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Woodard J, Zheng W, Zhang Y. Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders. PLoS Comput Biol 2021; 17:e1009370. [PMID: 34529671 PMCID: PMC8478239 DOI: 10.1371/journal.pcbi.1009370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/28/2021] [Accepted: 08/21/2021] [Indexed: 12/15/2022] Open
Abstract
Three-dimensional structures of proteins can provide important clues into the efficacy of personalized treatment. We perform a structural analysis of variants within three inherited lysosomal storage disorders, comparing variants responsive to pharmacological chaperone treatment to those unresponsive to such treatment. We find that predicted ΔΔG of mutation is higher on average for variants unresponsive to treatment, in the case of datasets for both Fabry disease and Pompe disease, in line with previous findings. Using both a single decision tree and an advanced machine learning approach based on the larger Fabry dataset, we correctly predict responsiveness of three Gaucher disease variants, and we provide predictions for untested variants. Many variants are predicted to be responsive to treatment, suggesting that drug-based treatments may be effective for a number of variants in Gaucher disease. In our analysis, we observe dependence on a topological feature reporting on contact arrangements which is likely connected to the order of folding of protein residues, and we provide a potential justification for this observation based on steady-state cellular kinetics. Pharmacological chaperones are small molecule drugs that bind to proteins to help stabilize the folded state. One set of diseases for which this treatment has been effective is the lysosomal storage disorders, which are caused by defective lysosomal enzymes. However, not all genotypes are equally responsive to treatment. For instance, missense mutants that are particularly destabilized relative to WT are less likely to respond. The availability of datasets containing responsiveness data for large numbers of mutants, along with crystal structures of the protein involved in each disease, make machine learning methods incorporating sequence-based and structural data feasible. We hypothesize that data from two diseases, Fabry and Pompe disease, may be useful for predicting responsiveness of variants in the related Gaucher disease. Results suggest that many rare variants in Gaucher disease could be amenable to existing drugs. Results also suggest that drug responsiveness depends on protein topology in such a way that mutations in early-to-fold residues are more likely to be non-responsive to pharmacological chaperone treatment, which is consistent with a simple kinetic model of stability rescue. This study provides an example of how machine learning can be used to inform further studies towards personalized treatment in medicine.
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Affiliation(s)
- Jaie Woodard
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Chantadul V, Wright GSA, Amporndanai K, Shahid M, Antonyuk SV, Washbourn G, Rogers M, Roberts N, Pye M, O'Neill PM, Hasnain SS. Ebselen as template for stabilization of A4V mutant dimer for motor neuron disease therapy. Commun Biol 2020; 3:97. [PMID: 32139772 PMCID: PMC7058017 DOI: 10.1038/s42003-020-0826-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/13/2020] [Indexed: 11/09/2022] Open
Abstract
Mutations to the gene encoding superoxide dismutase-1 (SOD1) were the first genetic elements discovered that cause motor neuron disease (MND). These mutations result in compromised SOD1 dimer stability, with one of the severest and most common mutations Ala4Val (A4V) displaying a propensity to monomerise and aggregate leading to neuronal death. We show that the clinically used ebselen and related analogues promote thermal stability of A4V SOD1 when binding to Cys111 only. We have developed a A4V SOD1 differential scanning fluorescence-based assay on a C6S mutation background that is effective in assessing suitability of compounds. Crystallographic data show that the selenium atom of these compounds binds covalently to A4V SOD1 at Cys111 at the dimer interface, resulting in stabilisation. This together with chemical amenability for hit expansion of ebselen and its on-target SOD1 pharmacological chaperone activity holds remarkable promise for structure-based therapeutics for MND using ebselen as a template.
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Affiliation(s)
- Varunya Chantadul
- Faculty of Health and Life Sciences, Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Faculty of Dentistry, Department of Anatomy, Mahidol University, Bangkok, 10400, Thailand
| | - Gareth S A Wright
- Faculty of Health and Life Sciences, Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Kangsa Amporndanai
- Faculty of Health and Life Sciences, Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Munazza Shahid
- Department of Chemistry and Chemical Engineering, Lahore University of Management Sciences, Punjab, 54792, Pakistan
| | - Svetlana V Antonyuk
- Faculty of Health and Life Sciences, Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Gina Washbourn
- Faculty of Science and Engineering, Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Michael Rogers
- Faculty of Science and Engineering, Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Natalie Roberts
- Faculty of Science and Engineering, Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Matthew Pye
- Faculty of Science and Engineering, Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Paul M O'Neill
- Faculty of Science and Engineering, Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - S Samar Hasnain
- Faculty of Health and Life Sciences, Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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Yasir M, Turner AK, Bastkowski S, Baker D, Page AJ, Telatin A, Phan MD, Monahan L, Savva GM, Darling A, Webber MA, Charles IG. TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance. Genome Res 2020; 30:239-249. [PMID: 32051187 PMCID: PMC7050523 DOI: 10.1101/gr.254391.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 01/17/2020] [Indexed: 01/14/2023]
Abstract
Understanding the genetic basis for a phenotype is a central goal in biological research. Much has been learnt about bacterial genomes by creating large mutant libraries and looking for conditionally important genes. However, current genome-wide methods are largely unable to assay essential genes which are not amenable to disruption. To overcome this limitation, we developed a new version of "TraDIS" (transposon directed insertion-site sequencing) that we term "TraDIS-Xpress" that combines an inducible promoter into the transposon cassette. This allows controlled overexpression and repression of all genes owing to saturation of inserts adjacent to all open reading frames as well as conventional inactivation. We applied TraDIS-Xpress to identify responses to the biocide triclosan across a range of concentrations. Triclosan is endemic in modern life, but there is uncertainty about its mode of action with a concentration-dependent switch from bacteriostatic to bactericidal action unexplained. Our results show a concentration-dependent response to triclosan with different genes important in survival between static and cidal exposures. These genes include those previously reported to have a role in triclosan resistance as well as a new set of genes, including essential genes. Novel genes identified as being sensitive to triclosan exposure include those involved in barrier function, small molecule uptake, and integrity of transcription and translation. We anticipate the approach we show here, by allowing comparisons across multiple experimental conditions of TraDIS data, and including essential genes, will be a starting point for future work examining how different drug conditions impact bacterial survival mechanisms.
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Affiliation(s)
- Muhammad Yasir
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - A Keith Turner
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - Sarah Bastkowski
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - David Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Queensland, Australia
| | - Leigh Monahan
- Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - George M Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - Aaron Darling
- Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
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Amico G, Brandas C, Moran O, Baroni D. Unravelling the Regions of Mutant F508del-CFTR More Susceptible to the Action of Four Cystic Fibrosis Correctors. Int J Mol Sci 2019; 20:ijms20215463. [PMID: 31683989 PMCID: PMC6862496 DOI: 10.3390/ijms20215463] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) is a genetic disease associated with the defective function of the cystic fibrosis transmembrane conductance regulator (CFTR) protein that causes obstructive disease and chronic bacterial infections in airway epithelia. The most prevalent CF-causing mutation, the deletion of phenylalanine at position 508 (F508del), leads to CFTR misfolding, trafficking defects and premature degradation. A number of correctors that are able to partially rescue F508del-CFTR processing defects have been identified. Clinical trials have demonstrated that, unfortunately, mono-therapy with the best correctors identified to date does not ameliorate lung function or sweat chloride concentration in homozygous F508del patients. Understanding the mechanisms exerted by currently available correctors to increase mutant F508del-CFTR expression is essential for the development of new CF-therapeutics. We investigated the activity of correctors on the mutant F508del and wild type (WT) CFTR to identify the protein domains whose expression is mostly affected by the action of correctors, and we investigated their mechanisms of action. We found that the four correctors under study, lumacaftor (VX809), the quinazoline derivative VX325, the bithiazole compound corr4a, and the new molecule tezacaftor (VX661), do not influence either the total expression or the maturation of the WT-CFTR transiently expressed in human embryonic kidney 293 (HEK293) cells. Contrarily, they significantly enhance the expression and the maturation of the full length F508del molecule. Three out of four correctors, VX809, VX661 and VX325, seem to specifically improve the expression and the maturation of the mutant CFTR N-half (M1N1, residues 1–633). By contrast, the CFTR C-half (M2N2, residues 837–1480) appears to be the region mainly affected by corr4a. VX809 was shown to stabilize both the WT- and F508del-CFTR N-half isoforms, while VX661 and VX325 demonstrated the ability to enhance the stability only of the mutant F508del polypeptide.
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Affiliation(s)
- Giulia Amico
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 16149 Genova, Italy.
| | - Chiara Brandas
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 16149 Genova, Italy.
| | - Oscar Moran
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 16149 Genova, Italy.
| | - Debora Baroni
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 16149 Genova, Italy.
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Liu Q, Sabirzhanova I, Yanda MK, Bergbower EAS, Boinot C, Guggino WB, Cebotaru L. Rescue of CFTR NBD2 mutants N1303K and S1235R is influenced by the functioning of the autophagosome. J Cyst Fibros 2018; 17:582-594. [PMID: 29936070 DOI: 10.1016/j.jcf.2018.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/27/2018] [Accepted: 05/27/2018] [Indexed: 11/19/2022]
Abstract
The missing phenylalanine at position 508, located in nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane regulator (CFTR), is the most common cystic fibrosis mutation. Severe disease-causing mutations also occur in NBD2. To provide information on potential therapeutic strategies for mutations in NBD2, we used a combination of biochemical, cell biological and electrophysiological approaches and newly created cell lines to study two disease-causing NBD2 mutants, N1303K and S1235R. We observed that neither was sensitive to E64, a cysteine protease inhibitor. However, further investigation showed that when treated with a combination of correctors, C4 + C18, both mutants also responded to E64. Further exploration to assess aggresome throughput using the autophagy regulator LC3 as a marker showed that, in the absence of correctors, N1303K showed a stalled throughput of LC3-II to the aggresome. The throughput became active again after treatment with the corrector combination C4 + C18. Confocal microscopic studies showed that the N1303K and S1235R mutant proteins both co-localized with LC3, but this co-localization was abolished by the corrector combination and, to a lesser extent, by VX-809. Both the corrector combination and VX-809 increased the CFTR chloride channel function of both mutants. We conclude that correctors have a dual effect, particularly on N1303K: they improve trafficking and function at the plasma membrane and reduce the association with autophagosomes. After treatment with correctors persistent degradation by the autophagosome may limit restoration of function. Thus, mutations in NBD2 of CFTR, in contrast to ΔF508-CFTR, may require additional personalized strategies to rescue them.
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Affiliation(s)
- Qiangni Liu
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Physiology, Johns Hopkins University, Baltimore, MD, USA
| | - Inna Sabirzhanova
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Physiology, Johns Hopkins University, Baltimore, MD, USA
| | - Murali K Yanda
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Physiology, Johns Hopkins University, Baltimore, MD, USA
| | - Emily A S Bergbower
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Physiology, Johns Hopkins University, Baltimore, MD, USA
| | - Clément Boinot
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Physiology, Johns Hopkins University, Baltimore, MD, USA
| | - William B Guggino
- Department of Physiology, Johns Hopkins University, Baltimore, MD, USA
| | - Liudmila Cebotaru
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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DeStefano S, Gees M, Hwang TC. Physiological and pharmacological characterization of the N1303K mutant CFTR. J Cyst Fibros 2018; 17:573-581. [PMID: 29887518 DOI: 10.1016/j.jcf.2018.05.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/13/2018] [Accepted: 05/21/2018] [Indexed: 11/18/2022]
Abstract
BACKGROUND N1303K, one of the common, severe disease-causing mutations in the CFTR gene, causes both defective biogenesis and gating abnormalities of the CFTR protein. The goals of the present study are to quantitatively assess the gating defects associated with the N1303K mutation and its pharmacological response to CFTR modulators including potentiators VX-770 and GLPG1837 and correctors VX-809, and VX-661. METHODS Gating behavior and pharmacological responses to CFTR potentiators were assessed using patch-clamp technique in the excised, inside-out mode. We also examined the effects of GLPG1837, VX-770, VX-809 and VX-661 on N1303K-CFTR surface expression using Western blot analysis. RESULTS Like wild-type (WT) CFTR, N1303K-CFTR channels were activated by protein kinase A-dependent phosphorylation, but the open probability (Po) of phosphorylated N1303K-CFTR was extremely low (~0.03 vs ~0.45 in WT channels). N1303K mutants showed abnormal responses to ATP analogs or mutations that disrupt ATP hydrolysis and/or dimerization of CFTR's two nucleotide-binding domains (NBDs). However, the Po of N1303K-CFTR was dramatically increased by GLPG1837 (~17-fold) and VX-770 (~8-fold). VX-809 or VX-661 enhanced N1303K-CFTR maturation by 2-3 fold, and co-treatment with GLPG1837 or VX-770 did not show any negative drug-drug interaction. CONCLUSION N1303K has a severe gating defect, reduced ATP-dependence and aberrant response to ATP analogs. These results suggest a defective function of the NBDs in N1303K-CFTR. An improvement of channel function by GLPG1837 or VX-770 and an increase of Band C protein by VX-809 or VX-661 support a therapeutic strategy of combining CFTR potentiator and corrector for patients carrying the N1303K mutation.
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Affiliation(s)
- Samantha DeStefano
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, United States; Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO 65211, United States
| | | | - Tzyh-Chang Hwang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, United States; Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO 65211, United States.
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Simon M, Mesmar F, Helguero L, Williams C. Genome-wide effects of MELK-inhibitor in triple-negative breast cancer cells indicate context-dependent response with p53 as a key determinant. PLoS One 2017; 12:e0172832. [PMID: 28235006 PMCID: PMC5325553 DOI: 10.1371/journal.pone.0172832] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 02/10/2017] [Indexed: 12/18/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive, highly recurrent breast cancer subtype, affecting approximately one-fifth of all breast cancer patients. Subpopulations of treatment-resistant cancer stem cells within the tumors are considered to contribute to disease recurrence. A potential druggable target for such cells is the maternal embryonic leucine-zipper kinase (MELK). MELK expression is upregulated in mammary stem cells and in undifferentiated cancers, where it correlates with poor prognosis and potentially mediates treatment resistance. Several MELK inhibitors have been developed, of which one, OTSSP167, is currently in clinical trials. In order to better understand how MELK and its inhibition influence TNBC, we verified its anti-proliferative and apoptotic effects in claudin-low TNBC cell lines MDA-MB-231 and SUM-159 using MTS assays and/or trypan blue viability assays together with analysis of PARP cleavage. Then, using microarrays, we explored which genes were affected by OTSSP167. We demonstrate that different sets of genes are regulated in MDA-MB-231 and SUM-159, but in both cell lines genes involved in cell cycle, mitosis and protein metabolism and folding were regulated. We identified p53 (TP53) as a potential upstream regulator of the regulated genes. Using western blot we found that OTSSP167 downregulates mutant p53 in all tested TNBC cell lines (MDA-MB-231, SUM-159, and BT-549), but upregulates wild-type p53 in the luminal A subtype MCF-7 cell line. We propose that OTSSP167 might have context-dependent or off-target effects, but that one consistent mechanism of action could involve the destabilization of mutant p53.
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Affiliation(s)
- Marisa Simon
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Texas, United States of America
| | - Fahmi Mesmar
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Texas, United States of America
| | - Luisa Helguero
- Institute for Research in Biomedicine, Department of Biosciences, University of Aveiro, Aveiro, Portugal
| | - Cecilia Williams
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Texas, United States of America
- Division of Proteomics, SciLifeLab, School of Biotechnology, KTH – Royal Institute of Technology, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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Cui B, Yang Q, Guan H, Shi B, Hou P, Ji M. PRIMA-1, a mutant p53 reactivator, restores the sensitivity of TP53 mutant-type thyroid cancer cells to the histone methylation inhibitor 3-Deazaneplanocin A. J Clin Endocrinol Metab 2014; 99:E962-70. [PMID: 24512488 DOI: 10.1210/jc.2013-3147] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT 3-Deazaneplanocin A (DZNep) depletes enhancer of zeste homolog 2 (EZH2), a core component of polycomb repressive complex 2 (PRC2), which is frequently overexpressed in human cancers. DZNep exhibits promising antitumor activity, and its responsiveness in cancer cells is determined by certain genetic factors. OBJECTIVES Our aims were (1) to test the therapeutic potential of DZNep and explore the genetic determinants affecting the DZNep response in thyroid cancer cells and (2) to test the combined therapeutic effect of DZNep and PRIMA-1, a mutant p53 reactivator, in thyroid cancer. EXPERIMENTAL DESIGN We evaluated the phenotypic effects of DZNep in thyroid cancer cells and examined the effects of DZNep alone or in combination with PRIMA-1 on cell proliferation, the cell cycle, apoptosis, and xenograft tumor growth. RESULTS DZNep induced enhancer of zeste homolog 2 depletion and trimethylated lysine 27 in H3 histone (H3K27me3) mark reduction in all thyroid cancer cells; however, only TP53 wild-type cells exhibited growth inhibition with DZNep treatment. In these cells, DZNep caused p53 protein accumulation through up-regulation of USP10 expression, resulting in activation of the p53 pathway, contributing to inhibition of cell growth. Conversely, TP53 mutant-type cells were resistant to DZNep. Strikingly, the combination of DZNep with PRIMA-1 restored the sensitivity of TP53 mutant-type cells to DZNep. A similar antitumor effect of DZNep and PRIMA-1 alone or in combination was also seen in xenograft tumor models. CONCLUSION Our data demonstrated that DZNep responsiveness was strongly associated with TP53 genomic status in thyroid cancer cells. Reactivation of p53 restored the sensitivity of TP53 mutant-type cells to DZNep. Thus, a combined therapeutic strategy may be effective in treating thyroid cancer cells (or patients) harboring mutant p53.
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Affiliation(s)
- Bo Cui
- Department of Endocrinology (B.C., Q.Y., B.S., P.H.) and Center for Translational Medicine (M.J.), The First Affiliated Hospital of Xi'an Jiao tong University School of Medicine, Xi'an 710061, the People's Republic of China; and Department of Endocrinology and Metabolism (H.G.), The First Affiliated Hospital of China Medical University, Shenyang 110001, the People's Republic of China
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Tenne SJ, Schwaneberg U. First insights on organic cosolvent effects on FhuA wildtype and FhuA Δ1-159. Int J Mol Sci 2012; 13:2459-2471. [PMID: 22408464 PMCID: PMC3292033 DOI: 10.3390/ijms13022459] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 02/09/2012] [Accepted: 02/13/2012] [Indexed: 11/24/2022] Open
Abstract
Circular dichroism (CD) and deconvolution were used to study the structural integrity of a "plugged" and an "open" FhuA transmembrane channel protein in the presence of varied concentrations of tetrahydrofuran (THF), ethanol (EtOH) and chloroform/methanol (C/M). FhuA is an Escherichia coli outer membrane protein (78.9 kDa) consisting of 22 β-sheets and an internal globular cork domain which acts as an iron transporter. FhuA and the deletion variant FhuA Δ1-159 showed comparable and remarkable resistance in the presence of THF (≤40 vol%) and EtOH (≤10 vol%). In C/M, significant differences in structural resistance were observed (FhuA stable ≤10 vol%; FhuA Δ1-159 ≤1 vol%). Deconvolution of CD-spectra for FhuA and FhuA Δ1-159 yielded β-sheet contents of 61 % (FhuA) and 58% (FhuA Δ1-159). Interestingly, FhuA and FhuA Δ1-159 had comparable β-sheet contents in the presence and absence of all three organic cosolvents. Additionally, precipitated FhuA and FhuA Δ1-159 (in 40 vol% C/M or 65 vol% THF) redissolved by supplementing the detergent n-octyl-oligo-oxyethylene (oPOE).
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Affiliation(s)
- Stefanie-Joana Tenne
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringer Weg 1, Aachen, D-52074, Germany; E-Mail:
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringer Weg 1, Aachen, D-52074, Germany; E-Mail:
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Abstract
Substitutive therapy has significantly ameliorated the quality of life of patients with coagulation factor deficiencies. However, there are some limitations that support research towards alternative therapeutic approaches. Here we focus on the rescue of coagulation factor biosynthesis by targeting the RNA processing and translation, which would permit restoration of the altered gene expression while maintaining the gene regulation in the physiological tissues. The essential prerequisite of the three reported RNA-based correction approaches (i-iii), which rely on mutation types and are applicable even to large size mRNAs, is the presence in cells of the precursor (pre-mRNA) or mature mRNA forms. (i) In the F7 gene, modification of the small nuclear RNA U1 (U1 snRNA), the key component of the spliceosomal U1 ribonucleoprotein, re-directs correct usage of a mutated exon-intron junction, triggering synthesis of correct mRNA and secretion of functional factor (F)VII. (ii) Spliceosome-mediated RNA trans-splicing (SMaRT) between mutated and engineered pre-mRNAs produces normal FVIII mRNA and secretion of functional protein. (iii) Aminoglycoside drugs induce ribosome readthrough and suppress premature translation termination caused by nonsense mutations in FVII, VIII and IX. The rescued expression levels ranged from very low (aminoglycosides) to moderate (U1 snRNA and SMaRT), which could result in amelioration of the disease phenotypes. These findings prompt further studies aimed at demonstrating the clinical translatability of RNA-based strategies, which might open new avenues in the treatment of coagulation factor deficiencies.
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Affiliation(s)
- M Pinotti
- Department of Biochemistry and Molecular Biology, University of Ferrara, Trieste, Italy
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Kopecká J, Krijt J, Raková K, Kožich V. Restoring assembly and activity of cystathionine β-synthase mutants by ligands and chemical chaperones. J Inherit Metab Dis 2011; 34:39-48. [PMID: 20490928 PMCID: PMC3026675 DOI: 10.1007/s10545-010-9087-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 02/28/2010] [Accepted: 03/19/2010] [Indexed: 11/28/2022]
Abstract
Misfolding and aggregation of mutant enzymes have been proposed to play role in the pathogenesis of homocystinuria due to cystathionine β-synthase (CBS) deficiency. Chemical chaperones have been recently shown to facilitate proper assembly of several CBS mutants. To asses the number of patients that may respond to chaperone therapy, we examined the effect of selected CBS ligands and osmolytes on assembly and activity of 27 CBS mutants that represent 70% of known CBS alleles. The mutant enzymes were expressed in a bacterial system, and their properties were assessed by native Western blotting and sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) assay, respectively. We studied the chaperoning activity of δ-aminolevulinic acid (δ-ALA)-a heme precursor-and of three osmolytes betaine, 2-aminoethanesulfonic acid (taurine), and glycerol. Fourteen mutants responded by at least 30% increase in the amount of correctly assembled tetramers and enzymatic activity to the coexpressional presence of either 0.5 mM δ-ALA, 100 mM betaine, and/or 750 mM glycerol. Eight of these mutants (p.R266K, p.P49L, p.R125Q, p.K102N, p.R369C, p.V180A, p.P78R, p.S466L) were rescuable by all of these three substances. Four mutants showed increased formation of tetramers that was not accompanied by changes in activity. Topology of mutations appeared to determine the chaperone responsiveness, as 11 of 14 solvent-exposed mutations were substantially more responsive than three of 13 buried mutations. This study identified chaperone-responsive mutants that represent 56 of 713 known patient-derived CBS alleles and may serve as a basis for exploring pharmacological approaches aimed at correcting misfolding in homocystinuria.
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Affiliation(s)
- Jana Kopecká
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, 128 08 Praha 2, Czech Republic
| | - Jakub Krijt
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, 128 08 Praha 2, Czech Republic
| | - Kateřina Raková
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, 128 08 Praha 2, Czech Republic
| | - Viktor Kožich
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, 128 08 Praha 2, Czech Republic
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Zache N, Lambert JMR, Rökaeus N, Shen J, Hainaut P, Bergman J, Wiman KG, Bykov VJN. Mutant p53 targeting by the low molecular weight compound STIMA-1. Mol Oncol 2008; 2:70-80. [PMID: 19383329 DOI: 10.1016/j.molonc.2008.02.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2007] [Revised: 02/25/2008] [Accepted: 02/28/2008] [Indexed: 12/13/2022] Open
Abstract
Reactivation of mutant p53 in human tumor cells should induce cell death by apoptosis and thus eliminate the tumor. Several small molecules that reactivate mutant p53 have been identified. Here we show that STIMA-1, a low molecular weight compound with some structural similarities to the previously identified molecule CP-31398, can stimulate mutant p53 DNA binding in vitro and induce expression of p53 target proteins and trigger apoptosis in mutant p53-expressing human tumor cells. Human diploid fibroblasts are significantly more resistant to STIMA-1 than mutant or wild type p53-carrying tumor cells. STIMA-1 may provide new insights into possible mechanisms of mutant p53 reactivation and thus facilitate the development of novel anticancer drugs that target mutant p53-carrying tumors.
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Affiliation(s)
- Nicole Zache
- Karolinska Institutet, Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska University Hospital, Stockholm, Sweden
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13
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Martínez-Rodríguez S, Andújar-Sánchez M, Neira JL, Clemente-Jiménez JM, Jara-Pérez V, Rodríguez-Vico F, Las Heras-Vázquez FJ. Site-directed mutagenesis indicates an important role of cysteines 76 and 181 in the catalysis of hydantoin racemase from Sinorhizobium meliloti. Protein Sci 2007; 15:2729-38. [PMID: 17132860 PMCID: PMC2242435 DOI: 10.1110/ps.062452106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Hydantoin racemase enzyme plays a crucial role in the reaction cascade known as "hydantoinase process." In conjunction with a stereoselective hydantoinase and a stereospecific carbamoylase, it allows the total conversion from D,L-5-monosubstituted hydantoins, with a low rate of racemization, to optically pure D- or L-amino acids. Residues Cys76 and Cys181 belonging to hydantoin racemase from Sinorhizobium meliloti (SmeHyuA) have been proved to be involved in catalysis. Here, we report biophysical data of SmeHyuA Cys76 and Cys181 to alanine mutants, which point toward a two-base mechanism for the racemization of 5-monosubstituted hydantoins. The secondary and the tertiary structure of the mutants were not significantly affected, as shown by circular dichroism. Calorimetric and fluorescence experiments have shown that Cys76 is responsible for recognition and proton retrieval of D-isomers, while Cys181 is responsible for L-isomer recognition and racemization. This recognition process is further supported by measurements of protein stability followed by chemical denaturation in the presence of the corresponding compound.
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Affiliation(s)
- Sergio Martínez-Rodríguez
- Departamento Química Física, Bioquímica y Química Inorgánica, Universidad de Almería, 04120 Almería, Spain
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Surín S, Cubonová L, Majerník AI, Smigán P. Amiloride resistance in the methanoarcheon Methanothermobacter thermoautotrophicus: characterization of membrane-associated proteins. Folia Microbiol (Praha) 2006; 51:313-6. [PMID: 17007434 DOI: 10.1007/bf02931822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
An amiloride-resistant mutant with diminished Na+/H+ antiporter activity was isolated from Methanothermobacter thermoautotrophicus. To define the protein basis of amiloride resistance, the composition of membrane-associated proteins was partially characterized and compared with that of the wild type strain. An abundant 670-kDa membrane-associated protein that was present only in the mutant strain was analyzed by MALDI-TOF MS and identified as a coenzyme F420-reducing hydrogenase. The amiloride resistance was not accompanied by changes in protein size or changes in the level of subunits A or B of the A1A0-type ATP synthase; on the other hand, the SDS-PAGE patterns of the chloroform-methanol extract of membranes from both strains were different. Two bands with calculated molecular mass 16 and 11 kDa were identified as MtrD and AtpK, respectively. The observed over-expression of a 22.7-kDa protein in the mutant cells may represent the multimeric form of the MtrD subunit. These results show that the impairment of the Na+/H+ antiporter system in the amiloride-resistant mutant of Methanothermobacter thermoautotrophicus is accompanied by only small changes in a few membrane-associated proteins.
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Affiliation(s)
- S Surín
- Institute of Animal Biochemistry and Genetics, Slovak Academy of Sciences, Ivanka pri Dunaji, Slovakia
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Zahradník I, Györke S, Zahradníková A. Calcium activation of ryanodine receptor channels--reconciling RyR gating models with tetrameric channel structure. ACTA ACUST UNITED AC 2006; 126:515-27. [PMID: 16260840 PMCID: PMC2266604 DOI: 10.1085/jgp.200509328] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite its importance and abundance of experimental data, the molecular mechanism of RyR2 activation by calcium is poorly understood. Recent experimental studies involving coexpression of wild-type (WT) RyR2 together with a RyR2 mutant deficient in calcium-dependent activation (Li, P., and S.R. Chen. 2001. J. Gen. Physiol. 118:33–44) revealed large variations of calcium sensitivity of the RyR tetramers with their monomer composition. Together with previous results on kinetics of Ca activation (Zahradníková, A., I. Zahradník, I. Györke, and S. Györke. 1999. J. Gen. Physiol. 114:787–798), these data represent benchmarks for construction and testing of RyR models that would reproduce RyR behavior and be structurally realistic as well. Here we present a theoretical study of the effects of RyR monomer substitution by a calcium-insensitive mutant on the calcium dependence of RyR activation. Three published models of tetrameric RyR channels were used either directly or after adaptation to provide allosteric regulation. Additionally, two alternative RyR models with Ca binding sites created jointly by the monomers were developed. The models were modified for description of channels composed of WT and mutant monomers. The parameters of the models were optimized to provide the best approximation of published experimental data. For reproducing the observed calcium dependence of RyR tetramers containing mutant monomers (a) single, independent Ca binding sites on each monomer were preferable to shared binding sites; (b) allosteric models were preferable to linear models; (c) in the WT channel, probability of opening to states containing a Ca2+-free monomer had to be extremely low; and (d) models with fully Ca-bound closed states, additional to those of an Monod-Wyman-Changeaux model, were preferable to models without such states. These results provide support for the concept that RyR activation is possible (albeit vanishingly small in WT channels) in the absence of Ca2+ binding. They also suggest further avenues toward understanding RyR gating.
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Affiliation(s)
- Ivan Zahradník
- Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovakia
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