1
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Maiti S, Bhattacharya K, Wider D, Hany D, Panasenko O, Bernasconi L, Hulo N, Picard D. Hsf1 and the molecular chaperone Hsp90 support a 'rewiring stress response' leading to an adaptive cell size increase in chronic stress. eLife 2023; 12:RP88658. [PMID: 38059913 DOI: 10.7554/elife.88658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023] Open
Abstract
Cells are exposed to a wide variety of internal and external stresses. Although many studies have focused on cellular responses to acute and severe stresses, little is known about how cellular systems adapt to sublethal chronic stresses. Using mammalian cells in culture, we discovered that they adapt to chronic mild stresses of up to two weeks, notably proteotoxic stresses such as heat, by increasing their size and translation, thereby scaling the amount of total protein. These adaptations render them more resilient to persistent and subsequent stresses. We demonstrate that Hsf1, well known for its role in acute stress responses, is required for the cell size increase, and that the molecular chaperone Hsp90 is essential for coupling the cell size increase to augmented translation. We term this translational reprogramming the 'rewiring stress response', and propose that this protective process of chronic stress adaptation contributes to the increase in size as cells get older, and that its failure promotes aging.
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Affiliation(s)
- Samarpan Maiti
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
| | - Kaushik Bhattacharya
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
| | - Diana Wider
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
| | - Dina Hany
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
- On leave from: Department of Pharmacology and Therapeutics, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria, Egypt
| | - Olesya Panasenko
- BioCode: RNA to Proteins Core Facility, Département de Microbiologie et Médecine Moléculaire, Faculté de Médecine, Université de Genève, Genève, Switzerland
| | - Lilia Bernasconi
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
| | - Nicolas Hulo
- Institute of Genetics and Genomics of Geneva, Université de Genève, Genève, Switzerland
| | - Didier Picard
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Genève, Switzerland
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2
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Yin K, Wu R. Investigation of cellular response to the HSP90 inhibition in human cells through thermal proteome profiling. Mol Cell Proteomics 2023; 22:100560. [PMID: 37119972 DOI: 10.1016/j.mcpro.2023.100560] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 03/31/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023] Open
Abstract
Heat shock proteins are chaperones and they are responsible for protein folding in cells. HSP90 is one of the most important chaperones in human cells, and its inhibition is promising for cancer therapy. However, despite the development of multiple HSP90 inhibitors, none of them has been approved for disease treatment due to unexpected cellular toxicity and side-effects. Hence, a more comprehensive investigation of cellular response to HSP90 inhibitors can aid in a better understanding of the molecular mechanisms of the cytotoxicity and side effects of these inhibitors. The thermal stability shifts of proteins, which represent protein structure and interaction alterations, can provide valuable information complementary to the results obtained from commonly used abundance-based proteomics analysis. Here, we systematically investigated cell response to different HSP90 inhibitors through global quantification of protein thermal stability changes using thermal proteome profiling, together with measurement of protein abundance changes. Besides the targets and potential off-targets of the drugs, proteins with significant thermal stability changes under the HSP90 inhibition are found to be involved in cell stress responses and the translation process. Moreover, proteins with thermal stability shifts under the inhibition are upstream of those with altered expression. These findings indicate that the HSP90 inhibition perturbs cell transcription and translation processes. The current study provides a different perspective for achieving a better understanding of cellular response to the chaperone inhibition.
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Affiliation(s)
- Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
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3
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Samant RS, Batista S, Larance M, Ozer B, Milton CI, Bludau I, Wu E, Biggins L, Andrews S, Hervieu A, Johnston HE, Al-Lazikhani B, Lamond AI, Clarke PA, Workman P. Native Size-Exclusion Chromatography-Based Mass Spectrometry Reveals New Components of the Early Heat Shock Protein 90 Inhibition Response Among Limited Global Changes. Mol Cell Proteomics 2023; 22:100485. [PMID: 36549590 PMCID: PMC9898794 DOI: 10.1016/j.mcpro.2022.100485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/16/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
The molecular chaperone heat shock protein 90 (HSP90) works in concert with co-chaperones to stabilize its client proteins, which include multiple drivers of oncogenesis and malignant progression. Pharmacologic inhibitors of HSP90 have been observed to exert a wide range of effects on the proteome, including depletion of client proteins, induction of heat shock proteins, dissociation of co-chaperones from HSP90, disruption of client protein signaling networks, and recruitment of the protein ubiquitylation and degradation machinery-suggesting widespread remodeling of cellular protein complexes. However, proteomics studies to date have focused on inhibitor-induced changes in total protein levels, often overlooking protein complex alterations. Here, we use size-exclusion chromatography in combination with mass spectrometry (SEC-MS) to characterize the early changes in native protein complexes following treatment with the HSP90 inhibitor tanespimycin (17-AAG) for 8 h in the HT29 colon adenocarcinoma cell line. After confirming the signature cellular response to HSP90 inhibition (e.g., induction of heat shock proteins, decreased total levels of client proteins), we were surprised to find only modest perturbations to the global distribution of protein elution profiles in inhibitor-treated HT29 cells at this relatively early time-point. Similarly, co-chaperones that co-eluted with HSP90 displayed no clear difference between control and treated conditions. However, two distinct analysis strategies identified multiple inhibitor-induced changes, including known and unknown components of the HSP90-dependent proteome. We validate two of these-the actin-binding protein Anillin and the mitochondrial isocitrate dehydrogenase 3 complex-as novel HSP90 inhibitor-modulated proteins. We present this dataset as a resource for the HSP90, proteostasis, and cancer communities (https://www.bioinformatics.babraham.ac.uk/shiny/HSP90/SEC-MS/), laying the groundwork for future mechanistic and therapeutic studies related to HSP90 pharmacology. Data are available via ProteomeXchange with identifier PXD033459.
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Affiliation(s)
- Rahul S Samant
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom; Signalling Programme, The Babraham Institute, Cambridge, United Kingdom.
| | - Silvia Batista
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Mark Larance
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, United Kingdom
| | - Bugra Ozer
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Christopher I Milton
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Isabell Bludau
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Estelle Wu
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Laura Biggins
- Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Alexia Hervieu
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Harvey E Johnston
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Bissan Al-Lazikhani
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Angus I Lamond
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, United Kingdom
| | - Paul A Clarke
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Paul Workman
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom.
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4
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Bhattacharya K, Maiti S, Zahoran S, Weidenauer L, Hany D, Wider D, Bernasconi L, Quadroni M, Collart M, Picard D. Translational reprogramming in response to accumulating stressors ensures critical threshold levels of Hsp90 for mammalian life. Nat Commun 2022; 13:6271. [PMID: 36270993 PMCID: PMC9587034 DOI: 10.1038/s41467-022-33916-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
The cytosolic molecular chaperone Hsp90 is essential for eukaryotic life. Although reduced Hsp90 levels correlate with aging, it was unknown whether eukaryotic cells and organisms can tune the basal Hsp90 levels to alleviate physiologically accumulated stress. We have investigated whether and how mice adapt to the deletion of three out of four alleles of the two genes encoding cytosolic Hsp90, with one Hsp90β allele being the only remaining one. While the vast majority of such mouse embryos die during gestation, survivors apparently manage to increase their Hsp90β protein to at least wild-type levels. Our studies reveal an internal ribosome entry site in the 5' untranslated region of the Hsp90β mRNA allowing translational reprogramming to compensate for the genetic loss of Hsp90 alleles and in response to stress. We find that the minimum amount of total Hsp90 required to support viability of mammalian cells and organisms is 50-70% of what is normally there. Those that fail to maintain a threshold level are subject to accelerated senescence, proteostatic collapse, and ultimately death. Therefore, considering that Hsp90 levels can be reduced ≥100-fold in the unicellular budding yeast, critical threshold levels of Hsp90 have markedly increased during eukaryotic evolution.
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Affiliation(s)
- Kaushik Bhattacharya
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Samarpan Maiti
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Szabolcs Zahoran
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Lorenz Weidenauer
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Dina Hany
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Diana Wider
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Lilia Bernasconi
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Martine Collart
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Didier Picard
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
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5
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Kelly V, Al-Rawi A, Lewis D, Kustatscher G, Ly T. Low Cell Number Proteomic Analysis Using In-Cell Protease Digests Reveals a Robust Signature for Cell Cycle State Classification. Mol Cell Proteomics 2022; 21:100169. [PMID: 34742921 PMCID: PMC8760417 DOI: 10.1016/j.mcpro.2021.100169] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/02/2021] [Accepted: 10/25/2021] [Indexed: 12/04/2022] Open
Abstract
Comprehensive proteome analysis of rare cell phenotypes remains a significant challenge. We report a method for low cell number MS-based proteomics using protease digestion of mildly formaldehyde-fixed cells in cellulo, which we call the "in-cell digest." We combined this with averaged MS1 precursor library matching to quantitatively characterize proteomes from low cell numbers of human lymphoblasts. About 4500 proteins were detected from 2000 cells, and 2500 proteins were quantitated from 200 lymphoblasts. The ease of sample processing and high sensitivity makes this method exceptionally suited for the proteomic analysis of rare cell states, including immune cell subsets and cell cycle subphases. To demonstrate the method, we characterized the proteome changes across 16 cell cycle states (CCSs) isolated from an asynchronous TK6 cells, avoiding synchronization. States included late mitotic cells present at extremely low frequency. We identified 119 pseudoperiodic proteins that vary across the cell cycle. Clustering of the pseudoperiodic proteins showed abundance patterns consistent with "waves" of protein degradation in late S, at the G2&M border, midmitosis, and at mitotic exit. These clusters were distinguished by significant differences in predicted nuclear localization and interaction with the anaphase-promoting complex/cyclosome. The dataset also identifies putative anaphase-promoting complex/cyclosome substrates in mitosis and the temporal order in which they are targeted for degradation. We demonstrate that a protein signature made of these 119 high-confidence cell cycle-regulated proteins can be used to perform unbiased classification of proteomes into CCSs. We applied this signature to 296 proteomes that encompass a range of quantitation methods, cell types, and experimental conditions. The analysis confidently assigns a CCS for 49 proteomes, including correct classification for proteomes from synchronized cells. We anticipate that this robust cell cycle protein signature will be crucial for classifying cell states in single-cell proteomes.
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Affiliation(s)
- Van Kelly
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Aymen Al-Rawi
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - David Lewis
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Georg Kustatscher
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Tony Ly
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK; Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.
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6
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Maurizy C, Abeza C, Lemmers B, Gabola M, Longobardi C, Pinet V, Ferrand M, Paul C, Bremond J, Langa F, Gerbe F, Jay P, Verheggen C, Tinari N, Helmlinger D, Lattanzio R, Bertrand E, Hahne M, Pradet-Balade B. The HSP90/R2TP assembly chaperone promotes cell proliferation in the intestinal epithelium. Nat Commun 2021; 12:4810. [PMID: 34376666 PMCID: PMC8355188 DOI: 10.1038/s41467-021-24792-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
The R2TP chaperone cooperates with HSP90 to integrate newly synthesized proteins into multi-subunit complexes, yet its role in tissue homeostasis is unknown. Here, we generated conditional, inducible knock-out mice for Rpap3 to inactivate this core component of R2TP in the intestinal epithelium. In adult mice, Rpap3 invalidation caused destruction of the small intestinal epithelium and death within 10 days. Levels of R2TP substrates decreased, with strong effects on mTOR, ATM and ATR. Proliferative stem cells and progenitors deficient for Rpap3 failed to import RNA polymerase II into the nucleus and they induced p53, cell cycle arrest and apoptosis. Post-mitotic, differentiated cells did not display these alterations, suggesting that R2TP clients are preferentially built in actively proliferating cells. In addition, high RPAP3 levels in colorectal tumors from patients correlate with bad prognosis. Here, we show that, in the intestine, the R2TP chaperone plays essential roles in normal and tumoral proliferation.
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Affiliation(s)
- Chloé Maurizy
- IGMM, Univ Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, Paris, France
| | - Claire Abeza
- IGMM, Univ Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, Paris, France
| | | | | | | | | | | | | | | | - Francina Langa
- Centre d'Ingénierie Génétique Murine, Institut Pasteur, Paris, France
| | - François Gerbe
- Equipe labélisée Ligue Nationale Contre le Cancer, Paris, France
- IGF, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Philippe Jay
- Equipe labélisée Ligue Nationale Contre le Cancer, Paris, France
- IGF, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Céline Verheggen
- IGMM, Univ Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, Paris, France
- IGH, Univ Montpellier, CNRS, Montpellier, France
| | - Nicola Tinari
- Department of Medical, Oral and Biotechnological Sciences, Center for Advanced Studies and Technology (CAST), 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | | | - Rossano Lattanzio
- Department of Innovative Technologies in Medicine & Dentistry, Center for Advanced Studies and Technology (CAST), 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Edouard Bertrand
- IGMM, Univ Montpellier, CNRS, Montpellier, France.
- Equipe labélisée Ligue Nationale Contre le Cancer, Paris, France.
- IGH, Univ Montpellier, CNRS, Montpellier, France.
| | | | - Bérengère Pradet-Balade
- Equipe labélisée Ligue Nationale Contre le Cancer, Paris, France.
- CRBM, Univ Montpellier, CNRS, Montpellier, France.
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7
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Fauvet B, Finka A, Castanié-Cornet MP, Cirinesi AM, Genevaux P, Quadroni M, Goloubinoff P. Bacterial Hsp90 Facilitates the Degradation of Aggregation-Prone Hsp70-Hsp40 Substrates. Front Mol Biosci 2021. [PMID: 33937334 DOI: 10.1101/451989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
In eukaryotes, the 90-kDa heat shock proteins (Hsp90s) are profusely studied chaperones that, together with 70-kDa heat shock proteins (Hsp70s), control protein homeostasis. In bacteria, however, the function of Hsp90 (HtpG) and its collaboration with Hsp70 (DnaK) remains poorly characterized. To uncover physiological processes that depend on HtpG and DnaK, we performed comparative quantitative proteomic analyses of insoluble and total protein fractions from unstressed wild-type (WT) Escherichia coli and from knockout mutants ΔdnaKdnaJ (ΔKJ), ΔhtpG (ΔG), and ΔdnaKdnaJΔhtpG (ΔKJG). Whereas the ΔG mutant showed no detectable proteomic differences with wild-type, ΔKJ expressed more chaperones, proteases and ribosomes and expressed dramatically less metabolic and respiratory enzymes. Unexpectedly, we found that the triple mutant ΔKJG showed higher levels of metabolic and respiratory enzymes than ΔKJ, suggesting that bacterial Hsp90 mediates the degradation of aggregation-prone Hsp70-Hsp40 substrates. Further in vivo experiments suggest that such Hsp90-mediated degradation possibly occurs through the HslUV protease.
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Affiliation(s)
- Bruno Fauvet
- Department of Plant Molecular Biology (DBMV), University of Lausanne, Lausanne, Switzerland
| | - Andrija Finka
- Department of Ecology, Agronomy and Aquaculture, University of Zadar, Zadar, Croatia
| | - Marie-Pierre Castanié-Cornet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Center de Biologie Intégrative, CNRS, Université de Toulouse, Toulouse, France
| | - Anne-Marie Cirinesi
- Laboratoire de Microbiologie et de Génétique Moléculaires, Center de Biologie Intégrative, CNRS, Université de Toulouse, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, Center de Biologie Intégrative, CNRS, Université de Toulouse, Toulouse, France
| | - Manfredo Quadroni
- Protein Analysis Facility, University of Lausanne, Lausanne, Switzerland
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology (DBMV), University of Lausanne, Lausanne, Switzerland
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8
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Bhattacharya K, Weidenauer L, Luengo TM, Pieters EC, Echeverría PC, Bernasconi L, Wider D, Sadian Y, Koopman MB, Villemin M, Bauer C, Rüdiger SGD, Quadroni M, Picard D. The Hsp70-Hsp90 co-chaperone Hop/Stip1 shifts the proteostatic balance from folding towards degradation. Nat Commun 2020; 11:5975. [PMID: 33239621 PMCID: PMC7688965 DOI: 10.1038/s41467-020-19783-w] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
Hop/Stip1/Sti1 is thought to be essential as a co-chaperone to facilitate substrate transfer between the Hsp70 and Hsp90 molecular chaperones. Despite this proposed key function for protein folding and maturation, it is not essential in a number of eukaryotes and bacteria lack an ortholog. We set out to identify and to characterize its eukaryote-specific function. Human cell lines and the budding yeast with deletions of the Hop/Sti1 gene display reduced proteasome activity due to inefficient capping of the core particle with regulatory particles. Unexpectedly, knock-out cells are more proficient at preventing protein aggregation and at promoting protein refolding. Without the restraint by Hop, a more efficient folding activity of the prokaryote-like Hsp70-Hsp90 complex, which can also be demonstrated in vitro, compensates for the proteasomal defect and ensures the proteostatic equilibrium. Thus, cells may act on the level and/or activity of Hop to shift the proteostatic balance between folding and degradation. Hop, also known as Stip1 or Sti1, facilitates substrate transfer between the Hsp70 and Hsp90 molecular chaperones. Characterization of proteostasis-related pathways in STIP1 knock-out cell lines reveals that in eukaryotes Stip1 modulates the balance between protein folding and degradation.
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Affiliation(s)
- Kaushik Bhattacharya
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Lorenz Weidenauer
- Protein Analysis Facility, Center for Integrative Genomics, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Tania Morán Luengo
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Ellis C Pieters
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Pablo C Echeverría
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland.,European Association for the Study of the Liver, 1203, Genève, Switzerland
| | - Lilia Bernasconi
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Diana Wider
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Yashar Sadian
- Bioimaging Center, Université de Genève, Sciences II, 1211, Genève 4, Switzerland
| | - Margreet B Koopman
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Matthieu Villemin
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Christoph Bauer
- Bioimaging Center, Université de Genève, Sciences II, 1211, Genève 4, Switzerland
| | - Stefan G D Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Manfredo Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Didier Picard
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland.
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9
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Joshi A, Dai L, Liu Y, Lee J, Ghahhari NM, Segala G, Beebe K, Jenkins LM, Lyons GC, Bernasconi L, Tsai FTF, Agard DA, Neckers L, Picard D. The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis. BMC Biol 2020; 18:10. [PMID: 31987035 PMCID: PMC6986101 DOI: 10.1186/s12915-020-0740-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 01/16/2020] [Indexed: 01/01/2023] Open
Abstract
Background The molecular chaperone TRAP1, the mitochondrial isoform of cytosolic HSP90, remains poorly understood with respect to its pivotal role in the regulation of mitochondrial metabolism. Most studies have found it to be an inhibitor of mitochondrial oxidative phosphorylation (OXPHOS) and an inducer of the Warburg phenotype of cancer cells. However, others have reported the opposite, and there is no consensus on the relevant TRAP1 interactors. This calls for a more comprehensive analysis of the TRAP1 interactome and of how TRAP1 and mitochondrial metabolism mutually affect each other. Results We show that the disruption of the gene for TRAP1 in a panel of cell lines dysregulates OXPHOS by a metabolic rewiring that induces the anaplerotic utilization of glutamine metabolism to replenish TCA cycle intermediates. Restoration of wild-type levels of OXPHOS requires full-length TRAP1. Whereas the TRAP1 ATPase activity is dispensable for this function, it modulates the interactions of TRAP1 with various mitochondrial proteins. Quantitatively by far, the major interactors of TRAP1 are the mitochondrial chaperones mtHSP70 and HSP60. However, we find that the most stable stoichiometric TRAP1 complex is a TRAP1 tetramer, whose levels change in response to both a decline and an increase in OXPHOS. Conclusions Our work provides a roadmap for further investigations of how TRAP1 and its interactors such as the ATP synthase regulate cellular energy metabolism. Our results highlight that TRAP1 function in metabolism and cancer cannot be understood without a focus on TRAP1 tetramers as potentially the most relevant functional entity.
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Affiliation(s)
- Abhinav Joshi
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland.,Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Li Dai
- Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Yanxin Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94143, USA
| | - Jungsoon Lee
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: Department of Pediatrics, Tropical Medicine, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nastaran Mohammadi Ghahhari
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Gregory Segala
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Kristin Beebe
- Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Gaelyn C Lyons
- Laboratory of Cell Biology, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Lilia Bernasconi
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Francis T F Tsai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94143, USA
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Didier Picard
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland.
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10
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Zhou C, Zhang C, Zhu H, Liu Z, Su H, Zhang X, Chen T, Zhong Y, Hu H, Xiong M, Zhou H, Xu Y, Zhang A, Zhang N. Allosteric Regulation of Hsp90α's Activity by Small Molecules Targeting the Middle Domain of the Chaperone. iScience 2020; 23:100857. [PMID: 32058968 PMCID: PMC6997908 DOI: 10.1016/j.isci.2020.100857] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/20/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Hsp90 is a target for anti-cancer drug development. Both the conformational events tuned by ATP/ADP and co-chaperones and the chaperoning cycle timing are required for Hsp90's fully functional display. Interfering with either one of the conformational events or the cycle timing will down-regulate Hsp90's function. In this manuscript, non-covalent allosteric modulators (SOMCL-16-171 and SOMCL-16-175) targeting Hsp90α’s middle domain (Hsp90M) were developed for the first time. Multiple techniques were then applied to characterize the interactions between two active compounds and Hsp90α. Two loops and one α-helix (F349-N360, K443-E451, and D372-G387) in Hsp90M were identified responsible for the recognition of SOMCL-16-171 and SOMCL-16-175. Meanwhile, the binding of SOMCL-16-171 and SOMCL-16-175 to Hsp90M was demonstrated to allosterically modulate the structure and function of Hsp90α’s N-terminal domain. Finally, cellular assays were conducted to evaluate the cellular activity of SOMCL-16-175, and the results indicate that SOMCL-16-175 destabilizes Hsp90's client proteins and reduces cell viability. Allosteric modulators targeting Hsp90α's middle domain were developed for the first time Key elements in Hsp90M for the recognition of allosteric modulators were identified Compound SOMCL-16-175 promotes Hsp90α’s ATPase activity and reduces cell viability SOMCL-16-175 destabilizes Hsp90's clients without triggering heat shock response
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Affiliation(s)
- Chen Zhou
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Chi Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongwen Zhu
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhijun Liu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Haixia Su
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xianglei Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Tingting Chen
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yan Zhong
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Huifang Hu
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Muya Xiong
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hu Zhou
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Ao Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Naixia Zhang
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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11
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Quantitative proteomics analysis provides insight into the biological role of Hsp90 in BmNPV infection in Bombyx mori. J Proteomics 2019; 203:103379. [PMID: 31102755 DOI: 10.1016/j.jprot.2019.103379] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/14/2019] [Accepted: 05/06/2019] [Indexed: 12/14/2022]
Abstract
Heat shock protein 90, an essential chaperone responsible for the correct maturation of key proteins, has been confirmed to facilitate Bombyx mori nucleopolyhedrovirus (BmNPV) proliferation but the mechanism is not clear. In this study, we use quantitative proteomics analysis to investigate the mechanism of Hsp90 in BmNPV replication. In total, 195 differentially expressed proteins (DEPs) were identified with 136 up-regulated proteins and 59 down-regulated proteins. The protein expression level of small heat shock proteins, immune-related proteins, cellular DNA repair-related proteins and zinc finger proteins is significantly enhanced while that of protein kinases is declined. KEGG pathway analysis reveals that DEPs are involved in longevity regulating pathway, mTOR signaling pathway, FoxO signaling pathway and Toll and Imd signaling pathway. Based on the DEPs results, we speculate that inhibition of Hsp90 suppresses the BmNPV infection may because it could not only stimulate the host innate immune, induce small heat shock proteins expression to maintain the cellular proteostasis but activate host transcription factors to bind to virus DNA or protein and subsequently hinder virus replication. The results will help understand the roles of Hsp90 in BmNPV infection and shed light on new clue to illustrate the molecular mechanism of silkworm-virus interaction. SIGNIFICANCE: This is the first report on Hsp90 roles in BmNPV infection based on proteomic analysis. Our findings may provide new clue and research orientation to illustrate the molecular mechanism of silkworm-virus interaction and a set of BmHsp90 candidate clients, which may involve in BmNPV infection in BmN cells.
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12
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Echeverria PC, Bhattacharya K, Joshi A, Wang T, Picard D. The sensitivity to Hsp90 inhibitors of both normal and oncogenically transformed cells is determined by the equilibrium between cellular quiescence and activity. PLoS One 2019; 14:e0208287. [PMID: 30726209 PMCID: PMC6364869 DOI: 10.1371/journal.pone.0208287] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/11/2019] [Indexed: 12/11/2022] Open
Abstract
The molecular chaperone Hsp90 is an essential and highly abundant central node in the interactome of eukaryotic cells. Many of its large number of client proteins are relevant to cancer. A hallmark of Hsp90-dependent proteins is that their accumulation is compromised by Hsp90 inhibitors. Combined with the anecdotal observation that cancer cells may be more sensitive to Hsp90 inhibitors, this has led to clinical trials aiming to develop Hsp90 inhibitors as anti-cancer agents. However, the sensitivity to Hsp90 inhibitors has not been studied in rigorously matched normal versus cancer cells, and despite the discovery of important regulators of Hsp90 activity and inhibitor sensitivity, it has remained unclear, why cancer cells might be more sensitive. To revisit this issue more systematically, we have generated an isogenic pair of normal and oncogenically transformed NIH-3T3 cell lines. Our proteomic analysis of the impact of three chemically different Hsp90 inhibitors shows that these affect a substantial portion of the oncogenic program and that indeed, transformed cells are hypersensitive. Targeting the oncogenic signaling pathway reverses the hypersensitivity, and so do inhibitors of DNA replication, cell growth, translation and energy metabolism. Conversely, stimulating normal cells with growth factors or challenging their proteostasis by overexpressing an aggregation-prone sensitizes them to Hsp90 inhibitors. Thus, the differential sensitivity to Hsp90 inhibitors may not stem from any particular intrinsic difference between normal and cancer cells, but rather from a shift in the balance between cellular quiescence and activity.
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Affiliation(s)
- Pablo C. Echeverria
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Genève, Switzerland
| | - Kaushik Bhattacharya
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Genève, Switzerland
| | - Abhinav Joshi
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Genève, Switzerland
| | - Tai Wang
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Genève, Switzerland
| | - Didier Picard
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Genève, Switzerland
- * E-mail:
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13
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Sager RA, Woodford MR, Backe SJ, Makedon AM, Baker-Williams AJ, DiGregorio BT, Loiselle DR, Haystead TA, Zachara NE, Prodromou C, Bourboulia D, Schmidt LS, Linehan WM, Bratslavsky G, Mollapour M. Post-translational Regulation of FNIP1 Creates a Rheostat for the Molecular Chaperone Hsp90. Cell Rep 2019; 26:1344-1356.e5. [PMID: 30699359 PMCID: PMC6370319 DOI: 10.1016/j.celrep.2019.01.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/12/2018] [Accepted: 01/04/2019] [Indexed: 11/25/2022] Open
Abstract
The molecular chaperone Hsp90 stabilizes and activates client proteins. Co-chaperones and post-translational modifications tightly regulate Hsp90 function and consequently lead to activation of clients. However, it is unclear whether this process occurs abruptly or gradually in the cellular context. We show that casein kinase-2 phosphorylation of the co-chaperone folliculin-interacting protein 1 (FNIP1) on priming serine-938 and subsequent relay phosphorylation on serine-939, 941, 946, and 948 promotes its gradual interaction with Hsp90. This leads to incremental inhibition of Hsp90 ATPase activity and gradual activation of both kinase and non-kinase clients. We further demonstrate that serine/threonine protein phosphatase 5 (PP5) dephosphorylates FNIP1, allowing the addition of O-GlcNAc (O-linked N-acetylglucosamine) to the priming serine-938. This process antagonizes phosphorylation of FNIP1, preventing its interaction with Hsp90, and consequently promotes FNIP1 lysine-1119 ubiquitination and proteasomal degradation. These findings provide a mechanism for gradual activation of the client proteins through intricate crosstalk of post-translational modifications of the co-chaperone FNIP1.
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Affiliation(s)
- Rebecca A Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Alan M Makedon
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Alexander J Baker-Williams
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Bryanna T DiGregorio
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - David R Loiselle
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy A Haystead
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Natasha E Zachara
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Laura S Schmidt
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Gennady Bratslavsky
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
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14
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Voruganti S, Kline JT, Balch MJ, Rogers J, Matts RL, Hartson SD. Proteomic Profiling of Hsp90 Inhibitors. Methods Mol Biol 2018; 1709:139-162. [PMID: 29177657 DOI: 10.1007/978-1-4939-7477-1_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Mass spectrometry assays demonstrate that Hsp90 inhibitors alter the expression of approximately one-quarter of the assayable proteome in mammalian cells. These changes are extraordinarily robust and reproducible, making "proteomics profiling" the gold standard for validating the effects of new Hsp90 inhibitors on cultured cells. Proteomics assays can also suggest novel hypotheses regarding drug mechanisms. To assist investigators in adopting this approach, this Chapter provides detailed protocols for conducting simple proteomics assays of Hsp90 inhibition. The protocols present a robust label-free approach that utilizes pre-fractionation of protein samples by SDS-PAGE, thereby providing reasonably good penetration into the proteome while addressing common issues with sample quality. The actual programming and operation of liquid chromatography-tandem mass spectrometers is not covered, but expectations for achievable performance are discussed, as are alternative approaches, common challenges, and software for data analysis.
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Affiliation(s)
- Sudhakar Voruganti
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.,Bristol-Myers Squibb, Pennington, NJ, USA
| | - Jake T Kline
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Maurie J Balch
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Janet Rogers
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Robert L Matts
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Steven D Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
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15
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Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M. Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis. Cell 2018; 173:260-274.e25. [PMID: 29551266 PMCID: PMC5871718 DOI: 10.1016/j.cell.2018.02.030] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 12/01/2017] [Accepted: 02/09/2018] [Indexed: 02/07/2023]
Abstract
Protein degradation plays important roles in biological processes and is tightly regulated. Further, targeted proteolysis is an emerging research tool and therapeutic strategy. However, proteome-wide technologies to investigate the causes and consequences of protein degradation in biological systems are lacking. We developed “multiplexed proteome dynamics profiling” (mPDP), a mass-spectrometry-based approach combining dynamic-SILAC labeling with isobaric mass tagging for multiplexed analysis of protein degradation and synthesis. In three proof-of-concept studies, we uncover different responses induced by the bromodomain inhibitor JQ1 versus a JQ1 proteolysis targeting chimera; we elucidate distinct modes of action of estrogen receptor modulators; and we comprehensively classify HSP90 clients based on their requirement for HSP90 constitutively or during synthesis, demonstrating that constitutive HSP90 clients have lower thermal stability than non-clients, have higher affinity for the chaperone, vary between cell types, and change upon external stimuli. These findings highlight the potential of mPDP to identify dynamically controlled degradation mechanisms in cellular systems. Multiplexed proteome dynamics profiling, mPDP, measures changes in proteostasis JQ1-PROTAC degrades a key mRNA export factor and blocks protein synthesis Raloxifene induces TMEM97 degradation dysregulating cholesterol homeostasis Characterization of proteins dependent on HSP90 constitutively or during synthesis
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Affiliation(s)
- Mikhail M Savitski
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Nico Zinn
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Daniel Poeckel
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephan Gade
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anne J Wagner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Katrin Strohmer
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephanie Melchert
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Massimo Petretich
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anna Rutkowska
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Johanna Vappiani
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Holger Franken
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Michael Steidel
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gavain M Sweetman
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Rab K Prinjha
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Giovanna Bergamini
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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16
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Weidenauer L, Wang T, Joshi S, Chiosis G, Quadroni MR. Proteomic interrogation of HSP90 and insights for medical research. Expert Rev Proteomics 2017; 14:1105-1117. [PMID: 28990809 PMCID: PMC6027630 DOI: 10.1080/14789450.2017.1389649] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Heat shock protein 90 (HSP90) regulates protein homeostasis in eukaryotes. As a 'professional interactor', HSP90 binds to and chaperones many proteins and has both housekeeping and disease-related functions but its regulation remains in part elusive. HSP90 complexes are a target for therapy, notably against cancer, and several inhibitors are currently in clinical trials. Proteomic studies have revealed the vast interaction network of HSP90 and, in doing so, the extent of cellular processes the chaperone takes part in, especially in yeast and human cells. Furthermore, small-molecule inhibitors were used to probe the global impact of its inhibition on the proteome. Areas covered: We review here recent HSP90-related interactomics and total proteome studies and their relevance for research on cancer, neurodegenerative and pathogen diseases. Expert commentary: Proteomics experiments are our best chance to identify the context-dependent global proteome of HSP90 and thus uncover and understand its disease-specific biology. However, understanding the complexity of HSP90 will require multiple complementary, quantitative approaches and novel bioinformatics to translate interactions into ordered functional networks and pathways. Developing therapies will necessitate more knowledge on HSP90 complexes and networks with disease relevance and on total proteome changes induced by their perturbation. Most work has been done in cancer, thus a lot remains to be done in the context of other diseases.
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Affiliation(s)
- Lorenz Weidenauer
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Tai Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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17
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Flees J, Rajaei-Sharifabadi H, Greene E, Beer L, Hargis BM, Ellestad L, Porter T, Donoghue A, Bottje WG, Dridi S. Effect of Morinda citrifolia (Noni)-Enriched Diet on Hepatic Heat Shock Protein and Lipid Metabolism-Related Genes in Heat Stressed Broiler Chickens. Front Physiol 2017; 8:919. [PMID: 29230177 PMCID: PMC5711822 DOI: 10.3389/fphys.2017.00919] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/30/2017] [Indexed: 12/31/2022] Open
Abstract
Heat stress (HS) has been reported to alter fat deposition in broilers, however the underlying molecular mechanisms are not well-defined. The objectives of the current study were, therefore: (1) to determine the effects of acute (2 h) and chronic (3 weeks) HS on the expression of key molecular signatures involved in hepatic lipogenic and lipolytic programs, and (2) to assess if diet supplementation with dried Noni medicinal plant (0.2% of the diet) modulates these effects. Broilers (480 males, 1 d) were randomly assigned to 12 environmental chambers, subjected to two environmental conditions (heat stress, HS, 35°C vs. thermoneutral condition, TN, 24°C) and fed two diets (control vs. Noni) in a 2 × 2 factorial design. Feed intake and body weights were recorded, and blood and liver samples were collected at 2 h and 3 weeks post-heat exposure. HS depressed feed intake, reduced body weight, and up regulated the hepatic expression of heat shock protein HSP60, HSP70, HSP90 as well as key lipogenic proteins (fatty acid synthase, FASN; acetyl co-A carboxylase alpha, ACCα and ATP citrate lyase, ACLY). HS down regulated the hepatic expression of lipoprotein lipase (LPL) and hepatic triacylglycerol lipase (LIPC), but up-regulated ATGL. Although it did not affect growth performance, Noni supplementation regulated the hepatic expression of lipogenic proteins in a time- and gene-specific manner. Prior to HS, Noni increased ACLY and FASN in the acute and chronic experimental conditions, respectively. During acute HS, Noni increased ACCα, but reduced FASN and ACLY expression. Under chronic HS, Noni up regulated ACCα and FASN but it down regulated ACLY. In vitro studies, using chicken hepatocyte cell lines, showed that HS down-regulated the expression of ACCα, FASN, and ACLY. Treatment with quercetin, one bioactive ingredient in Noni, up-regulated the expression of ACCα, FASN, and ACLY under TN conditions, but it appeared to down-regulate ACCα and increase ACLY levels under HS exposure. In conclusion, our findings indicate that HS induces hepatic lipogenesis in chickens and this effect is probably mediated via HSPs. The modulation of hepatic HSP expression suggest also that Noni might be involved in modulating the stress response in chicken liver.
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Affiliation(s)
- Joshua Flees
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | | | - Elizabeth Greene
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Lesleigh Beer
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Billy M Hargis
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Laura Ellestad
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
| | - Tom Porter
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
| | - Annie Donoghue
- USDA, Agricultural Research Service, Fayetteville, AR, United States
| | - Walter G Bottje
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Sami Dridi
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
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18
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Wang Y, Koay YC, McAlpine SR. How Selective are Hsp90 Inhibitors for Cancer Cells over Normal Cells? ChemMedChem 2017; 12:353-357. [PMID: 28139075 DOI: 10.1002/cmdc.201600595] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/26/2017] [Indexed: 12/13/2022]
Abstract
Selectively inhibiting target proteins in cancer cells over normal cells is one of the most critical features of a successful protein inhibitor for clinical applications. By evaluating and comparing the impact of a clinical N-terminal heat shock protein 90 (Hsp90) inhibitor, AUY922 (luminespib), on Hsp90 inhibition-associated cellular events in cancer cells versus normal cells, we found that it produces similar phenotype characteristics in both cell types, indicating that AUY922 is not selective for targeting Hsp90 in tumor cells. By comparison, the C-terminal Hsp90 modulator SM258 suppresses cell proliferation, triggers apoptosis, regulates the expression of Hsp90-associated heat shock proteins, and enhances the degradation of Hsp90's client proteins preferentially in cancer cells over normal cells. Our findings support a new paradigm that AUY922 is not tumor selective, whereas SM258 is more selective and likely acts through an Hsp90-dependent mechanism.
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Affiliation(s)
- Yao Wang
- Department of Medicine, University of New South Wales, 2052, Australia
| | - Yen Chin Koay
- School of Chemistry, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Shelli R McAlpine
- School of Chemistry, University of New South Wales, Sydney, NSW, 2052, Australia
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19
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Wang Y, McAlpine SR. Regulating the cytoprotective response in cancer cells using simultaneous inhibition of Hsp90 and Hsp70. Org Biomol Chem 2015; 13:2108-16. [PMID: 25526223 DOI: 10.1039/c4ob02531h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Both heat shock protein 90 and 70 (Hsp90, Hsp70) are cytoprotective proteins that regulate cell death by stabilizing and folding proteins. Taking a two-pronged approach, involving simultaneous inhibition of Hsp90 and Hsp70, leads to synergistic cell death, which makes this is an appealing clinical therapy.
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Affiliation(s)
- Y Wang
- Department of Chemistry, Gate 2 High street, Dalton 219. and University of New South Wales, Sydney, NSW 2052, Australia.
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20
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Wang Y, McAlpine SR. Combining an Hsp70 inhibitor with either an N- or C-terminal Hsp90 inhibitor produces mechanistically distinct phenotypes. Org Biomol Chem 2015; 13:3691-8. [PMID: 25679754 DOI: 10.1039/c5ob00147a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Blocking the function of both heat shock protein 90 and 70 (Hsp90 and Hsp70) simultaneously limits these chaperones' cytoprotective effects on cancer cells. The unique phenotype associated with modulating Hsp90's C-terminus, when used in combination with Hsp70 inhibitors, produces a synergistic and highly relevant dual chemotherapy regimen.
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Affiliation(s)
- Y Wang
- Department of Chemistry, Gate 2 High street, Dalton 219, University of New South Wales, Sydney, NSW 2052, Australia.
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21
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Vartholomaiou E, Echeverría PC, Picard D. Unusual Suspects in the Twilight Zone Between the Hsp90 Interactome and Carcinogenesis. Adv Cancer Res 2015; 129:1-30. [PMID: 26915999 DOI: 10.1016/bs.acr.2015.08.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The molecular chaperone Hsp90 has attracted a lot of interest in cancer research ever since cancer cells were found to be more sensitive to Hsp90 inhibition than normal cells. Why that is has remained a matter of debate and is still unclear. In addition to increased Hsp90 dependence for some mutant cancer proteins and modifications of the Hsp90 machinery itself, a number of other characteristics of cancer cells probably contribute to this phenomenon; these include aneuploidy and overall increased numbers and levels of defective and mutant proteins, which all contribute to perturbed proteostasis. Work over the last two decades has demonstrated that many cancer-related proteins are Hsp90 clients, and yet only few of them have been extensively investigated, selected either on the basis of their obvious function as cancer drivers or because they proved to be convenient biomarkers for monitoring the effects of Hsp90 inhibitors. The purpose of our review is to go beyond these "usual suspects." We established a workflow to select poorly studied proteins that are related to cancer processes and qualify as Hsp90 clients. By discussing and taking a fresh look at these "unusual suspects," we hope to stimulate others to revisit them as novel therapeutic targets or diagnostic markers.
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Affiliation(s)
| | - Pablo C Echeverría
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Geneva, Switzerland
| | - Didier Picard
- Département de Biologie Cellulaire, Université de Genève, Sciences III, Geneva, Switzerland.
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22
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Yuzefovych Y, Blasczyk R, Huyton T. Oncogenic acidic nuclear phosphoproteins ANP32C/D are novel clients of heat shock protein 90. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2338-48. [DOI: 10.1016/j.bbamcr.2015.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 11/27/2022]
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23
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Sattin S, Tao J, Vettoretti G, Moroni E, Pennati M, Lopergolo A, Morelli L, Bugatti A, Zuehlke A, Moses M, Prince T, Kijima T, Beebe K, Rusnati M, Neckers L, Zaffaroni N, Agard DA, Bernardi A, Colombo G. Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands. Chemistry 2015; 21:13598-608. [PMID: 26286886 PMCID: PMC5921052 DOI: 10.1002/chem.201502211] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 12/25/2022]
Abstract
Hsp90 is a molecular chaperone of pivotal importance for multiple cell pathways. ATP-regulated internal dynamics are critical for its function and current pharmacological approaches block the chaperone with ATP-competitive inhibitors. Herein, a general approach to perturb Hsp90 through design of new allosteric ligands aimed at modulating its functional dynamics is proposed. Based on the characterization of a first set of 2-phenylbenzofurans showing stimulatory effects on Hsp90 ATPase and conformational dynamics, new ligands were developed that activate Hsp90 by targeting an allosteric site, located 65 Å from the active site. Specifically, analysis of protein responses to first-generation activators was exploited to guide the design of novel derivatives with improved ability to stimulate ATP hydrolysis. The molecules' effects on Hsp90 enzymatic, conformational, co-chaperone and client-binding properties were characterized through biochemical, biophysical and cellular approaches. These designed probes act as allosteric activators of the chaperone and affect the viability of cancer cell lines for which proper functioning of Hsp90 is necessary.
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Affiliation(s)
- Sara Sattin
- Dipartimento di Chimica, Università degli Studi di Milano via Golgi, 19, 20133, Milan (Italy)
| | - Jiahui Tao
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, 600 16th Street, San Francisco, 94158 (USA)
| | - Gerolamo Vettoretti
- Istituto di Chimica del Riconoscimento Molecolare, CNR via Mario Bianco, 9, 20131, Milan (Italy)
| | - Elisabetta Moroni
- Istituto di Chimica del Riconoscimento Molecolare, CNR via Mario Bianco, 9, 20131, Milan (Italy)
| | - Marzia Pennati
- Dept. Experimental Oncology and Molecular Medicine, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori via Amadeo, 42, 20133 Milano (Italy)
| | - Alessia Lopergolo
- Dept. Experimental Oncology and Molecular Medicine, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori via Amadeo, 42, 20133 Milano (Italy)
| | - Laura Morelli
- Dipartimento di Chimica, Università degli Studi di Milano via Golgi, 19, 20133, Milan (Italy)
| | - Antonella Bugatti
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia (Italy)
| | - Abbey Zuehlke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Mike Moses
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Thomas Prince
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Toshiki Kijima
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Kristin Beebe
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Marco Rusnati
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia (Italy)
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
| | - Nadia Zaffaroni
- Dept. Experimental Oncology and Molecular Medicine, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori via Amadeo, 42, 20133 Milano (Italy)
| | - David A Agard
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, 600 16th Street, San Francisco, 94158 (USA)
| | - Anna Bernardi
- Dipartimento di Chimica, Università degli Studi di Milano via Golgi, 19, 20133, Milan (Italy)
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR via Mario Bianco, 9, 20131, Milan (Italy).
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Schwartz H, Scroggins B, Zuehlke A, Kijima T, Beebe K, Mishra A, Neckers L, Prince T. Combined HSP90 and kinase inhibitor therapy: Insights from The Cancer Genome Atlas. Cell Stress Chaperones 2015; 20:729-41. [PMID: 26070366 PMCID: PMC4529871 DOI: 10.1007/s12192-015-0604-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/06/2015] [Accepted: 05/08/2015] [Indexed: 12/13/2022] Open
Abstract
The merging of knowledge from genomics, cellular signal transduction and molecular evolution is producing new paradigms of cancer analysis. Protein kinases have long been understood to initiate and promote malignant cell growth and targeting kinases to fight cancer has been a major strategy within the pharmaceutical industry for over two decades. Despite the initial success of kinase inhibitors (KIs), the ability of cancer to evolve resistance and reprogram oncogenic signaling networks has reduced the efficacy of kinase targeting. The molecular chaperone HSP90 physically supports global kinase function while also acting as an evolutionary capacitor. The Cancer Genome Atlas (TCGA) has compiled a trove of data indicating that a large percentage of tumors overexpress or possess mutant kinases that depend on the HSP90 molecular chaperone complex. Moreover, the overexpression or mutation of parallel activators of kinase activity (PAKA) increases the number of components that promote malignancy and indirectly associate with HSP90. Therefore, targeting HSP90 is predicted to complement kinase inhibitors by inhibiting oncogenic reprogramming and cancer evolution. Based on this hypothesis, consideration should be given by both the research and clinical communities towards combining kinase inhibitors and HSP90 inhibitors (H90Ins) in combating cancer. The purpose of this perspective is to reflect on the current understanding of HSP90 and kinase biology as well as promote the exploration of potential synergistic molecular therapy combinations through the utilization of The Cancer Genome Atlas.
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Affiliation(s)
- Harvey Schwartz
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Brad Scroggins
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Abbey Zuehlke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Toshiki Kijima
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Kristin Beebe
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Alok Mishra
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
| | - Thomas Prince
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 USA
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25
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Finka A, Sood V, Quadroni M, Rios PDL, Goloubinoff P. Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs. Cell Stress Chaperones 2015; 20:605-20. [PMID: 25847399 PMCID: PMC4463922 DOI: 10.1007/s12192-015-0583-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 03/08/2015] [Accepted: 03/10/2015] [Indexed: 11/18/2022] Open
Abstract
Classic semiquantitative proteomic methods have shown that all organisms respond to a mild heat shock by an apparent massive accumulation of a small set of proteins, named heat-shock proteins (HSPs) and a concomitant slowing down in the synthesis of the other proteins. Yet unexplained, the increased levels of HSP messenger RNAs (mRNAs) may exceed 100 times the ensuing relative levels of HSP proteins. We used here high-throughput quantitative proteomics and targeted mRNA quantification to estimate in human cell cultures the mass and copy numbers of the most abundant proteins that become significantly accumulated, depleted, or unchanged during and following 4 h at 41 °C, which we define as mild heat shock. This treatment caused a minor across-the-board mass loss in many housekeeping proteins, which was matched by a mass gain in a few HSPs, predominantly cytosolic HSPCs (HSP90s) and HSPA8 (HSC70). As the mRNAs of the heat-depleted proteins were not significantly degraded and less ribosomes were recruited by excess new HSP mRNAs, the mild depletion of the many housekeeping proteins during heat shock was attributed to their slower replenishment. This differential protein expression pattern was reproduced by isothermal treatments with Hsp90 inhibitors. Unexpectedly, heat-treated cells accumulated 55 times more new molecules of HSPA8 (HSC70) than of the acknowledged heat-inducible isoform HSPA1A (HSP70), implying that when expressed as net copy number differences, rather than as mere "fold change" ratios, new biologically relevant information can be extracted from quantitative proteomic data. Raw data are available via ProteomeXchange with identifier PXD001666.
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Affiliation(s)
- Andrija Finka
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
- Laboratoire de Biophysique Statistique, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Vishal Sood
- Laboratoire de Biophysique Statistique, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Manfredo Quadroni
- Department of Biochemistry, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Paolo De Los Rios
- Laboratoire de Biophysique Statistique, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
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26
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Characterization of CLL exosomes reveals a distinct microRNA signature and enhanced secretion by activation of BCR signaling. Blood 2015; 125:3297-305. [PMID: 25833959 DOI: 10.1182/blood-2014-12-618470] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/22/2015] [Indexed: 12/19/2022] Open
Abstract
Multiple studies show that chronic lymphocytic leukemia (CLL) cells are heavily dependent on their microenvironment for survival. Communication between CLL cells and the microenvironment is mediated through direct cell contact, soluble factors, and extracellular vesicles. Exosomes are small particles enclosed with lipids, proteins, and small RNAs that can convey biological materials to surrounding cells. Our data herein demonstrate that CLL cells release significant amounts of exosomes in plasma that exhibit abundant CD37, CD9, and CD63 expression. Our work also pinpoints the regulation of B-cell receptor (BCR) signaling in the release of CLL exosomes: BCR activation by α-immunoglobulin (Ig)M induces exosome secretion, whereas BCR inactivation via ibrutinib impedes α-IgM-stimulated exosome release. Moreover, analysis of serial plasma samples collected from CLL patients on an ibrutinib clinical trial revealed that exosome plasma concentration was significantly decreased following ibrutinib therapy. Furthermore, microRNA (miR) profiling of plasma-derived exosomes identified a distinct exosome microRNA signature, including miR-29 family, miR-150, miR-155, and miR-223 that have been associated with CLL disease. Interestingly, expression of exosome miR-150 and miR-155 increases with BCR activation. In all, this study successfully characterized CLL exosomes, demonstrated the control of BCR signaling in the release of CLL exosomes, and uncovered a disease-relevant exosome microRNA profile.
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27
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Quadroni M, Potts A, Waridel P. Hsp90 inhibition induces both protein-specific and global changes in the ubiquitinome. J Proteomics 2015; 120:215-29. [PMID: 25782750 DOI: 10.1016/j.jprot.2015.02.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/09/2015] [Accepted: 02/27/2015] [Indexed: 10/23/2022]
Abstract
UNLABELLED Inhibition of the essential chaperone Hsp90 with drugs causes a global perturbation of protein folding and the depletion of direct substrates of Hsp90, also called clients. Ubiquitination and proteasomal degradation play a key role in cellular stress responses, but the impact of Hsp90 inhibition on the ubiquitinome has not been characterized on a global scale. We used stable isotope labeling and antibody-based peptide enrichment to quantify more than 1500 protein sites modified with a Gly-Gly motif, the remnant of ubiquitination, in human T-cells treated with an Hsp90 inhibitor. We observed rapid changes in GlyGly-modification sites, with strong increases for some Hsp90 clients but also decreases for a majority of cellular proteins. A comparison with changes in total protein levels and protein synthesis and decay rates from a previous study revealed a complex picture with different regulatory patterns observed for different protein families. Overall the data support the notion that for Hsp90 clients GlyGly-modification correlates with targeting by the ubiquitin-proteasome system and decay, while for other proteins levels of GlyGly-modification appear to be mainly influenced by their synthesis rates. Therefore a correct interpretation of changes in ubiquitination requires knowledge of multiple parameters. Data are available via ProteomeXchange with identifier PXD001549. BIOLOGICAL SIGNIFICANCE Proteostasis, i.e. the capacity of the cell to maintain proper synthesis and maturation of proteins, is a fundamental biological process and its perturbations have far-reaching medical implications e.g. in cancer or neurodegenerative diseases. Hsp90 is an essential chaperone responsible for the correct maturation and stability of a number of key proteins. Inhibition of Hsp90 triggers a global stress response caused by accumulation of misfolded chains, which have to be either refolded or eliminated by protein degradation pathways such as the Ubiquitin-Proteasome System (UPS). We present the first global assessment of the changes in the ubiquitinome, the subset of ubiquitin-modified proteins, following Hsp90 inhibition in human T-cells. The results provide clues on how cells respond to a specific proteostasis challenge. Furthermore, our data also suggest that basal ubiquitination levels for most proteins are influenced by synthesis rates. This has broad significance as it implies that a proper interpretation of data on ubiquitination levels necessitates simultaneous knowledge of other parameters.
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Affiliation(s)
- Manfredo Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
| | - Alexandra Potts
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Patrice Waridel
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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28
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Helou YA, Salomon AR. Protein networks and activation of lymphocytes. Curr Opin Immunol 2015; 33:78-85. [PMID: 25687331 DOI: 10.1016/j.coi.2015.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/30/2015] [Accepted: 01/30/2015] [Indexed: 12/30/2022]
Abstract
The signal transduction pathways initiated by lymphocyte activation play a critical role in regulating host immunity. High-resolution mass spectrometry has accelerated the investigation of these complex and dynamic pathways by enabling the qualitative and quantitative investigation of thousands of proteins and phosphoproteins simultaneously. In addition, the unbiased and wide-scale identification of protein-protein interaction networks and protein kinase substrates in lymphocyte signaling pathways can be achieved by mass spectrometry-based approaches. Critically, the integration of these discovery-driven strategies with single-cell analysis using mass cytometry can facilitate the understanding of complex signaling phenotypes in distinct immunophenotypes.
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Affiliation(s)
- Ynes A Helou
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Arthur R Salomon
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA.
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29
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Sha K, Cao W. Structural and energetic insight into the isoform-selective inhibitors of tumour marker Hsp90 against Grp94. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2014.999239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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30
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Gopinath RK, You ST, Chien KY, Swamy KBS, Yu JS, Schuyler SC, Leu JY. The Hsp90-dependent proteome is conserved and enriched for hub proteins with high levels of protein-protein connectivity. Genome Biol Evol 2014; 6:2851-65. [PMID: 25316598 PMCID: PMC4224352 DOI: 10.1093/gbe/evu226] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hsp90 is one of the most abundant and conserved proteins in the cell. Reduced levels or activity of Hsp90 causes defects in many cellular processes and also reveals genetic and nongenetic variation within a population. Despite information about Hsp90 protein–protein interactions, a global view of the Hsp90-regulated proteome in yeast is unavailable. To investigate the degree of dependency of individual yeast proteins on Hsp90, we used the “stable isotope labeling by amino acids in cell culture” method coupled with mass spectrometry to quantify around 4,000 proteins in low-Hsp90 cells. We observed that 904 proteins changed in their abundance by more than 1.5-fold. When compared with the transcriptome of the same population of cells, two-thirds of the misregulated proteins were observed to be affected posttranscriptionally, of which the majority were downregulated. Further analyses indicated that the downregulated proteins are highly conserved and assume central roles in cellular networks with a high number of protein interacting partners, suggesting that Hsp90 buffers genetic and nongenetic variation through regulating protein network hubs. The downregulated proteins were enriched for essential proteins previously not known to be Hsp90-dependent. Finally, we observed that downregulation of transcription factors and mating pathway components by attenuating Hsp90 function led to decreased target gene expression and pheromone response, respectively, providing a direct link between observed proteome regulation and cellular phenotypes.
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Affiliation(s)
- Rajaneesh Karimpurath Gopinath
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Ting You
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Kun-Yi Chien
- Molecular Medicine Research Center, Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | | | - Jau-Song Yu
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Scott C Schuyler
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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31
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Bhat R, Tummalapalli SR, Rotella DP. Progress in the discovery and development of heat shock protein 90 (Hsp90) inhibitors. J Med Chem 2014; 57:8718-28. [PMID: 25141341 DOI: 10.1021/jm500823a] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The discovery and clinical development of heat shock protein 90 (Hsp90) inhibitors continue to progress. A number of Hsp90 inhibitors are in clinical trials, and preclinical discoveries of new chemotypes that bind to distinct regions in the protein as well as isoform selective compounds are active areas of research. This review will highlight progress in the field since 2010.
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Affiliation(s)
- Rohit Bhat
- Department of Chemistry and Biochemistry, Sokol Institute for Pharmaceutical Life Sciences, Montclair State University , Montclair, New Jersey 07043, United States
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32
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Koay YC, McConnell JR, Wang Y, Kim SJ, Buckton LK, Mansour F, McAlpine SR. Chemically accessible hsp90 inhibitor that does not induce a heat shock response. ACS Med Chem Lett 2014; 5:771-6. [PMID: 25050163 DOI: 10.1021/ml500114p] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/13/2014] [Indexed: 02/01/2023] Open
Abstract
Recent cancer therapies have focused on targeting biology networks through a single regulatory protein. Heat shock protein 90 (hsp90) is an ideal oncogenic target as it regulates over 400 client proteins and cochaperones. However, clinical inhibitors of hsp90 have had limited success; the primary reason being that they induce a heat shock response. We describe the synthesis and biological evaluation of a new hsp90 inhibitor, SM253. The previous generation on which SM253 is based (SM145) has poor overall synthetic yields, low solubility, and micromolar cytotoxicity. By comparison SM253 has relatively high overall yields, good aqueous solubility, and is more cytotoxic than its parent compound. Verification that hsp90 is SM253's target was accomplished using pull-down and protein folding assays. SM253 is superior to both SM145 and the clinical candidate 17-AAG as it decreases proteins related to the heat shock response by 2-fold, versus a 2-4-fold increase observed when cells are treated with 17-AAG.
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Affiliation(s)
- Yen Chin Koay
- The University of New South Wales, Sydney, NSW 2052, Australia
| | | | - Yao Wang
- The University of New South Wales, Sydney, NSW 2052, Australia
| | - Seong Jong Kim
- The University of New South Wales, Sydney, NSW 2052, Australia
| | | | - Flora Mansour
- The University of New South Wales, Sydney, NSW 2052, Australia
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33
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Zhao J, Zhao H, Hall JA, Brown D, Brandes E, Bazzill J, Grogan PT, Subramanian C, Vielhauer G, Cohen MS, Blagg BSJ. Triazole Containing Novobiocin and Biphenyl Amides as Hsp90 C-Terminal Inhibitors. MEDCHEMCOMM 2014; 5:1317-1323. [PMID: 25328661 DOI: 10.1039/c4md00102h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hsp90 C-terminal inhibitors are advantageous for the development of new cancer chemotherapeutics due to their ability to segregate client protein degradation from induction of the prosurvival heat shock response, which is a major detriment associated with Hsp90 N-terminal inhibitors under clinical investigation. Based upon prior SAR trends, a 1,2,3-triazole side chain was placed in lieu of the aryl side chain and attached to both the coumarin and biphenyl scaffold. Antiproliferative studies against SKBr3 and MCF-7 breast cancer cell lines demonstrated these triazole-containing compounds to exhibit improved activity. These compounds were shown to manifest Hsp90 inhibitory activity through Western blot analysis and represent a new scaffold upon which more potent inhibitors can be pursued.
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Affiliation(s)
- Jinbo Zhao
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, Kansas 66045, USA
| | - Huiping Zhao
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, Kansas 66045, USA
| | - Jessica A Hall
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, Kansas 66045, USA
| | - Douglas Brown
- Department of Urology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Mail Stop 1016, Kansas City, KS 66160, USA
| | - Eileen Brandes
- Department of Surgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joseph Bazzill
- Department of Pharmaceutical Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Patrick T Grogan
- Department of Surgery, University of Michigan, Ann Arbor, MI, 48109, USA ; Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, 3901 Rainbow Blvd., Mail Stop 1016, Kansas City, KS 66160, USA
| | - Chitra Subramanian
- Department of Surgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - George Vielhauer
- Department of Urology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Mail Stop 1016, Kansas City, KS 66160, USA
| | - Mark S Cohen
- Department of Surgery, University of Michigan, Ann Arbor, MI, 48109, USA ; Department of Pharmaceutical Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA ; Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, 3901 Rainbow Blvd., Mail Stop 1016, Kansas City, KS 66160, USA
| | - Brian S J Blagg
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, Kansas 66045, USA
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