1
|
Regunath K, Fomin V, Liu Z, Wang P, Hoque M, Tian B, Rabadan R, Prives C. Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types. Mol Cancer Res 2024; 22:555-571. [PMID: 38393317 DOI: 10.1158/1541-7786.mcr-23-0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/04/2023] [Accepted: 02/21/2024] [Indexed: 02/25/2024]
Abstract
The p53 tumor suppressor protein, a sequence-specific DNA binding transcription factor, regulates the expression of a large number of genes, in response to various forms of cellular stress. Although the protein coding target genes of p53 have been well studied, less is known about its role in regulating long noncoding genes and their functional relevance to cancer. Here we report the genome-wide identification of a large set (>1,000) of long noncoding RNAs (lncRNA), which are putative p53 targets in a colon cancer cell line and in human patient datasets from five different common types of cancer. These lncRNAs have not been annotated by other studies of normal unstressed systems. In the colon cancer cell line, a high proportion of these lncRNAs are uniquely induced by different chemotherapeutic agents that activate p53, whereas others are induced by more than one agent tested. Further, subsets of these lncRNAs independently predict overall and disease-free survival of patients across the five different common cancer types. Interestingly, both genetic alterations and patient survival associated with different lncRNAs are unique to each cancer tested, indicating extraordinary tissue-specific variability in the p53 noncoding response. The newly identified noncoding p53 target genes have allowed us to construct a classifier for tumor diagnosis and prognosis. IMPLICATIONS Our results not only identify myriad p53-regulated long noncoding (lncRNA), they also reveal marked drug-induced, as well as tissue- and tumor-specific heterogeneity in these putative p53 targets and our findings have enabled the construction of robust classifiers for diagnosis and prognosis.
Collapse
Affiliation(s)
- Kausik Regunath
- Department of Biological Sciences, Columbia University, New York, New York
| | - Vitalay Fomin
- Department of Biological Sciences, Columbia University, New York, New York
| | - Zhaoqi Liu
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Pingzhang Wang
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Mainul Hoque
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Raul Rabadan
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, New York
| |
Collapse
|
2
|
Psatha K, Kollipara L, Drakos E, Deligianni E, Brintakis K, Patsouris E, Sickmann A, Rassidakis GZ, Aivaliotis M. Interruption of p53-MDM2 Interaction by Nutlin-3a in Human Lymphoma Cell Models Initiates a Cell-Dependent Global Effect on Transcriptome and Proteome Level. Cancers (Basel) 2023; 15:3903. [PMID: 37568720 PMCID: PMC10417430 DOI: 10.3390/cancers15153903] [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] [Received: 05/10/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 08/13/2023] Open
Abstract
In most lymphomas, p53 signaling pathway is inactivated by various mechanisms independent to p53 gene mutations or deletions. In many cases, p53 function is largely regulated by alterations in the protein abundance levels by the action of E3 ubiquitin-protein ligase MDM2, targeting p53 to proteasome-mediated degradation. In the present study, an integrating transcriptomics and proteomics analysis was employed to investigate the effect of p53 activation by a small-molecule MDM2-antagonist, nutlin-3a, on three lymphoma cell models following p53 activation. Our analysis revealed a system-wide nutlin-3a-associated effect in all examined lymphoma types, identifying in total of 4037 differentially affected proteins involved in a plethora of pathways, with significant heterogeneity among lymphomas. Our findings include known p53-targets and novel p53 activation effects, involving transcription, translation, or degradation of protein components of pathways, such as a decrease in key members of PI3K/mTOR pathway, heat-shock response, and glycolysis, and an increase in key members of oxidative phoshosphorylation, autophagy and mitochondrial translation. Combined inhibition of HSP90 or PI3K/mTOR pathway with nutlin-3a-mediated p53-activation enhanced the apoptotic effects suggesting a promising strategy against human lymphomas. Integrated omic profiling after p53 activation offered novel insights on the regulatory role specific proteins and pathways may have in lymphomagenesis.
Collapse
Affiliation(s)
- Konstantina Psatha
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, 70013 Heraklion, Greece; (K.P.); (E.D.)
- Department of Pathology, Medical School, University of Crete, 70013 Heraklion, Greece;
- First Department of Pathology, National and Kapodistrian University of Athens, 15772 Athens, Greece;
- Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), 54124 Thessaloniki, Greece
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften–ISAS–e.V., 44139 Dortmund, Germany; (L.K.); (A.S.)
| | - Elias Drakos
- Department of Pathology, Medical School, University of Crete, 70013 Heraklion, Greece;
| | - Elena Deligianni
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, 70013 Heraklion, Greece; (K.P.); (E.D.)
| | - Konstantinos Brintakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology—Hellas, 71110 Heraklion, Greece;
| | - Eustratios Patsouris
- First Department of Pathology, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften–ISAS–e.V., 44139 Dortmund, Germany; (L.K.); (A.S.)
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
- Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - George Z. Rassidakis
- Department of Oncology-Pathology, Karolinska Institute, 17164 Stockholm, Sweden;
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, 70013 Heraklion, Greece; (K.P.); (E.D.)
- Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), 54124 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| |
Collapse
|
3
|
Li R, Zatloukalova P, Muller P, Gil-Mir M, Kote S, Wilkinson S, Kemp AJ, Hernychova L, Wang Y, Ball KL, Tao K, Hupp T, Vojtesek B. The MDM2 ligand Nutlin-3 differentially alters expression of the immune blockade receptors PD-L1 and CD276. Cell Mol Biol Lett 2020; 25:41. [PMID: 32874188 PMCID: PMC7457494 DOI: 10.1186/s11658-020-00233-w] [Citation(s) in RCA: 10] [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: 04/04/2020] [Accepted: 08/21/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The links between the p53/MDM2 pathway and the expression of pro-oncogenic immune inhibitory receptors in tumor cells are undefined. In this report, we evaluate whether there is p53 and/or MDM2 dependence in the expression of two key immune receptors, CD276 and PD-L1. METHODS Proximity ligation assays were used to quantify protein-protein interactions in situ in response to Nutlin-3. A panel of p53-null melanoma cells was created using CRISPR-Cas9 guide RNA mediated genetic ablation. Flow cytometric analyses were used to assess the impact of TP53 or ATG5 gene ablation, as well as the effects of Nutlin-3 and an ATM inhibitor on cell surface PD-L1 and CD276. Targeted siRNA was used to deplete CD276 to assess changes in cell cycle parameters by flow cytometry. A T-cell proliferation assay was used to assess activity of CD4+ T-cells as a function of ATG5 genotype. RESULTS CD276 forms protein-protein interactions with MDM2 in response to Nutlin-3, similar to the known MDM2 interactors p53 and HSP70. Isogenic HCT116 p53-wt/null cancer cells demonstrated that CD276 is induced on the cell surface by Nutlin-3 in a p53-dependent manner. PD-L1 was also unexpectedly induced by Nutlin-3, but PD-L1 does not bind MDM2. The ATM inhibitor KU55993 reduced the levels of PD-L1 under conditions where Nutlin-3 induces PD-L1, indicating that MDM2 and ATM have opposing effects on PD-L1 steady-state levels. PD-L1 is also up-regulated in response to genetic ablation of TP53 in A375 melanoma cell clones under conditions in which CD276 remains unaffected. A549 cells with a deletion in the ATG5 gene up-regulated only PD-L1, further indicating that PD-L1 and CD276 are under distinct genetic control. CONCLUSION Genetic inactivation of TP53, or the use of the MDM2 ligand Nutlin-3, alters the expression of the immune blockade receptors PD-L1 and CD276. The biological function of elevated CD276 is to promote altered cell cycle progression in response to Nutlin-3, whilst the major effect of elevated PD-L1 is T-cell suppression. These data indicate that TP53 gene status, ATM and MDM2 influence PD-L1 and CD276 paralogs on the cell surface. These data have implications for the use of drugs that target the p53 pathway as modifiers of immune checkpoint receptor expression.
Collapse
Affiliation(s)
- Ruidong Li
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland EH4 2XR UK
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | - Petr Muller
- RECAMO, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Maria Gil-Mir
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland EH4 2XR UK
| | - Sachin Kote
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Simon Wilkinson
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland EH4 2XR UK
| | - Alain J. Kemp
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland EH4 2XR UK
| | - Lenka Hernychova
- RECAMO, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Yaxin Wang
- Department of Anesthesiology and Critical Care, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kathryn L. Ball
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland EH4 2XR UK
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ted Hupp
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland EH4 2XR UK
- RECAMO, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| |
Collapse
|
4
|
Kobayashi M, Ishizaki Y, Owaki M, Matsumoto Y, Kakiyama Y, Hoshino S, Tagawa R, Sudo Y, Okita N, Akimoto K, Higami Y. Nutlin-3a suppresses poly (ADP-ribose) polymerase 1 by mechanisms different from conventional PARP1 suppressors in a human breast cancer cell line. Oncotarget 2020; 11:1653-1665. [PMID: 32405340 PMCID: PMC7210013 DOI: 10.18632/oncotarget.27581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) plays important roles in single strand DNA repair. PARP1 inhibitors enhance the effects of DNA damaging drugs in homologous recombination-deficient tumors including tumors with breast cancer susceptibility gene (BRCA1) mutation. Nutlin-3a, an analog of cis-imidazoline, inhibits degradation of murine double minute 2 (MDM2) and stabilizes p53. We previously reported that nutlin-3a induces PARP1 degradation in p53-dependent manner in mouse fibroblasts, suggesting nutlin-3a may be a PARP1 suppressor. Here, we investigated the effects of nutlin-3a on PARP1 in MCF-7, a human breast cancer cell line. Consistent with our previous results, nutlin-3a reduced PARP1 levels in dose- and time-dependent manners in MCF-7 cells, but this reduction was suppressed in p53 knockdown cells. RITA, a p53 stabilizer that binds to p53 itself, failed to reduce PARP1 protein levels. Moreover, transient MDM2 knockdown repressed nutlin-3a-mediated PARP1 reduction. The MG132 proteasome inhibitor, and knockdown of checkpoint with forkhead and ring finger domains (CHFR) and ring finger protein 146 (RNF146), E3 ubiquitin ligases targeting PARP1, suppressed nutlin-3a-induced PARP1 reduction. Short-term nutlin-3a treatment elevated the levels of PARylated PARP1, suggesting nutlin-3a promoted PARylation of PARP1, thereby inducing its proteasomal degradation. Furthermore, nutlin-3a-induced PARP1 degradation enhanced DNA-damaging effects of cisplatin in BRCA1 knockdown cells. Our study revealed that nutlin-3a is a PARP1 suppressor that induces PARP1 proteasomal degradation by binding to MDM2 and promoting autoPARylation of PARP1. Further analysis of the mechanisms in nutlin-3a-induced PARP1 degradation may lead to the development of novel PARP1 suppressors applicable for cancers with BRCA1 mutation.
Collapse
Affiliation(s)
- Masaki Kobayashi
- Laboratory of Molecular Pathology & Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan.,Translational Research Center, Research Institute of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan.,Co-first authors
| | - Yuka Ishizaki
- Laboratory of Molecular Pathology & Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan.,Co-first authors
| | - Mika Owaki
- Laboratory of Molecular Pathology & Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan.,Co-first authors
| | - Yoko Matsumoto
- Laboratory of Molecular Pathology & Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yuri Kakiyama
- Laboratory of Molecular Pathology & Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Shunsuke Hoshino
- Laboratory of Molecular Pathology & Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan.,Translational Research Center, Research Institute of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Ryoma Tagawa
- Laboratory of Molecular Pathology & Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yuka Sudo
- Translational Research Center, Research Institute of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Naoyuki Okita
- Division of Pathological Biochemistry, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-onoda, Yamaguchi 756-0884, Japan
| | - Kazunori Akimoto
- Translational Research Center, Research Institute of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan.,Laboratory of Medicinal and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yoshikazu Higami
- Laboratory of Molecular Pathology & Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan.,Translational Research Center, Research Institute of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| |
Collapse
|
5
|
Dey L, Mukhopadhyay A. Biclustering-based association rule mining approach for predicting cancer-associated protein interactions. IET Syst Biol 2020; 13:234-242. [PMID: 31538957 DOI: 10.1049/iet-syb.2019.0045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Protein-protein interactions (PPIs) have been widely used to understand different biological processes and cellular functions associated with several diseases like cancer. Although some cancer-related protein interaction databases are available, lack of experimental data and conflicting PPI data among different available databases have slowed down the cancer research. Therefore, in this study, the authors have focused on various proteins that are directly related to different types of cancer disease. They have prepared a PPI database between cancer-associated proteins with the rest of the human proteins. They have also incorporated the annotation type and direction of each interaction. Subsequently, a biclustering-based association rule mining algorithm is applied to predict new interactions with type and direction. This study shows the prediction power of association rule mining algorithm over the traditional classifier model without choosing a negative data set. The time complexity of the biclustering-based association rule mining is also analysed and compared to traditional association rule mining. The authors are able to discover 38 new PPIs which are not present in the cancer database. The biological relevance of these newly predicted interactions is analysed by published literature. Recognition of such interactions may accelerate a way of developing new drugs to prevent different cancer-related diseases.
Collapse
Affiliation(s)
- Lopamudra Dey
- Department of Computer Science and Engineering, Heritage Institute of Technology, 994 Madurdaha, Kolkata 700 107, West Bengal, India.
| | - Anirban Mukhopadhyay
- Department of Computer Science and Engineering, University of Kalyani, Nadia, Kalyani 741235, West Bengal, India
| |
Collapse
|
6
|
Tommasi C, Rogerson C, Depledge DP, Jones M, Naeem AS, Venturini C, Frampton D, Tutill HJ, Way B, Breuer J, O'Shaughnessy RFL. Kallikrein-Mediated Cytokeratin 10 Degradation Is Required for Varicella Zoster Virus Propagation in Skin. J Invest Dermatol 2019; 140:774-784.e11. [PMID: 31626786 DOI: 10.1016/j.jid.2019.08.448] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 11/30/2022]
Abstract
Varicella zoster virus (VZV) is a skin-tropic virus that infects epidermal keratinocytes and causes chickenpox. Although common, VZV infection can be life-threatening, particularly in the immunocompromized. Therefore, understanding VZV-keratinocyte interactions is important to find new treatments beyond vaccination and antiviral drugs. In VZV-infected skin, kallikrein 6 and the ubiquitin ligase MDM2 are upregulated concomitant with keratin 10 (KRT10) downregulation. MDM2 binds to KRT10, targeting it for degradation via the ubiquitin-proteasome pathway. Preventing KRT10 degradation reduced VZV propagation in culture and prevented epidermal disruption in skin explants. KRT10 knockdown induced expression of NR4A1 and enhanced viral propagation in culture. NR4A1 knockdown prevented viral propagation in culture, reduced LC3 levels, and increased LAMP2 expression. We therefore describe a drug-able pathway whereby MDM2 ubiquitinates and degrades KRT10, increasing NR4A1 expression and allowing VZV replication and propagation.
Collapse
Affiliation(s)
- Cristina Tommasi
- Livingstone Skin Research Centre, Immunobiology and Dermatology, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Clare Rogerson
- Centre for Cell Biology and Cutaneous Research, Queen Mary University of London, London, United Kingdom
| | - Daniel P Depledge
- Infection and Immunity, University College London, London, United Kingdom; Department of Microbiology, New York University, New York, New York
| | - Meleri Jones
- Centre for Cell Biology and Cutaneous Research, Queen Mary University of London, London, United Kingdom; Infection and Immunity, University College London, London, United Kingdom
| | - Aishath S Naeem
- Livingstone Skin Research Centre, Immunobiology and Dermatology, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Cristina Venturini
- Infection and Immunity, University College London, London, United Kingdom
| | - Dan Frampton
- Infection and Immunity, University College London, London, United Kingdom
| | - Helena J Tutill
- Infection and Immunity, University College London, London, United Kingdom
| | - Benjamin Way
- Livingstone Skin Research Centre, Immunobiology and Dermatology, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Judith Breuer
- Infection and Immunity, University College London, London, United Kingdom
| | - Ryan F L O'Shaughnessy
- Livingstone Skin Research Centre, Immunobiology and Dermatology, University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Centre for Cell Biology and Cutaneous Research, Queen Mary University of London, London, United Kingdom.
| |
Collapse
|
7
|
Walter RFH, Sydow SR, Berg E, Kollmeier J, Christoph DC, Christoph S, Eberhardt WEE, Mairinger T, Wohlschlaeger J, Schmid KW, Mairinger FD. Bortezomib sensitivity is tissue dependent and high expression of the 20S proteasome precludes good response in malignant pleural mesothelioma. Cancer Manag Res 2019; 11:8711-8720. [PMID: 31576173 PMCID: PMC6765394 DOI: 10.2147/cmar.s194337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 07/22/2019] [Indexed: 01/13/2023] Open
Abstract
Background Bortezomib is an approved proteasome inhibitor for the treatment of certain lymphoma subtypes. Two clinical trials investigated bortezomib in patients with malignant pleural mesothelioma (MPM) and failed to improve outcome. We present a potential explanation for this event. Methods 171 patients with MPM were analyzed for their mRNA expression of proteasomal subunits PSMA1, PSMA5, PSMB1, PSMB2, PSMB4 and PSMB5 via qPCR (n=84) or sequencing (n=87 TCGA/cBioPortal data set “Mesothelioma”). Outcome and subunit expression were correlated. Four mesothelial and one fibroblast cell line were treated with bortezomib and cisplatin. Cellular response was measured after 0, 6, 12, 24, 48 and 72 hrs. Enzyme activity of proteasomal subunits was assessed via functional enzyme activity assays. Results Patients with MPM presented with elevated expression of proteasomal subunits compared to benign controls (p<0.001). PSMB4 correlated with outcome (Cox propotiortional-hazards model (COXPH): p<0.0175, TCGA/cBioPortal data). In cell lines, apoptosis was the main event with a peak after 48 hr incubation for bortezomib or cisplatin. Only two cell lines with comparably low proteasome activity (PSMB2 and PSMB5) responded to 50 nM and 100 nM bortezomib better than to cisplatin (MRC-5, NCI-H2052). MSTO-211H responded to cisplatin only, whereas the other two cell lines were considered therapy resistant (Met-5A, NCI-H2452). Interpretation Two clinical trials testing bortezomib in MPM failed, although MPM presents with high proteasome expression, which predicts bortezomib sensitivity in several tumors. Bortezomib induced apoptosis in MPM cell lines with low proteasome activity only. Bortezomib is not suitable for the treatment of MPM, and biomarker-based stratification could have improved both clinical trials. Trial registration NCT00513877 and NCT00458913
Collapse
Affiliation(s)
- Robert Fred Henry Walter
- Ruhrlandklinik, West German Lung Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | | - Erika Berg
- Institute of Pathology, Charité Universitaetsmedizin, Berlin, Germany
| | - Jens Kollmeier
- Institute of Pathology, Helios Klinikum Emil Von Behring, Berlin, Germany
| | - Daniel Christian Christoph
- Department of Oncology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Internistic Oncology, Kliniken Essen Mitte, Essen, Germany
| | - Sandra Christoph
- Department of Bone Marrow Transplantation, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | | - Thomas Mairinger
- Institute of Pathology, Helios Klinikum Emil Von Behring, Berlin, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | |
Collapse
|
8
|
Shuvalov O, Kizenko A, Shakirova A, Fedorova O, Petukhov A, Aksenov N, Vasileva E, Daks A, Barlev N. Nutlin sensitizes lung carcinoma cells to interferon-alpha treatment in MDM2-dependent but p53-independent manner. Biochem Biophys Res Commun 2018; 495:1233-1239. [DOI: 10.1016/j.bbrc.2017.11.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 11/19/2017] [Indexed: 12/21/2022]
|
9
|
Way L, Faktor J, Dvorakova P, Nicholson J, Vojtesek B, Graham D, Ball KL, Hupp T. Rearrangement of mitochondrial pyruvate dehydrogenase subunit dihydrolipoamide dehydrogenase protein-protein interactions by the MDM2 ligand nutlin-3. Proteomics 2017; 16:2327-44. [PMID: 27273042 PMCID: PMC5026170 DOI: 10.1002/pmic.201500501] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 04/27/2016] [Accepted: 06/03/2016] [Indexed: 12/22/2022]
Abstract
Drugs targeting MDM2's hydrophobic pocket activate p53. However, these agents act allosterically and have agonist effects on MDM2's protein interaction landscape. Dominant p53‐independent MDM2‐drug responsive‐binding proteins have not been stratified. We used as a variable the differential expression of MDM2 protein as a function of cell density to identify Nutlin‐3 responsive MDM2‐binding proteins that are perturbed independent of cell density using SWATH‐MS. Dihydrolipoamide dehydrogenase, the E3 subunit of the mitochondrial pyruvate dehydrogenase complex, was one of two Nutlin‐3 perturbed proteins identified fours hour posttreatment at two cell densities. Immunoblotting confirmed that dihydrolipoamide dehydrogenase was induced by Nutlin‐3. Depletion of MDM2 using siRNA also elevated dihydrolipoamide dehydrogenase in Nutlin‐3 treated cells. Mitotracker confirmed that Nutlin‐3 inhibits mitochondrial activity. Enrichment of mitochondria using TOM22+ immunobeads and TMT labeling defined key changes in the mitochondrial proteome after Nutlin‐3 treatment. Proximity ligation identified rearrangements of cellular protein–protein complexes in situ. In response to Nutlin‐3, a reduction of dihydrolipoamide dehydrogenase/dihydrolipoamide acetyltransferase protein complexes highlighted a disruption of the pyruvate dehydrogenase complex. This coincides with an increase in MDM2/dihydrolipoamide dehydrogenase complexes in the nucleus that was further enhanced by the nuclear export inhibitor Leptomycin B. The data suggest one therapeutic impact of MDM2 drugs might be on the early perturbation of specific protein–protein interactions within the mitochondria. This methodology forms a blueprint for biomarker discovery that can identify rearrangements of MDM2 protein–protein complexes in drug‐treated cells.
Collapse
Affiliation(s)
- Luke Way
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Jakub Faktor
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Petra Dvorakova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Judith Nicholson
- CRUK & MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Borek Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Kathryn L Ball
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK.,Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ted Hupp
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK. .,Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic.
| |
Collapse
|
10
|
Expressions Profiles of the Proteins Associated with Carbohydrate Metabolism in Rat Liver Regeneration. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8428926. [PMID: 28752099 PMCID: PMC5511655 DOI: 10.1155/2017/8428926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 05/11/2017] [Accepted: 05/28/2017] [Indexed: 01/20/2023]
Abstract
Liver has a very amazing ability to regenerate from the remnant liver after injury or partial hepatectomy (PH). Carbohydrate metabolism plays a critical role in regeneration. Many signaling pathways are involved in the metabolism process. We analyzed the changes of proteins at 0–36 h after PH in rats using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with LC-MS/MS-based quantitative proteomics strategy. The results showed that 110 proteins and 5 signaling pathways related to carbohydrate metabolism in rat LR changed significantly. Based on a motif discovery method performed by iRegulon, we identified for the first time that the transcription factor SPIB whose motif was enriched among the differentiated genes associated with carbohydrate metabolism may play an important role in liver regeneration for the first time. The findings of this research provide a molecular basis for further unrevealing the mechanism of regeneration at priming stage (0–6 h) and proliferation stage (6–36 h) of LR in rats. At the same time, our studies provide more novel evidence for the signaling pathways which regulate carbohydrate metabolism from proteomics level. This study can provide some new thinking of liver regeneration and treatment of diseases associated with glucose metabolism.
Collapse
|
11
|
Hünten S, Kaller M, Drepper F, Oeljeklaus S, Bonfert T, Erhard F, Dueck A, Eichner N, Friedel CC, Meister G, Zimmer R, Warscheid B, Hermeking H. p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses. Mol Cell Proteomics 2015; 14:2609-29. [PMID: 26183718 DOI: 10.1074/mcp.m115.050237] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 12/20/2022] Open
Abstract
We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics (pulsed stable isotope labeling with amino acids in cell culture/pSILAC) in the colorectal cancer cell line SW480. This was combined with mRNA and noncoding RNA expression analyses by next generation sequencing (RNA-, miR-Seq). Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated proteins (542 up, 569 down), mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down) and lncRNAs (270 up, 123 down). Changes in protein and mRNA expression levels showed a positive correlation (r = 0.50, p < 0.0001). In total, we detected 133 direct p53 target genes that were differentially expressed and displayed p53 occupancy in the vicinity of their promoter. More transcriptionally induced genes displayed occupied p53 binding sites (4.3% mRNAs, 7.2% miRNAs, 6.3% lncRNAs, 5.9% proteins) than repressed genes (2.4% mRNAs, 3.2% miRNAs, 0.8% lncRNAs, 1.9% proteins), suggesting indirect mechanisms of repression. Around 50% of the down-regulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3'-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed up-regulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibits proliferation in SW480 cells. Furthermore, KLF12, HMGB1 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486-5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of KLF12, HMGB1 and CIT was detected in advanced stages of cancer. In conclusion, the integration of multiple omics methods allowed the comprehensive identification of direct and indirect effectors of p53 that provide new insights and leads into the mechanisms of p53-mediated tumor suppression.
Collapse
Affiliation(s)
- Sabine Hünten
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany
| | - Markus Kaller
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany
| | - Friedel Drepper
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Silke Oeljeklaus
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Bonfert
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Florian Erhard
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Anne Dueck
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Norbert Eichner
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Caroline C Friedel
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Gunter Meister
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Ralf Zimmer
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Bettina Warscheid
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; **Center for Biological Systems Analysis (ZBSA), University of Freiburg, 79104 Freiburg, Germany
| | - Heiko Hermeking
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany; §German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany; ¶German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany;
| |
Collapse
|
12
|
Geng X, Wang G, Qin Y, Zang X, Li P, Geng Z, Xue D, Dong Z, Ma K, Chen G, Xu C. iTRAQ-Based Quantitative Proteomic Analysis of the Initiation of Head Regeneration in Planarians. PLoS One 2015; 10:e0132045. [PMID: 26131905 PMCID: PMC4488856 DOI: 10.1371/journal.pone.0132045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 06/09/2015] [Indexed: 02/07/2023] Open
Abstract
The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians at transcriptional level, but the initiation mechanism of planarian head regeneration (PHR) remains unclear at the protein level. Here, a global analysis of proteome dynamics during the early stage of PHR was performed using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy, and our data are available via ProteomeXchange with identifier PXD002100. The results showed that 162 proteins were differentially expressed at 2 h and 6 h following amputation. Furthermore, the analysis of expression patterns and functional enrichment of the differentially expressed proteins showed that proteins involved in muscle contraction, oxidation reduction and protein synthesis were up-regulated in the initiation of PHR. Moreover, ingenuity pathway analysis showed that predominant signaling pathways such as ILK, calcium, EIF2 and mTOR signaling which were associated with cell migration, cell proliferation and protein synthesis were likely to be involved in the initiation of PHR. The results for the first time demonstrated that muscle contraction and ILK signaling might played important roles in the initiation of PHR at the global protein level. The findings of this research provide a molecular basis for further unraveling the mechanism of head regeneration initiation in planarians.
Collapse
Affiliation(s)
- Xiaofang Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
| | - Gaiping Wang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Yanli Qin
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Pengfei Li
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Zhi Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Deming Xue
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Zimei Dong
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Kexue Ma
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
| | - Guangwen Chen
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
- * E-mail: (CSX); (GWC)
| | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, Henan Province, China
- Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang, Henan Province, China
- College of Life Science, Henan Normal University, Xinxiang, Henan Province, China
- * E-mail: (CSX); (GWC)
| |
Collapse
|
13
|
Phosphomimetic mutation of the N-terminal lid of MDM2 enhances the polyubiquitination of p53 through stimulation of E2-ubiquitin thioester hydrolysis. J Mol Biol 2014; 427:1728-47. [PMID: 25543083 DOI: 10.1016/j.jmb.2014.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 11/24/2022]
Abstract
Mouse double minute 2 (MDM2) has a phosphorylation site within a lid motif at Ser17 whose phosphomimetic mutation to Asp17 stimulates MDM2-mediated polyubiquitination of p53. MDM2 lid deletion, but not Asp17 mutation, induced a blue shift in the λ(max) of intrinsic fluorescence derived from residues in the central domain including Trp235, Trp303, Trp323, and Trp329. This indicates that the Asp17 mutation does not alter the conformation of MDM2 surrounding the tryptophan residues. In addition, Phe235 mutation enhanced MDM2 binding to p53 but did not stimulate its ubiquitination function, thus uncoupling increases in p53 binding from its E3 ubiquitin ligase function. However, the Asp17 mutation in MDM2 stimulated its discharge of the UBCH5a-ubiquitin thioester adduct (UBCH5a is a ubiquitin-conjugating enzyme E2D 1 UBC4/5 homolog yeast). This stimulation of ubiquitin discharge from E2 was independent of the p53 substrate. There are now four known effects of the Asp17 mutation on MDM2: (i) it alters the conformation of the isolated N-terminus as defined by NMR; (ii) it induces increased thermostability of the isolated N-terminal domain; (iii) it stimulates the allosteric interaction of MDM2 with the DNA-binding domain of p53; and (iv) it stimulates a novel protein-protein interaction with the E2-ubiquitin complex in the absence of substrate p53 that, in turn, increases hydrolysis of the E2-ubiquitin thioester bond. These data also suggest a new strategy to disrupt MDM2 function by targeting the E2-ubiquitin discharge reaction.
Collapse
|
14
|
p53-directed translational control can shape and expand the universe of p53 target genes. Cell Death Differ 2014; 21:1522-34. [PMID: 24926617 DOI: 10.1038/cdd.2014.79] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 04/23/2014] [Accepted: 04/30/2014] [Indexed: 01/20/2023] Open
Abstract
The increasing number of genome-wide transcriptome analyses focusing on p53-induced cellular responses in many cellular contexts keeps adding to the already numerous p53-regulated transcriptional networks. To investigate post-transcriptional controls as an additional dimension of p53-directed gene expression responses, we performed a translatome analysis through polysomal profiling on MCF7 cells upon 16 hours of doxorubicin or nutlin-3a treatment. The comparison between the transcriptome and the translatome revealed a considerable level of uncoupling, characterized by genes whose transcription variations did not correlate with translation variations. Interestingly, uncoupled genes were associated with apoptosis, DNA and RNA metabolism and cell cycle functions, suggesting that post-transcriptional control can modulate classical p53-regulated responses. Furthermore, even for well-established p53 targets that were differentially expressed both at the transcriptional and translational levels, quantitative differences between the transcriptome, subpolysomal and polysomal RNAs were evident. As we searched mechanisms underlying gene expression uncoupling, we identified the p53-dependent modulation of six RNA-binding proteins, where hnRNPD (AUF1) and CPEB4 are direct p53 transcriptional targets, whereas SRSF1, DDX17, YBX1 and TARDBP are indirect targets (genes modulated preferentially in the subpolysomal or polysomal mRNA level) modulated at the translational level in a p53-dependent manner. In particular, YBX1 translation appeared to be reduced by p53 via two different mechanisms, one related to mTOR inhibition and the other to miR-34a expression. Overall, we established p53 as a master regulator of translational control and identified new p53-regulated genes affecting translation that can contribute to p53-dependent cellular responses.
Collapse
|
15
|
Haaland I, Opsahl JA, Berven FS, Reikvam H, Fredly HK, Haugse R, Thiede B, McCormack E, Lain S, Bruserud Ø, Gjertsen BT. Molecular mechanisms of nutlin-3 involve acetylation of p53, histones and heat shock proteins in acute myeloid leukemia. Mol Cancer 2014; 13:116. [PMID: 24885082 PMCID: PMC4032636 DOI: 10.1186/1476-4598-13-116] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/29/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The small-molecule MDM2 antagonist nutlin-3 has proved to be an effective p53 activating therapeutic compound in several preclinical cancer models, including acute myeloid leukemia (AML). We and others have previously reported a vigorous acetylation of the p53 protein by nutlin-treatment. In this study we aimed to investigate the functional role of this p53 acetylation in nutlin-sensitivity, and further to explore if nutlin-induced protein acetylation in general could indicate novel targets for the enhancement of nutlin-based therapy. RESULTS Nutlin-3 was found to enhance the acetylation of p53 in the human AML cell line MOLM-13 (wild type TP53) and in TP53 null cells transfected with wild type p53 cDNA. Stable isotope labeling with amino acids in cell culture (SILAC) in combination with immunoprecipitation using an anti-acetyl-lysine antibody and mass spectrometry analysis identified increased levels of acetylated Histone H2B, Hsp27 and Hsp90 in MOLM-13 cells after nutlin-treatment, accompanied by downregulation of total levels of Hsp27 and Hsp90. Intracellular levels of heat shock proteins Hsp27, Hsp40, Hsp60, Hsp70 and Hsp90α were correlated to nutlin-sensitivity for primary AML cells (n = 40), and AML patient samples with low sensitivity to nutlin-3 tended to express higher levels of heat shock proteins than more responsive samples. Combination therapy of nutlin-3 and Hsp90 inhibitor geldanamycin demonstrated synergistic induction of apoptosis in AML cell lines and primary AML cells. Finally, TP53 null cells transfected with a p53 acetylation defective mutant demonstrated decreased heat shock protein acetylation and sensitivity to nutlin-3 compared to wild type p53 expressing cells. CONCLUSIONS Altogether, our results demonstrate that nutlin-3 induces acetylation of p53, histones and heat shock proteins, and indicate that p53 acetylation status and the levels of heat shock proteins may participate in modulation of nutlin-3 sensitivity in AML.
Collapse
MESH Headings
- Acetylation
- Antineoplastic Agents/pharmacology
- Benzoquinones/pharmacology
- Cell Line, Tumor
- Drug Synergism
- Gene Expression Regulation, Leukemic
- HSP27 Heat-Shock Proteins/genetics
- HSP27 Heat-Shock Proteins/metabolism
- HSP90 Heat-Shock Proteins/genetics
- HSP90 Heat-Shock Proteins/metabolism
- Histones/genetics
- Histones/metabolism
- Humans
- Imidazoles/pharmacology
- Lactams, Macrocyclic/pharmacology
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Piperazines/pharmacology
- Primary Cell Culture
- Signal Transduction
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
Collapse
Affiliation(s)
- Ingvild Haaland
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Jill A Opsahl
- Department of Biomedicine, Proteomics Unit at University of Bergen (PROBE), University of Bergen, Bergen N-5021, Norway
| | - Frode S Berven
- Department of Biomedicine, Proteomics Unit at University of Bergen (PROBE), University of Bergen, Bergen N-5021, Norway
| | - Håkon Reikvam
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Hanne K Fredly
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Ragnhild Haugse
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
| | - Bernd Thiede
- The Biotechnology Centre of Oslo, University of Oslo, Oslo N-0317, Norway
| | - Emmet McCormack
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
- Department of Internal Medicine, Haukeland University Hospital, Bergen N-5021, Norway
| | - Sonia Lain
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm SE-171777, Sweden
| | - Øystein Bruserud
- Department of Clinical Science, Hematology Section, University of Bergen, Bergen N-5021, Norway
- Department of Internal Medicine, Haukeland University Hospital, Bergen N-5021, Norway
| | - Bjørn Tore Gjertsen
- Department of Internal Medicine, Haukeland University Hospital, Bergen N-5021, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen N-5021, Norway
| |
Collapse
|
16
|
Selivanova G. Wild type p53 reactivation: from lab bench to clinic. FEBS Lett 2014; 588:2628-38. [PMID: 24726725 DOI: 10.1016/j.febslet.2014.03.049] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 12/17/2022]
Abstract
The p53 tumor suppressor is the most frequently inactivated gene in cancer. Several mouse models have demonstrated that the reconstitution of the p53 function suppresses the growth of established tumors. These facts, taken together, promote the idea of p53 reactivation as a strategy to combat cancer. This review will focus on recent advances in the development of small molecules which restore the function of wild type p53 by blocking its inhibitors Mdm2 and MdmX or their upstream regulators and discuss the impact of different p53 functions for tumor prevention and tumor eradication. Finally, the recent progress in p53 research will be analyzed concerning the role of p53 cofactors and cellular environment in the biological response upon p53 reactivation and how this can be applied in clinic.
Collapse
Affiliation(s)
- Galina Selivanova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobelsvag 16, SE-17177 Stockholm, Sweden.
| |
Collapse
|
17
|
Murray E, Hernychová L, Scigelova M, Ho J, Nekulova M, O’Neill JR, Nenutil R, Vesely K, Dundas SR, Dhaliwal C, Henderson H, Hayward RL, Salter DM, Vojtěšek B, Hupp TR. Quantitative Proteomic Profiling of Pleomorphic Human Sarcoma Identifies CLIC1 as a Dominant Pro-Oncogenic Receptor Expressed in Diverse Sarcoma Types. J Proteome Res 2014; 13:2543-59. [DOI: 10.1021/pr4010713] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Euan Murray
- University of Edinburgh, Institute of Genetics and
Molecular Medicine, Edinburgh Cancer Research Centre, South Crewe Road, Edinburgh EH4 2XR, United Kingdom
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Lenka Hernychová
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Michaela Scigelova
- Thermo Fisher Scientific, Hanna-Kunath-Strasse
11, 28199 Bremen, Germany
| | - Jenny Ho
- Thermo Fisher Scientific, 1
Boundary Park, Hemel Hempstead HP2 7GE, United Kingdom
| | - Marta Nekulova
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - John Robert O’Neill
- University of Edinburgh, Institute of Genetics and
Molecular Medicine, Edinburgh Cancer Research Centre, South Crewe Road, Edinburgh EH4 2XR, United Kingdom
| | - Rudolf Nenutil
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Karel Vesely
- Masaryk University and St. Annés University Hospital, First Department of Pathological Anatomy, Pekařská 53, 656 91 Brno, Czech Republic
| | - Sinclair R. Dundas
- Department
of Pathology, University of Aberdeen, University Medical Buildings, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Catharine Dhaliwal
- Department
of Pathology, Royal Infirmary of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SA, United Kingdom
| | - Hannah Henderson
- Department
of Pathology, Royal Infirmary of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SA, United Kingdom
| | - Richard L. Hayward
- University of Edinburgh, Institute of Genetics and
Molecular Medicine, Edinburgh Cancer Research Centre, South Crewe Road, Edinburgh EH4 2XR, United Kingdom
| | - Donald M. Salter
- University of Edinburgh, Institute of Genetics and
Molecular Medicine, Edinburgh Cancer Research Centre, South Crewe Road, Edinburgh EH4 2XR, United Kingdom
| | - Bořivoj Vojtěšek
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Ted R. Hupp
- University of Edinburgh, Institute of Genetics and
Molecular Medicine, Edinburgh Cancer Research Centre, South Crewe Road, Edinburgh EH4 2XR, United Kingdom
- RECAMO, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| |
Collapse
|
18
|
Sim AYL, Joseph T, Lane DP, Verma C. Mechanism of Stapled Peptide Binding to MDM2: Possible Consequences for Peptide Design. J Chem Theory Comput 2014; 10:1753-61. [DOI: 10.1021/ct4009238] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Adelene Y. L. Sim
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
| | - Thomas Joseph
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
| | - David P. Lane
- p53
Laboratory (p53Lab, A*STAR), 8A Biomedical Grove, #06-06, Immunos, Singapore 138648
| | - Chandra Verma
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551
- Department
of Biological Sciences, National University of Singapore, 14 Science
Drive 4, Singapore 117543
| |
Collapse
|
19
|
Nicholson J, Scherl A, Way L, Blackburn EA, Walkinshaw MD, Ball KL, Hupp TR. A systems wide mass spectrometric based linear motif screen to identify dominant in-vivo interacting proteins for the ubiquitin ligase MDM2. Cell Signal 2014; 26:1243-57. [PMID: 24583282 DOI: 10.1016/j.cellsig.2014.02.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 02/21/2014] [Indexed: 12/24/2022]
Abstract
Linear motifs mediate protein-protein interactions (PPI) that allow expansion of a target protein interactome at a systems level. This study uses a proteomics approach and linear motif sub-stratifications to expand on PPIs of MDM2. MDM2 is a multi-functional protein with over one hundred known binding partners not stratified by hierarchy or function. A new linear motif based on a MDM2 interaction consensus is used to select novel MDM2 interactors based on Nutlin-3 responsiveness in a cell-based proteomics screen. MDM2 binds a subset of peptide motifs corresponding to real proteins with a range of allosteric responses to MDM2 ligands. We validate cyclophilin B as a novel protein with a consensus MDM2 binding motif that is stabilised by Nutlin-3 in vivo, thus identifying one of the few known interactors of MDM2 that is stabilised by Nutlin-3. These data invoke two modes of peptide binding at the MDM2 N-terminus that rely on a consensus core motif to control the equilibrium between MDM2 binding proteins. This approach stratifies MDM2 interacting proteins based on the linear motif feature and provides a new biomarker assay to define clinically relevant Nutlin-3 responsive MDM2 interactors.
Collapse
Affiliation(s)
- Judith Nicholson
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom; Department of Radiation Oncology and Biology, University of Oxford, OX3 7DQ, United Kingdom
| | - Alex Scherl
- Proteomics Core Facility, University of Geneva, Switzerland
| | - Luke Way
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom
| | - Elizabeth A Blackburn
- Edinburgh Centre for Chemical Biology, University of Edinburgh, EH9 3JG, United Kingdom
| | - Malcolm D Walkinshaw
- Edinburgh Centre for Chemical Biology, University of Edinburgh, EH9 3JG, United Kingdom
| | - Kathryn L Ball
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom
| | - Ted R Hupp
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom.
| |
Collapse
|
20
|
Hernychova L, Man P, Verma C, Nicholson J, Sharma CA, Ruckova E, Teo JY, Ball K, Vojtesek B, Hupp TR. Identification of a second Nutlin-3 responsive interaction site in the N-terminal domain of MDM2 using hydrogen/deuterium exchange mass spectrometry. Proteomics 2014; 13:2512-25. [PMID: 23776060 DOI: 10.1002/pmic.201300029] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 05/01/2013] [Accepted: 05/13/2013] [Indexed: 11/07/2022]
Abstract
MDM2 is a multidomain protein that functions as an E3 ubiquitin ligase, transcription repressor, mRNA-binding protein, translation factor, and molecular chaperone. The small molecule Nutlin-3 has been engineered to bind to the N-terminal hydrophobic pocket domain of MDM2. This binding of Nutlin-3 has two consequences: (i) antagonistic effects through competitive disruption of the MDM2-p53 complex and (ii) agonist effects that allosterically stabilize MDM2 protein-protein interactions that increase p53 ubiquitination as well as nucleophosmin deoligomerization. We present a methodology using a hydrogen/deuterium (H/D) exchange platform that measures Nutlin-3 binding to the N-terminal domain of MDM2 (MDM2(1-126)) in order to begin to develop dynamic assays that evaluate MDM2 allostery. In order to localize the regions in MDM2 being suppressed by Nutlin-3, MDM2 was incubated with the ligand and H/D amide exchange was measured after pepsin digestion. One dynamic segment containing amino acids 55-60 exhibited slower deuterium exchange after Nutlin-3 binding, reflecting ligand binding within the hydrophobic pocket. However, another dominant suppression of H/D exchange was observed in a motif from amino acids 103-107 that reflects surface hydrophobic residues surrounding the hydrophobic pocket of MDM2. In order to explore the consequences of this latter Nutlin-3 interaction site on MDM2, the Y104G and L107G mutant series was constructed. The MDM2(Y104G) and MDM2(L107G) mutants were fully active in p53 binding. However, the authentic p53-derived peptide:MDM2(Y104G) complex exhibited partial resistance to Nutlin-3 inhibition, while the p53-mimetic 12.1 peptide:MDM2(Y104G) complex retained normal Nutlin-3 responsiveness. These data reveal the existence of a second functional Nutlin-3-binding site in a surface hydrophobic patch of MDM2, flanking the hydrophobic pocket. This reveals two modes of peptide binding by MDM2 and highlights the utility of H/D exchange as an assay for measuring allosteric effects in MDM2.
Collapse
Affiliation(s)
- Lenka Hernychova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Fåhraeus R, Olivares-Illana V. MDM2's social network. Oncogene 2013; 33:4365-76. [PMID: 24096477 DOI: 10.1038/onc.2013.410] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/17/2013] [Accepted: 08/17/2013] [Indexed: 12/22/2022]
Abstract
MDM2 is considered a hub protein due to its capacity to interact with a large number of different partners of which p53 is most well described. MDM2 is an E3 ubiquitin ligase, and many, but not all, of its interactions relate directly to this activity, such as substrates, adaptors or bridges, promoters, inhibitors or complementary factors. Some interactions serve regulatory functions that in response to cellular stresses control the localisation and functions of MDM2 including protein kinases, ribosomal proteins and proteases. Moreover, interactions with nucleotides serve other functions such as mRNA to regulate protein synthesis and DNA to control transcription. To perform such a pleiotropic panorama of different functions, MDM2 is subjected to a multitude of post-translational modifications and is expressed in different isoforms. The large and diverse interactome is made possible due to the plasticity of MDM2 and in this review we have listed the MDM2 interactions until now and we will discuss how this multifaceted protein can interact with such a variety of substrates to provide a key intermediary role in different signalling pathways.
Collapse
Affiliation(s)
- R Fåhraeus
- Cibles Therapeutiques, Equipe Labellisée Ligue Contre le Cancer, INSERM Unité 940, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St Louis, 27 rue Juliette Dodu, Paris, France
| | - V Olivares-Illana
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Av. Manuel Nava, Zona Universitaria, San Luis Potosí, México
| |
Collapse
|
22
|
Identifying a hyperkeratosis signature in autosomal recessive congenital ichthyosis: Mdm2 inhibition prevents hyperkeratosis in a rat ARCI model. J Invest Dermatol 2013; 134:858-861. [PMID: 24005053 DOI: 10.1038/jid.2013.374] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
23
|
Gray TA, Murray E, Nowicki MW, Remnant L, Scherl A, Muller P, Vojtesek B, Hupp TR. Development of a fluorescent monoclonal antibody-based assay to measure the allosteric effects of synthetic peptides on self-oligomerization of AGR2 protein. Protein Sci 2013; 22:1266-78. [PMID: 23780840 DOI: 10.1002/pro.2299] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/10/2013] [Accepted: 06/10/2013] [Indexed: 11/12/2022]
Abstract
Many regulatory proteins are homo-oligomeric and designing assays that measure self-assembly will provide novel approaches to study protein allostery and screen for novel small molecule modulators of protein interactions. We present an assay to begin to define the biochemical determinants that regulate dimerization of the cancer-associated oncoprotein AGR2. A two site-sandwich microtiter assay ((2S) MTA) was designed using a DyLight800-labeled monoclonal antibody that binds to an epitope in AGR2 to screen for synthetic self-peptides that might regulate dimer stability. Peptides derived from the intrinsically disordered N-terminal region of AGR2 increase in trans oligomer stability as defined using the (2S) MTA assay. A DSS-crosslinking assay that traps the AGR2 dimer through K95-K95 adducts confirmed that Δ45-AGR2 was a more stable dimer using denaturing gel electrophoresis. A titration of wt-AGR2, Δ45-AGR2 (more stable dimer), and monomeric AGR2(E60A) revealed that Δ45-AGR2 was more active in binding to Reptin than either wt-AGR2 or the AGR2(E60A) mutant. Our data have defined a functional role for the AGR2 dimer in the binding to its most well characterized interacting protein, Reptin. The ability to regulate AGR2 oligomerization in trans opens the possibility for developing small molecules that regulate its' biochemical activity as potential cancer therapeutics. The data also highlight the utility of this oligomerization assay to screen chemical libraries for ligands that could regulate AGR2 dimer stability and its' oncogenic potential.
Collapse
Affiliation(s)
- Terry A Gray
- Institute of Genetics and Molecular Medicine, Cell Signaling Unit, University of Edinburgh, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Kessler BM. Ubiquitin - omics reveals novel networks and associations with human disease. Curr Opin Chem Biol 2013; 17:59-65. [PMID: 23339974 DOI: 10.1016/j.cbpa.2012.12.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 12/18/2012] [Accepted: 12/30/2012] [Indexed: 01/27/2023]
Abstract
Human neurodegenerative and infectious diseases and tumorigenesis are associated with alterations in ubiquitin pathways. Over 10% of the genome encode for genes that either bind or manipulate ubiquitin to affect a large proportion of biological processes. This has been the basis for the development of approaches allowing the enrichment of ubiquitinated proteins for comparisons using proteomics and mass spectrometry. Tools such as tagged tandem ubiquitin binding domains, chemically derivatized ubiquitin or anti-gly-gly-lys antibodies combined with mass spectrometry have contributed to surveys of poly-ubiquitinated proteins, poly-ubiquitin linkage diversity and protein ubiquitination sites and their relation to other posttranslational modifications at a proteome wide level, providing insights in to how dynamic alterations in ubiquitination and deubiquitination steps are associated with normal physiology and pathogenesis.
Collapse
Affiliation(s)
- Benedikt M Kessler
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, OX3 7BN, UK.
| |
Collapse
|