed Engl 2015; 55:983-6. [PMID: 26644280 PMCID: PMC4736688 DOI: 10.1002/anie.201509272] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Indexed: 12/19/2022]
Abstract
RAF kinases are key players in the MAPK signaling pathway and are important targets for personalized cancer therapy. RAF dimerization is part of the physiological activation mechanism, together with phosphorylation, and is known to convey resistance to RAF inhibitors. Herein, molecular dynamics simulations are used to show that phosphorylation of a key N-terminal acidic (NtA) motif facilitates RAF dimerization by introducing several interprotomer salt bridges between the αC-helix and charged residues upstream of the NtA motif. Additionally, we show that the R-spine of RAF interacts with a conserved Trp residue in the vicinity of the NtA motif, connecting the active sites of two protomers and thereby modulating the cooperative interactions in the RAF dimer. Our findings provide a first structure-based mechanism for the auto-transactivation of RAF and could be generally applicable to other kinases, opening new pathways for overcoming dimerization-related drug resistance.
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Affiliation(s)
- Pablo G Jambrina
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Nora Rauch
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Ruth Pilkington
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Katja Rybakova
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Lan K Nguyen
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, 4, Ireland.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, 3800, Australia
| | - Boris N Kholodenko
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptative Systems Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Walter Kolch
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland. .,School of Medicine & Medical Sciences, University College Dublin, Belfield, Dublin, 4, Ireland.
| | - Edina Rosta
- Department of Chemistry, King's College London, London, SE1 1DB, UK.
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Kolch W, Fey D, Halasz M, Rauch N, Munoz AG, Pilkington R, Kholodenko BN, Croucher DR, Kennedy SP, Hastings JF, Westermann F, Dreidax D, Fischer M, Duffy D, Krstic A, Schwarzl T. Abstract CN05-03: Personalized cancer diagnostics and therapeutics based on the computational modeling of signal transduction networks. Mol Cancer Ther 2015. [DOI: 10.1158/1535-7163.targ-15-cn05-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Signalling pathways exert finely tuned control over cell fate decisions that ultimately determine the behaviour of cancer cells. It could therefore be expected that the dynamics of key pathway activation may contain prognostically relevant information over and above that which is contained in the static nature of traditional biomarkers. To investigate this hypothesis we have characterised the network architecture regulating JNK stress signalling in neuroblastoma cells and applied an experimentally calibrated and validated computational model of this network to extract prognostic information from neuroblastoma patient-specific simulations of JNK activation. Survival analysis based upon the dynamics of these simulations revealed that an inability to initiate switch-like JNK signalling in silico was significantly associated with poor overall survival for both MYCN amplified and non-amplified neuroblastoma patients. Furthermore, our analysis demonstrated that in order to extract prognostic information from a signalling pathway, deciphering the extant network structure is a vital consideration in model development. We also show that network based analysis can lead to the discovery of new therapeutic targets.
Citation Format: Walter Kolch, Dirk Fey, Melinda Halasz, Nora Rauch, Amaya Garcia Munoz, Ruth Pilkington, Boris N. Kholodenko, David R. Croucher, Sean P. Kennedy, Jordan F. Hastings, Frank Westermann, Daniel Dreidax, Matthias Fischer, David Duffy, Aleksandar Krstic, Thomas Schwarzl. Personalized cancer diagnostics and therapeutics based on the computational modeling of signal transduction networks. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr CN05-03.
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Affiliation(s)
- Walter Kolch
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Dirk Fey
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Melinda Halasz
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Nora Rauch
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Amaya Garcia Munoz
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Ruth Pilkington
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Boris N. Kholodenko
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - David R. Croucher
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Sean P. Kennedy
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Jordan F. Hastings
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Frank Westermann
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Daniel Dreidax
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Matthias Fischer
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - David Duffy
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Aleksandar Krstic
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Thomas Schwarzl
- Systems Biology Ireland, Dublin, Ireland, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia, Department of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany, Department of Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
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Van Belle E, Juthier F, Vincentelli A, Hurt C, Debry N, Rauch N, Schurtz G, Auffray JL, Prat A, Susen S. Can the use of a direct thrombin inhibitor prevent the risk of brain emboli during TAVI procedures? Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht311.5933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Rauch N, Ullmer E, Matt D, Greminger P. Siebzehnjährige Schülerin mit therapieresistenter Pneumonie. Radiologe 2010; 50:548-52. [DOI: 10.1007/s00117-010-2021-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Saiz E, Tomsia AP, Rauch N, Scheu C, Ruehle M, Benhassine M, Seveno D, de Coninck J, Lopez-Esteban S. Nonreactive spreading at high temperature: molten metals and oxides on molybdenum. Phys Rev E Stat Nonlin Soft Matter Phys 2007; 76:041602. [PMID: 17994999 DOI: 10.1103/physreve.76.041602] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Indexed: 05/25/2023]
Abstract
The spontaneous spreading of small liquid metal (Cu, Ag, Au) and oxide drops on Mo substrates has been studied using a drop transfer setup combined with high-speed video. Under the experimental conditions used in this work, spreading occurs in the absence of interfacial reactions or ridging. The analysis of the spreading data indicates that dissipation at the triple junction (that can be described in terms of a triple-line friction) is playing a dominant role in the movement of the liquid front. This is due, in part, to the much stronger atomic interactions in high-temperature systems when compared to organic liquids. As a result of this analysis, a comprehensive view of spreading emerges in which the strength of the atomic interactions (solid-liquid, liquid-liquid) determines the relative roles of viscous impedance and dissipation at the triple junction in spreading kinetics.
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Affiliation(s)
- E Saiz
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Rauch N. Female habitat choice as a determinant of the reproductive success of the territorial male marine iguana (Amblyrhynchus cristatus). Behav Ecol Sociobiol 1985. [DOI: 10.1007/bf00295146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
We examined the patterns of cyclic AMP-dependent protein phosphorylation in membranes prepared from rat cortical synaptosomes following gel electrophoresis and autoradiography. We determined the optimum pH (6.2), time (20 s), Mg2+ concentration (10 mM) and cyclic AMP concentration (5 microM) for the reaction. We also found that the detergents Triton X-100 and gramicidin S enhanced cyclic AMP-dependent protein phosphorylation. Inhibitors of the Na+, K+ ATPase (ouabain, NaF, vanadate) enhanced protein phosphorylation. This effect occurred in the presence but not in the absence of detergent. The addition of purified bovine brain cyclic AMP-dependent protein kinase catalytic subunit enhanced membrane protein phosphorylation. The addition of homogeneous neural (bovine brain) and non-neural (bovine skeletal muscle) cyclic AMP-dependent protein kinase type II regulatory subunit partially inhibited protein phosphorylation. Both neural and non-neural regulatory subunits behaved similarly. In addition to cyclic AMP-dependent phosphorylation, the alpha-subunit of pyruvate dehydrogenase (Mr = 41,000) is phosphorylated in a cyclic AMP-independent fashion. We also examined the phosphorylation pattern of membranes prepared from rat heart and found that the number of acceptor substrates was much less than that from the nervous system.
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Schölmerich J, Becher MS, Köttgen E, Rauch N, Häussinger D, Löhle E, Vuilleumier JP, Gerok W. The influence of portosystemic shunting on zinc and vitamin A metabolism in liver cirrhosis. Hepatogastroenterology 1983; 30:143-7. [PMID: 6685108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
To elucidate the possible role of portosystemic shunting on zinc and vitamin A deficiency which has been described in patients with cirrhosis of the liver, a study on 37 hospitalized patients with liver cirrhosis was performed. Patients with surgical portosystemic shunt were found to have a significantly lower levels of zinc, vitamin A and retinol-binding protein (RBP) than controls and patients with cirrhosis without shunt. Patients with portal hypertension--considered to have spontaneous shunting--also has lower levels than those without this symptom. A significant correlation between zinc and vitamin A and RBP levels, respectively, was found. Also an increased renal zinc output was demonstrated. An influence of portosystemic shunting on zinc deficiency and subsequent vitamin A deficiency by decreased RBP release is concluded. The importance of these metabolic disorders for clinical symptoms is discussed.
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Roskoski R, Rauch N, Roskoski LM. Glutamate, aspartate, and gamma-aminobutyrate transport by membrane vesicles prepared from rat brain. Arch Biochem Biophys 1981; 207:407-15. [PMID: 7247412 DOI: 10.1016/0003-9861(81)90048-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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