1
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Fitzgerald MC, O'Halloran PJ, Kerrane SA, Ní Chonghaile T, Connolly NMC, Murphy BM. The identification of BCL-XL and MCL-1 as key anti-apoptotic proteins in medulloblastoma that mediate distinct roles in chemotherapy resistance. Cell Death Dis 2023; 14:705. [PMID: 37898609 PMCID: PMC10613306 DOI: 10.1038/s41419-023-06231-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 09/25/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023]
Abstract
Medulloblastoma is the most common malignant paediatric brain tumour, representing 20% of all paediatric intercranial tumours. Current aggressive treatment protocols and the use of radiation therapy in particular are associated with high levels of toxicity and significant adverse effects, and long-term sequelae can be severe. Therefore, improving chemotherapy efficacy could reduce the current reliance on radiation therapy. Here, we demonstrated that systems-level analysis of basal apoptosis protein expression and their signalling interactions can differentiate between medulloblastoma cell lines that undergo apoptosis in response to chemotherapy, and those that do not. Combining computational predictions with experimental BH3 profiling, we identified a therapeutically-exploitable dependence of medulloblastoma cells on BCL-XL, and experimentally validated that BCL-XL targeting, and not targeting of BCL-2 or MCL-1, can potentiate cisplatin-induced cytotoxicity in medulloblastoma cell lines with low sensitivity to cisplatin treatment. Finally, we identified MCL-1 as an anti-apoptotic mediator whose targeting is required for BCL-XL inhibitor-induced apoptosis. Collectively, our study identifies that BCL-XL and MCL-1 are the key anti-apoptotic proteins in medulloblastoma, which mediate distinct protective roles. While BCL-XL has a first-line role in protecting cells from apoptosis basally, MCL-1 represents a second line of defence that compensates for BCL-XL upon its inhibition. We provide rationale for the further evaluation of BCL-XL and MCL-1 inhibitors in the treatment of medulloblastoma, and together with current efforts to improve the cancer-specificity of BCL-2 family inhibitors, these novel treatment strategies have the potential to improve the future clinical management of medulloblastoma.
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Affiliation(s)
- Marie-Claire Fitzgerald
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D02 YN77, Ireland
- National Children's Research Centre at the Children's Health Ireland at Crumlin, Dublin, D12 N512, Ireland
| | - Philip J O'Halloran
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D02 YN77, Ireland
- Department of Neurosurgery, Queen Elizabeth Hospital, Birmingham, UK
| | - Sean A Kerrane
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D02 YN77, Ireland
- National Children's Research Centre at the Children's Health Ireland at Crumlin, Dublin, D12 N512, Ireland
| | - Triona Ní Chonghaile
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D02 YN77, Ireland
| | - Niamh M C Connolly
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D02 YN77, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D02 YN77, Ireland
| | - Brona M Murphy
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D02 YN77, Ireland.
- National Children's Research Centre at the Children's Health Ireland at Crumlin, Dublin, D12 N512, Ireland.
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2
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Vera J, Lai X, Baur A, Erdmann M, Gupta S, Guttà C, Heinzerling L, Heppt MV, Kazmierczak PM, Kunz M, Lischer C, Pützer BM, Rehm M, Ostalecki C, Retzlaff J, Witt S, Wolkenhauer O, Berking C. Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. Brief Bioinform 2022; 23:6761961. [PMID: 36252807 DOI: 10.1093/bib/bbac433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/28/2022] [Accepted: 09/08/2022] [Indexed: 12/19/2022] Open
Abstract
We live in an unprecedented time in oncology. We have accumulated samples and cases in cohorts larger and more complex than ever before. New technologies are available for quantifying solid or liquid samples at the molecular level. At the same time, we are now equipped with the computational power necessary to handle this enormous amount of quantitative data. Computational models are widely used helping us to substantiate and interpret data. Under the label of systems and precision medicine, we are putting all these developments together to improve and personalize the therapy of cancer. In this review, we use melanoma as a paradigm to present the successful application of these technologies but also to discuss possible future developments in patient care linked to them. Melanoma is a paradigmatic case for disruptive improvements in therapies, with a considerable number of metastatic melanoma patients benefiting from novel therapies. Nevertheless, a large proportion of patients does not respond to therapy or suffers from adverse events. Melanoma is an ideal case study to deploy advanced technologies not only due to the medical need but also to some intrinsic features of melanoma as a disease and the skin as an organ. From the perspective of data acquisition, the skin is the ideal organ due to its accessibility and suitability for many kinds of advanced imaging techniques. We put special emphasis on the necessity of computational strategies to integrate multiple sources of quantitative data describing the tumour at different scales and levels.
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Affiliation(s)
- Julio Vera
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Xin Lai
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Andreas Baur
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Michael Erdmann
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock 18051, Germany
| | - Cristiano Guttà
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Lucie Heinzerling
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany.,Department of Dermatology, LMU University Hospital, Munich, Germany
| | - Markus V Heppt
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | | | - Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig, 04103 Leipzig, Germany
| | - Christopher Lischer
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Brigitte M Pützer
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany.,Stuttgart Research Center Systems Biology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Christian Ostalecki
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Jimmy Retzlaff
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | | | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock 18051, Germany
| | - Carola Berking
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
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3
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Lindner AU, Salvucci M, McDonough E, Cho S, Stachtea X, O'Connell EP, Corwin AD, Santamaria-Pang A, Carberry S, Fichtner M, Van Schaeybroeck S, Laurent-Puig P, Burke JP, McNamara DA, Lawler M, Sood A, Graf JF, Rehm M, Dunne PD, Longley DB, Ginty F, Prehn JHM. An atlas of inter- and intra-tumor heterogeneity of apoptosis competency in colorectal cancer tissue at single-cell resolution. Cell Death Differ 2021; 29:806-817. [PMID: 34754079 PMCID: PMC8990071 DOI: 10.1038/s41418-021-00895-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Cancer cells’ ability to inhibit apoptosis is key to malignant transformation and limits response to therapy. Here, we performed multiplexed immunofluorescence analysis on tissue microarrays with 373 cores from 168 patients, segmentation of 2.4 million individual cells, and quantification of 18 cell lineage and apoptosis proteins. We identified an enrichment for BCL2 in immune, and BAK, SMAC, and XIAP in cancer cells. Ordinary differential equation-based modeling of apoptosis sensitivity at single-cell resolution was conducted and an atlas of inter- and intra-tumor heterogeneity in apoptosis susceptibility generated. Systems modeling at single-cell resolution identified an enhanced sensitivity of cancer cells to mitochondrial permeabilization and executioner caspase activation compared to immune and stromal cells, but showed significant inter- and intra-tumor heterogeneity.
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Affiliation(s)
- Andreas Ulrich Lindner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | | | | | - Xanthi Stachtea
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Emer P O'Connell
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Department of Surgery, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | | | | | - Steven Carberry
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | - Michael Fichtner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | - Sandra Van Schaeybroeck
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université de Paris, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - John P Burke
- Department of Surgery, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | - Deborah A McNamara
- Department of Surgery, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
| | - Mark Lawler
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Anup Sood
- GE Research, Niskayuna, NY, 12309, USA
| | | | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Philip D Dunne
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Daniel B Longley
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | | | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland. .,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.
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4
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The Role of Age, Neutrophil Infiltration and Antibiotics Timing in the Severity of Streptococcus pneumoniae Pneumonia. Insights from a Multi-Level Mathematical Model Approach. Int J Mol Sci 2020; 21:ijms21228428. [PMID: 33182614 PMCID: PMC7696447 DOI: 10.3390/ijms21228428] [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: 10/22/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/11/2022] Open
Abstract
Bacterial pneumonia is one of the most prevalent infectious diseases and has high mortality in sensitive patients (children, elderly and immunocompromised). Although an infection, the disease alters the alveolar epithelium homeostasis and hinders normal breathing, often with fatal consequences. A special case is hospitalized aged patients, which present a high risk of infection and death because of the community acquired version of the Streptococcus pneumoniae pneumonia. There is evidence that early antibiotics treatment decreases the inflammatory response during pneumonia. Here, we investigate mechanistically this strategy using a multi-level mathematical model, which describes the 24 first hours after infection of a single alveolus from the key signaling networks behind activation of the epithelium to the dynamics of the local immune response. With the model, we simulated pneumonia in aged and young patients subjected to different antibiotics timing. The results show that providing antibiotics to elderly patients 8 h in advance compared to young patients restores in aged individuals the effective response seen in young ones. This result suggests the use of early, probably prophylactic, antibiotics treatment in aged hospitalized people with high risk of pneumonia.
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5
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Albrecht M, Lucarelli P, Kulms D, Sauter T. Computational models of melanoma. Theor Biol Med Model 2020; 17:8. [PMID: 32410672 PMCID: PMC7222475 DOI: 10.1186/s12976-020-00126-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 04/29/2020] [Indexed: 02/08/2023] Open
Abstract
Genes, proteins, or cells influence each other and consequently create patterns, which can be increasingly better observed by experimental biology and medicine. Thereby, descriptive methods of statistics and bioinformatics sharpen and structure our perception. However, additionally considering the interconnectivity between biological elements promises a deeper and more coherent understanding of melanoma. For instance, integrative network-based tools and well-grounded inductive in silico research reveal disease mechanisms, stratify patients, and support treatment individualization. This review gives an overview of different modeling techniques beyond statistics, shows how different strategies align with the respective medical biology, and identifies possible areas of new computational melanoma research.
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Affiliation(s)
- Marco Albrecht
- Systems Biology Group, Life Science Research Unit, University of Luxembourg, 6, avenue du Swing, Belval, 4367 Luxembourg
| | - Philippe Lucarelli
- Systems Biology Group, Life Science Research Unit, University of Luxembourg, 6, avenue du Swing, Belval, 4367 Luxembourg
| | - Dagmar Kulms
- Experimental Dermatology, Department of Dermatology, Dresden University of Technology, Fetscherstraße 105, Dresden, 01307 Germany
| | - Thomas Sauter
- Systems Biology Group, Life Science Research Unit, University of Luxembourg, 6, avenue du Swing, Belval, 4367 Luxembourg
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6
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Fullstone G, Bauer TL, Guttà C, Salvucci M, Prehn JHM, Rehm M. The apoptosome molecular timer synergises with XIAP to suppress apoptosis execution and contributes to prognosticating survival in colorectal cancer. Cell Death Differ 2020; 27:2828-2842. [PMID: 32341447 PMCID: PMC7493894 DOI: 10.1038/s41418-020-0545-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/17/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023] Open
Abstract
The execution phase of apoptosis is a critical process in programmed cell death in response to a multitude of cellular stresses. A crucial component of this pathway is the apoptosome, a platform for the activation of pro-caspase 9 (PC9). Recent findings have shown that autocleavage of PC9 to Caspase 9 (C9) p35/p12 not only permits XIAP-mediated C9 inhibition but also temporally shuts down apoptosome activity, forming a molecular timer. In order to delineate the combined contributions of XIAP and the apoptosome molecular timer to apoptosis execution we utilised a systems modelling approach. We demonstrate that cooperative recruitment of PC9 to the apoptosome, based on existing PC9-apoptosome interaction data, is important for efficient formation of PC9 homodimers, autocatalytic cleavage and dual regulation by XIAP and the molecular timer across biologically relevant PC9 and APAF1 concentrations. Screening physiologically relevant concentration ranges of apoptotic proteins, we discovered that the molecular timer can prevent apoptosis execution in specific scenarios after complete or partial mitochondrial outer membrane permeabilisation (MOMP). Furthermore, its ability to prevent apoptosis is intricately tied to a synergistic combination with XIAP. Finally, we demonstrate that simulations of these processes are prognostic of survival in stage III colorectal cancer and that the molecular timer may promote apoptosis resistance in a subset of patients. Based on our findings, we postulate that the physiological function of the molecular timer is to aid XIAP in the shutdown of caspase-mediated apoptosis execution. This shutdown potentially facilitates switching to pro-inflammatory caspase-independent responses subsequent to Bax/Bak pore formation.
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Affiliation(s)
- Gavin Fullstone
- Institute for Cell Biology and Immunology, Allmandring 31, 70569, Stuttgart, Germany.,Stuttgart Research Centre Systems Biology, Nobelstraße 15, 70569, Stuttgart, Germany
| | - Tabea L Bauer
- Institute for Cell Biology and Immunology, Allmandring 31, 70569, Stuttgart, Germany
| | - Cristiano Guttà
- Institute for Cell Biology and Immunology, Allmandring 31, 70569, Stuttgart, Germany.,SimTech Cluster of Excellence, Pfaffenwaldring 5a, 70569, Stuttgart, Germany
| | - Manuela Salvucci
- SimTech Cluster of Excellence, Pfaffenwaldring 5a, 70569, Stuttgart, Germany.,Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland.,Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Jochen H M Prehn
- SimTech Cluster of Excellence, Pfaffenwaldring 5a, 70569, Stuttgart, Germany.,Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland.,Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Markus Rehm
- Institute for Cell Biology and Immunology, Allmandring 31, 70569, Stuttgart, Germany. .,Stuttgart Research Centre Systems Biology, Nobelstraße 15, 70569, Stuttgart, Germany. .,SimTech Cluster of Excellence, Pfaffenwaldring 5a, 70569, Stuttgart, Germany. .,Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland. .,Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
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7
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Low expression of pro-apoptotic proteins Bax, Bak and Smac indicates prolonged progression-free survival in chemotherapy-treated metastatic melanoma. Cell Death Dis 2020; 11:124. [PMID: 32054850 PMCID: PMC7018795 DOI: 10.1038/s41419-020-2309-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 12/30/2022]
Abstract
Despite the introduction of novel targeted therapies, chemotherapy still remains the primary treatment for metastatic melanoma in poorly funded healthcare environments or in case of disease relapse, with no reliable molecular markers for progression-free survival (PFS) available. As chemotherapy primarily eliminates cancer cells by apoptosis, we here evaluated if the expression of key apoptosis regulators (Bax, Bak, Bcl-2, Bcl-xL, Smac, Procaspase-9, Apaf-1, Procaspase-3 and XIAP) allows prognosticating PFS in stage III/IV melanoma patients. Following antibody validation, marker expression was determined by automated and manual scoring of immunohistochemically stained tissue microarrays (TMAs) constructed from treatment-naive metastatic melanoma biopsies. Interestingly and counter-intuitively, low expression of the pro-apoptotic proteins Bax, Bak and Smac indicated better prognosis (log-rank p < 0.0001, p = 0.0301 and p = 0.0227 for automated and p = 0.0422, p = 0.0410 and p = 0.0073 for manual scoring). These findings were independently validated in the cancer genome atlas (TCGA) metastatic melanoma cohort (TCGA-SKCM) at transcript level (log-rank p = 0.0004, p = 0.0104 and p = 0.0377). Taking expression heterogeneity between the markers in individual tumour samples into account allowed defining combinatorial Bax, Bak, Smac signatures that were associated with significantly increased PFS (p = 0.0002 and p = 0.0028 at protein and transcript level, respectively). Furthermore, combined low expression of Bax, Bak and Smac allowed predicting prolonged PFS (> 12 months) on a case-by-case basis (area under the receiver operating characteristic curve (ROC AUC) = 0.79). Taken together, our results therefore suggest that Bax, Bak and Smac jointly define a signature with potential clinical utility in chemotherapy-treated metastatic melanoma.
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8
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Rožanc J, Sakellaropoulos T, Antoranz A, Guttà C, Podder B, Vetma V, Rufo N, Agostinis P, Pliaka V, Sauter T, Kulms D, Rehm M, Alexopoulos LG. Phosphoprotein patterns predict trametinib responsiveness and optimal trametinib sensitisation strategies in melanoma. Cell Death Differ 2018; 26:1365-1378. [PMID: 30323272 DOI: 10.1038/s41418-018-0210-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/19/2018] [Accepted: 09/10/2018] [Indexed: 01/02/2023] Open
Abstract
Malignant melanoma is a highly aggressive form of skin cancer responsible for the majority of skin cancer-related deaths. Recent insight into the heterogeneous nature of melanoma suggests more personalised treatments may be necessary to overcome drug resistance and improve patient care. To this end, reliable molecular signatures that can accurately predict treatment responsiveness need to be identified. In this study, we applied multiplex phosphoproteomic profiling across a panel of 24 melanoma cell lines with different disease-relevant mutations, to predict responsiveness to MEK inhibitor trametinib. Supported by multivariate statistical analysis and multidimensional pattern recognition algorithms, the responsiveness of individual cell lines to trametinib could be predicted with high accuracy (83% correct predictions), independent of mutation status. We also successfully employed this approach to case specifically predict whether individual melanoma cell lines could be sensitised to trametinib. Our predictions identified that combining MEK inhibition with selective targeting of c-JUN and/or FAK, using siRNA-based depletion or pharmacological inhibitors, sensitised resistant cell lines and significantly enhanced treatment efficacy. Our study indicates that multiplex proteomic analyses coupled with pattern recognition approaches could assist in personalising trametinib-based treatment decisions in the future.
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Affiliation(s)
- Jan Rožanc
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg.,ProtATonce Ltd, Science Park Demokritos, Athens, Greece
| | | | - Asier Antoranz
- ProtATonce Ltd, Science Park Demokritos, Athens, Greece.,Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece
| | - Cristiano Guttà
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Biswajit Podder
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Vesna Vetma
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Nicole Rufo
- Laboratory for Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Laboratory for Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Vaia Pliaka
- ProtATonce Ltd, Science Park Demokritos, Athens, Greece
| | - Thomas Sauter
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Dagmar Kulms
- Experimental Dermatology, Department of Dermatology, Technical University Dresden, Dresden, Germany.,Center for Regenerative Therapies, Technical University Dresden, Dresden, Germany
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany.,Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.,Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leonidas G Alexopoulos
- ProtATonce Ltd, Science Park Demokritos, Athens, Greece. .,Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece.
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9
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Vera J, Santos G. Can Gamification Contribute to Computer Modeling-Driven Biomedical Research? Front Physiol 2018; 9:908. [PMID: 30072911 PMCID: PMC6060613 DOI: 10.3389/fphys.2018.00908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/21/2018] [Indexed: 01/23/2023] Open
Affiliation(s)
- Julio Vera
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen and Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Guido Santos
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen and Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
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10
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Santos G, Lai X, Eberhardt M, Vera J. Bacterial Adherence and Dwelling Probability: Two Drivers of Early Alveolar Infection by Streptococcus pneumoniae Identified in Multi-Level Mathematical Modeling. Front Cell Infect Microbiol 2018; 8:159. [PMID: 29868515 PMCID: PMC5962665 DOI: 10.3389/fcimb.2018.00159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 04/25/2018] [Indexed: 01/31/2023] Open
Abstract
Pneumococcal infection is the most frequent cause of pneumonia, and one of the most prevalent diseases worldwide. The population groups at high risk of death from bacterial pneumonia are infants, elderly and immunosuppressed people. These groups are more vulnerable because they have immature or impaired immune systems, the efficacy of their response to vaccines is lower, and antibiotic treatment often does not take place until the inflammatory response triggered is already overwhelming. The immune response to bacterial lung infections involves dynamic interactions between several types of cells whose activation is driven by intracellular molecular networks. A feasible approach to the integration of knowledge and data linking tissue, cellular and intracellular events and the construction of hypotheses in this area is the use of mathematical modeling. For this paper, we used a multi-level computational model to analyse the role of cellular and molecular interactions during the first 10 h after alveolar invasion of Streptococcus pneumoniae bacteria. By “multi-level” we mean that we simulated the interplay between different temporal and spatial scales in a single computational model. In this instance, we included the intracellular scale of processes driving lung epithelial cell activation together with the scale of cell-to-cell interactions at the alveolar tissue. In our analysis, we combined systematic model simulations with logistic regression analysis and decision trees to find genotypic-phenotypic signatures that explain differences in bacteria strain infectivity. According to our simulations, pneumococci benefit from a high dwelling probability and a high proliferation rate during the first stages of infection. In addition to this, the model predicts that during the very early phases of infection the bacterial capsule could be an impediment to the establishment of the alveolar infection because it impairs bacterial colonization.
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Affiliation(s)
- Guido Santos
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen and Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Xin Lai
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen and Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Martin Eberhardt
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen and Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Julio Vera
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen and Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
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11
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Predicting the cell death responsiveness and sensitization of glioma cells to TRAIL and temozolomide. Oncotarget 2018; 7:61295-61311. [PMID: 27494880 PMCID: PMC5308652 DOI: 10.18632/oncotarget.10973] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 07/18/2016] [Indexed: 12/28/2022] Open
Abstract
Genotoxic chemotherapy with temozolomide (TMZ) is a mainstay of treatment for glioblastoma (GBM); however, at best, TMZ provides only modest survival benefit to a subset of patients. Recent insight into the heterogeneous nature of GBM suggests a more personalized approach to treatment may be necessary to overcome cancer drug resistance and improve patient care. These include novel therapies that can be used both alone and with TMZ to selectively reactivate apoptosis within malignant cells. For this approach to work, reliable molecular signatures that can accurately predict treatment responsiveness need to be identified first. Here, we describe the first proof-of-principle study that merges quantitative protein-based analysis of apoptosis signaling networks with data- and knowledge-driven mathematical systems modeling to predict treatment responsiveness of GBM cell lines to various apoptosis-inducing stimuli. These include monotherapies with TMZ and TRAIL, which activate the intrinsic and extrinsic apoptosis pathways, respectively, as well as combination therapies of TMZ+TRAIL. We also successfully employed this approach to predict whether individual GBM cell lines could be sensitized to TMZ or TRAIL via the selective targeting of Bcl-2/Bcl-xL proteins with ABT-737. Our findings suggest that systems biology-based approaches could assist in personalizing treatment decisions in GBM to optimize cell death induction.
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12
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Kolluri KK, Alifrangis C, Kumar N, Ishii Y, Price S, Michaut M, Williams S, Barthorpe S, Lightfoot H, Busacca S, Sharkey A, Yuan Z, Sage EK, Vallath S, Le Quesne J, Tice DA, Alrifai D, von Karstedt S, Montinaro A, Guppy N, Waller DA, Nakas A, Good R, Holmes A, Walczak H, Fennell DA, Garnett M, Iorio F, Wessels L, McDermott U, Janes SM. Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells. eLife 2018; 7:e30224. [PMID: 29345617 PMCID: PMC5773178 DOI: 10.7554/elife.30224] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/13/2017] [Indexed: 12/29/2022] Open
Abstract
Malignant mesothelioma (MM) is poorly responsive to systemic cytotoxic chemotherapy and invariably fatal. Here we describe a screen of 94 drugs in 15 exome-sequenced MM lines and the discovery of a subset defined by loss of function of the nuclear deubiquitinase BRCA associated protein-1 (BAP1) that demonstrate heightened sensitivity to TRAIL (tumour necrosis factor-related apoptosis-inducing ligand). This association is observed across human early passage MM cultures, mouse xenografts and human tumour explants. We demonstrate that BAP1 deubiquitinase activity and its association with ASXL1 to form the Polycomb repressive deubiquitinase complex (PR-DUB) impacts TRAIL sensitivity implicating transcriptional modulation as an underlying mechanism. Death receptor agonists are well-tolerated anti-cancer agents demonstrating limited therapeutic benefit in trials without a targeting biomarker. We identify BAP1 loss-of-function mutations, which are frequent in MM, as a potential genomic stratification tool for TRAIL sensitivity with immediate and actionable therapeutic implications.
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Affiliation(s)
- Krishna Kalyan Kolluri
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | | | - Neelam Kumar
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Yuki Ishii
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Stacey Price
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | | | | | - Syd Barthorpe
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | | | - Sara Busacca
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | - Annabel Sharkey
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | - Zhenqiang Yuan
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Elizabeth K Sage
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Sabarinath Vallath
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - John Le Quesne
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | - David A Tice
- Oncology Research, MedImmune, Inc.GaithersburgUnited States
| | - Doraid Alrifai
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Sylvia von Karstedt
- Centre for Cell Death, Cancer and InflammationUCL Cancer Institute, University College LondonLondonUnited Kingdom
| | - Antonella Montinaro
- Centre for Cell Death, Cancer and InflammationUCL Cancer Institute, University College LondonLondonUnited Kingdom
| | - Naomi Guppy
- UCL Advanced DiagnosticsUniversity College LondonLondonUnited Kingdom
| | - David A Waller
- Department of Thoracic SurgeryGlenfield Hospital, University Hospitals of LeicesterLeicesterUnited Kingdom
| | - Apostolos Nakas
- Department of Thoracic SurgeryGlenfield Hospital, University Hospitals of LeicesterLeicesterUnited Kingdom
| | - Robert Good
- UCL School of PharmacyUniversity College LondonLondonUnited Kingdom
| | - Alan Holmes
- UCL School of PharmacyUniversity College LondonLondonUnited Kingdom
| | - Henning Walczak
- Centre for Cell Death, Cancer and InflammationUCL Cancer Institute, University College LondonLondonUnited Kingdom
| | - Dean A Fennell
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | | | - Francesco Iorio
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteCambridgeUnited Kingdom
| | | | | | - Samuel M Janes
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
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13
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López-Marín N, Mulet R. In silico modelling of apoptosis induced by photodynamic therapy. J Theor Biol 2017; 436:8-17. [PMID: 28966107 DOI: 10.1016/j.jtbi.2017.09.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 09/22/2017] [Accepted: 09/27/2017] [Indexed: 12/25/2022]
Abstract
Photodynamic therapy (PDT) is an emergent technique used for the treatment of several diseases. After PDT, cells die by necrosis, apoptosis or autophagy. Necrosis is produced immediately during photodynamic therapy by high concentration of reactive oxygen species, apoptosis and autophagy are triggered by mild or low doses of light and photosensitizer. In this work we model the cell response to low doses of PDT assuming a bi-dimensional matrix of interacting cells. For each cell of the matrix we simulate in detail, with the help of the Gillespie's algorithm, the two main chemical pathways leading to apoptosis. We unveil the role of both pathways in the cell death rate of the tumor, as well as the relevance of several molecules in the process. Our model suggests values of concentrations for several species of molecules to enhance the effectiveness of PDT.
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Affiliation(s)
- N López-Marín
- Group of Complex Systems and Statistical Physics. Department of General Physics, Physics Faculty, University of Havana, La Habana, CP 10400, Cuba.
| | - R Mulet
- Group of Complex Systems and Statistical Physics. Department of Theoretical Physics, Physics Faculty, University of Havana, La Habana, CP 10400, Cuba.
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14
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Vetma V, Rožanc J, Charles EM, Hellwig CT, Alexopoulos LG, Rehm M. Examining the In Vitro Efficacy of the IAP Antagonist Birinapant as a Single Agent or in Combination With Dacarbazine to Induce Melanoma Cell Death. Oncol Res 2017; 25:1489-1494. [PMID: 28337955 PMCID: PMC7841063 DOI: 10.3727/096504017x14897145996933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Antagonists of inhibitors of apoptosis proteins (IAPs), alone or in combination with genotoxic therapeutics, have been shown to efficiently induce cell death in various solid tumors. The IAP antagonist birinapant is currently being tested in phase II clinical trials. We herein aimed to investigate the antitumor efficacy of dacarbazine in vitro, both as a single agent and in combination with birinapant, in melanoma cell lines. Covering clinically relevant drug concentration ranges, we conducted a total of 5,400 measurements in a panel of 12 human melanoma cell lines representing different stages of disease progression. Surprisingly, functionally relevant synergies or response potentiation in combination treatments was not observed, and only one cell line modestly responded to birinapant single treatment (approximately 16% cell death). Although we did not study the underlying resistance mechanisms or more complex in vivo scenarios in which dacarbazine/birinapant response synergies may still possibly manifest, our findings are nevertheless noteworthy because IAP antagonists were demonstrated to strongly enhance responses to DNA-damaging agents in cell lines of other cancer types under comparable experimental conditions in vitro.
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15
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Naoum GE, Buchsbaum DJ, Tawadros F, Farooqi A, Arafat WO. Journey of TRAIL from Bench to Bedside and its Potential Role in Immuno-Oncology. Oncol Rev 2017; 11:332. [PMID: 28584572 PMCID: PMC5432952 DOI: 10.4081/oncol.2017.332] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 02/17/2017] [Accepted: 02/27/2017] [Indexed: 12/21/2022] Open
Abstract
Induction of apoptosis in cancer cells has increasingly been the focus of many therapeutic approaches in oncology field. Since its identification as a TNF family member, TRAIL (TNF-related apoptosis-inducing ligand) paved a new path in apoptosis inducing cancer therapies. Its selective ability to activate extrinsic and intrinsic cell death pathways in cancer cells only, independently from p53 mutations responsible for conventional therapeutics resistance, spotted TRAIL as a potent cancer apoptotic agent. Many recombinant preparations of TRAIL and death receptor targeting monoclonal antibodies have been developed and being tested pre-clinically and clinically both as a single agent and in combinations. Of note, the monoclonal antibodies were not the only type of antibodies developed to target TRAIL receptors. Recent technology has brought forth several single chain variable domains (scFv) designs fused recombinantly to TRAIL as well. Also, it is becoming progressively more understandable that field of nanotechnology has revolutionized cancer diagnosis and therapy. The recent breakthroughs in materials science and protein engineering have helped considerably in strategically loading drugs into nanoparticles or conjugating drugs to their surface. In this review we aim to comprehensively highlight the molecular knowledge of TRAIL in the context of its pathway, receptors and resistance factors. We also aim to review the clinical trials that have been done using TRAIL based therapies and to review various scFv designs, the arsenal of nano-carriers and molecules available to selectively target tumor cells with TRAIL.
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Affiliation(s)
| | | | | | | | - Waleed O. Arafat
- Alexandria Comprehensive Cancer Center, Alexandria, Egypt
- Univeristy of Alabama, Birmingham, AL, USA
- University of Alexandria, Faculty of Medicine, Egypt
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16
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Flusberg DA, Sorger PK. Surviving apoptosis: life-death signaling in single cells. Trends Cell Biol 2015; 25:446-58. [PMID: 25920803 PMCID: PMC4570028 DOI: 10.1016/j.tcb.2015.03.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/19/2015] [Accepted: 03/19/2015] [Indexed: 12/16/2022]
Abstract
Tissue development and homeostasis are regulated by opposing pro-survival and pro-death signals. An interesting feature of the Tumor Necrosis Factor (TNF) family of ligands is that they simultaneously activate opposing signals within a single cell via the same ligand-receptor complex. The magnitude of pro-death events such as caspase activation and pro-survival events such as Nuclear Factor (NF)-κB activation vary not only from one cell type to the next but also among individual cells of the same type due to intrinsic and extrinsic noise. The molecules involved in these pro-survival and/or pro-death pathways, and the different phenotypes that result from their activities, have been recently reviewed. Here we focus on the impact of cell-to-cell variability in the strength of these opposing signals on shaping cell fate decisions.
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Affiliation(s)
- Deborah A Flusberg
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
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17
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Roux J, Hafner M, Bandara S, Sims JJ, Hudson H, Chai D, Sorger PK. Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold. Mol Syst Biol 2015; 11:803. [PMID: 25953765 PMCID: PMC4461398 DOI: 10.15252/msb.20145584] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
When cells are exposed to death ligands such as TRAIL, a fraction undergoes apoptosis and a fraction survives; if surviving cells are re-exposed to TRAIL, fractional killing is once again observed. Therapeutic antibodies directed against TRAIL receptors also cause fractional killing, even at saturating concentrations, limiting their effectiveness. Fractional killing arises from cell-to-cell fluctuations in protein levels (extrinsic noise), but how this results in a clean bifurcation between life and death remains unclear. In this paper, we identify a threshold in the rate and timing of initiator caspase activation that distinguishes cells that live from those that die; by mapping this threshold, we can predict fractional killing of cells exposed to natural and synthetic agonists alone or in combination with sensitizing drugs such as bortezomib. A phenomenological model of the threshold also quantifies the contributions of two resistance genes (c-FLIP and Bcl-2), providing new insight into the control of cell fate by opposing pro-death and pro-survival proteins and suggesting new criteria for evaluating the efficacy of therapeutic TRAIL receptor agonists.
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Affiliation(s)
- Jérémie Roux
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Marc Hafner
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Samuel Bandara
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Joshua J Sims
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Diana Chai
- Merrimack Pharmaceuticals, Cambridge, MA, USA
| | - Peter K Sorger
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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18
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USP11-dependent selective cIAP2 deubiquitylation and stabilization determine sensitivity to Smac mimetics. Cell Death Differ 2015; 22:1463-76. [PMID: 25613375 DOI: 10.1038/cdd.2014.234] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 12/22/2022] Open
Abstract
Given their crucial role in apoptosis suppression, inhibitor of apoptosis proteins (IAPs) have recently become attractive targets for cancer therapy. Here, we report that cellular IAP2 (cIAP2) is specifically stabilized in several cancer cell lines, leading to resistance to Smac mimetics, such as BV6 and birinapant. In particular, our results showed that cIAP2 depletion, but not cIAP1 depletion, sensitized cancer cells to Smac mimetic-induced apoptosis. Ubiquitin-specific protease 11 (USP11) is a deubiquitylase that directly stabilizes cIAP2. USP11 overexpression is frequently found in colorectal cancer and melanoma and is correlated with poor survival. In our study, cancer cell lines expressing high levels of USP11 exhibited strong resistance to Smac mimetic-induced cIAP2 degradation. Furthermore, USP11 downregulation sensitized these cells to apoptosis induced by TRAIL and BV6 and suppressed tumor growth in a xenograft model. Finally, the TNFα/JNK pathway induced USP11 expression and maintained cIAP2 stability, suggesting an alternative TNFα-dependent cell survival pathway. Collectively, our data suggest that USP11-stabilized cIAP2 may serve as a barrier against IAP-targeted clinical approaches.
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19
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Charles EM, Rehm M. Key regulators of apoptosis execution as biomarker candidates in melanoma. Mol Cell Oncol 2014; 1:e964037. [PMID: 27308353 PMCID: PMC4904965 DOI: 10.4161/23723548.2014.964037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/11/2014] [Accepted: 08/12/2014] [Indexed: 01/22/2023]
Abstract
Resistance to apoptosis is frequently detected in malignant melanoma, a skin cancer with rapidly growing incidence rates. Apoptosis resistance may develop with disease progression and may be associated with the poor responsiveness of metastatic melanoma to apoptosis-inducing treatments, such as genotoxic chemotherapy and radiotherapy. Likewise, the efficacy of novel treatment options (targeted kinase inhibitors and immunotherapeutics) that indirectly lead to cell death may depend on the susceptibility of melanoma to apoptosis. At its core, apoptosis execution is regulated by the interplay between a comparatively small number of pro- and anti-apoptotic proteins, and consequently numerous studies have investigated the potential of these players as biomarker candidates. Here, we provide a comprehensive overview of biomarker discovery studies focusing on key regulators of apoptosis execution, critically review the findings of these studies, and outline strategies that address current limitations and challenges in exploiting regulators of apoptosis execution as prognostic or predictive biomarkers in melanoma.
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Affiliation(s)
- Emilie M Charles
- Department of Physiology & Medical Physics; Royal College of Physics; Royal College of Surgeons in Ireland; Dublin 2, Ireland; Centre for Systems Medicine; Royal College of Surgeons in Ireland; Dublin 2, Ireland
| | - Markus Rehm
- Department of Physiology & Medical Physics; Royal College of Physics; Royal College of Surgeons in Ireland; Dublin 2, Ireland; Centre for Systems Medicine; Royal College of Surgeons in Ireland; Dublin 2, Ireland
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20
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Würstle ML, Rehm M. A systems biology analysis of apoptosome formation and apoptosis execution supports allosteric procaspase-9 activation. J Biol Chem 2014; 289:26277-26289. [PMID: 25107908 DOI: 10.1074/jbc.m114.590034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The protease caspase-9 is activated on the apoptosome, a multiprotein signal transduction platform that assembles in response to mitochondria-dependent apoptosis initiation. Despite extensive molecular research, the assembly of the holo-apoptosome and the process of caspase-9 activation remain incompletely understood. Here, we therefore integrated quantitative data on the molecular interactions and proteolytic processes during apoptosome formation and apoptosis execution and conducted mathematical simulations to investigate the resulting biochemical signaling, quantitatively and kinetically. Interestingly, when implementing the homodimerization of procaspase-9 as a prerequisite for activation, the calculated kinetics of apoptosis execution and the efficacy of caspase-3 activation failed to replicate experimental data. In contrast, assuming a scenario in which procaspase-9 is activated allosterically upon binding to the apoptosome backbone, the mathematical simulations quantitatively and kinetically reproduced all experimental data. These data included a XIAP threshold concentration at which apoptosis execution is suppressed in HeLa cervical cancer cells, half-times of procaspase-9 processing, as well as the molecular timer function of the apoptosome. Our study therefore provides novel mechanistic insight into apoptosome-dependent apoptosis execution and suggests that caspase-9 is activated allosterically by binding to the apoptosome backbone. Our findings challenge the currently prevailing dogma that all initiator procaspases require homodimerization for activation.
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Affiliation(s)
- Maximilian L Würstle
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Markus Rehm
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
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21
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Lemke J, von Karstedt S, Zinngrebe J, Walczak H. Getting TRAIL back on track for cancer therapy. Cell Death Differ 2014; 21:1350-64. [PMID: 24948009 PMCID: PMC4131183 DOI: 10.1038/cdd.2014.81] [Citation(s) in RCA: 367] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/14/2014] [Accepted: 04/15/2014] [Indexed: 02/07/2023] Open
Abstract
Unlike other members of the TNF superfamily, the TNF-related apoptosis-inducing ligand (TRAIL, also known as Apo2L) possesses the unique capacity to induce apoptosis selectively in cancer cells in vitro and in vivo. This exciting discovery provided the basis for the development of TRAIL-receptor agonists (TRAs), which have demonstrated robust anticancer activity in a number of preclinical studies. Subsequently initiated clinical trials testing TRAs demonstrated, on the one hand, broad tolerability but revealed, on the other, that therapeutic benefit was rather limited. Several factors that are likely to account for TRAs' sobering clinical performance have since been identified. First, because of initial concerns over potential hepatotoxicity, TRAs with relatively weak agonistic activity were selected to enter clinical trials. Second, although TRAIL can induce apoptosis in several cancer cell lines, it has now emerged that many others, and importantly, most primary cancer cells are resistant to TRAIL monotherapy. Third, so far patients enrolled in TRA-employing clinical trials were not selected for likelihood of benefitting from a TRA-comprising therapy on the basis of a valid(ated) biomarker. This review summarizes and discusses the results achieved so far in TRA-employing clinical trials in the light of these three shortcomings. By integrating recent insight on apoptotic and non-apoptotic TRAIL signaling in cancer cells, we propose approaches to introduce novel, revised TRAIL-based therapeutic concepts into the cancer clinic. These include (i) the use of recently developed highly active TRAs, (ii) the addition of efficient, but cancer-cell-selective TRAIL-sensitizing agents to overcome TRAIL resistance and (iii) employing proteomic profiling to uncover resistance mechanisms. We envisage that this shall enable the design of effective TRA-comprising therapeutic concepts for individual cancer patients in the future.
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Affiliation(s)
- J Lemke
- 1] Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK [2] Clinic of General and Visceral Surgery, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - S von Karstedt
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - J Zinngrebe
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - H Walczak
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
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22
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Xia X, Owen MS, Lee REC, Gaudet S. Cell-to-cell variability in cell death: can systems biology help us make sense of it all? Cell Death Dis 2014; 5:e1261. [PMID: 24874733 PMCID: PMC4047886 DOI: 10.1038/cddis.2014.199] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/24/2014] [Accepted: 02/25/2014] [Indexed: 01/22/2023]
Abstract
One of the most common observations in cell death assays is that not all cells die at the same time, or at the same treatment dose. Here, using the perspective of the systems biology of apoptosis and the context of cancer treatment, we discuss possible sources of this cell-to-cell variability as well as its implications for quantitative measurements and computational models of cell death. Many different factors, both within and outside of the apoptosis signaling networks, have been correlated with the variable responses to various death-inducing treatments. Systems biology models offer us the opportunity to take a more synoptic view of the cell death process to identify multifactorial determinants of the cell death decision. Finally, with an eye toward 'systems pharmacology', we discuss how leveraging this new understanding should help us develop combination treatment strategies to compel cancer cells toward apoptosis by manipulating either the biochemical state of cancer cells or the dynamics of signal transduction.
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Affiliation(s)
- X Xia
- Department of Cancer Biology and Center for Cancer Systems Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - M S Owen
- Department of Cancer Biology and Center for Cancer Systems Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - R E C Lee
- Department of Cancer Biology and Center for Cancer Systems Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - S Gaudet
- Department of Cancer Biology and Center for Cancer Systems Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Biology/Genetics, Dana-Farber Cancer Institute/Harvard Medical School, 450 Brookline Avenue, Smith 836B, Boston, MA 02215, USA. Tel: +1 617 632 4269; Fax: +1 617 394 2898; E-mail:
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23
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Würstle ML, Zink E, Prehn JHM, Rehm M. From computational modelling of the intrinsic apoptosis pathway to a systems-based analysis of chemotherapy resistance: achievements, perspectives and challenges in systems medicine. Cell Death Dis 2014; 5:e1258. [PMID: 24874730 PMCID: PMC4047923 DOI: 10.1038/cddis.2014.36] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 12/20/2013] [Accepted: 01/02/2014] [Indexed: 12/14/2022]
Abstract
Our understanding of the mitochondrial or intrinsic apoptosis pathway and its role in chemotherapy resistance has increased significantly in recent years by a combination of experimental studies and mathematical modelling. This combined approach enhanced the quantitative and kinetic understanding of apoptosis signal transduction, but also provided new insights that systems-emanating functions (i.e., functions that cannot be attributed to individual network components but that are instead established by multi-component interplay) are crucial determinants of cell fate decisions. Among these features are molecular thresholds, cooperative protein functions, feedback loops and functional redundancies that provide systems robustness, and signalling topologies that allow ultrasensitivity or switch-like responses. The successful development of kinetic systems models that recapitulate biological signal transduction observed in living cells have now led to the first translational studies, which have exploited and validated such models in a clinical context. Bottom-up strategies that use pathway models in combination with higher-level modelling at the tissue, organ and whole body-level therefore carry great potential to eventually deliver a new generation of systems-based diagnostic tools that may contribute to the development of personalised and predictive medicine approaches. Here we review major achievements in the systems biology of intrinsic apoptosis signalling, discuss challenges for further model development, perspectives for higher-level integration of apoptosis models and finally discuss requirements for the development of systems medical solutions in the coming years.
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Affiliation(s)
- M L Würstle
- 1] Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland [2] Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - E Zink
- 1] Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland [2] Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - J H M Prehn
- 1] Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland [2] Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - M Rehm
- 1] Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland [2] Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
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Lavrik IN. Systems biology of death receptor networks: live and let die. Cell Death Dis 2014; 5:e1259. [PMID: 24874731 PMCID: PMC4047881 DOI: 10.1038/cddis.2014.160] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/11/2014] [Accepted: 03/13/2014] [Indexed: 12/21/2022]
Abstract
The extrinsic apoptotic pathway is initiated by death receptor activation. Death receptor activation leads to the formation of death receptor signaling platforms, resulting in the demolition of the cell. Despite the fact that death receptor-mediated apoptosis has been studied to a high level of detail, its quantitative regulation until recently has been poorly understood. This situation has dramatically changed in the last years. Creation of mathematical models of death receptor signaling led to an enormous progress in the quantitative understanding of the network regulation and provided fascinating insights into the mechanisms of apoptosis control. In the following sections, the models of the death receptor signaling and their biological implications will be addressed. Central attention will be given to the models of CD95/Fas/APO-1, an exemplified member of the death receptor signaling pathways. The CD95 death-inducing signaling complex (DISC) and regulation of CD95 DISC activity by its key inhibitor c-FLIP, have been vigorously investigated by modeling approaches, and therefore will be the major topic here. Furthermore, the non-linear dynamics of the DISC, positive feedback loops and bistability as well as stoichiometric switches in extrinsic apoptosis will be discussed. Collectively, this review gives a comprehensive view how the mathematical modeling supported by quantitative experimental approaches has provided a new understanding of the death receptor signaling network.
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Affiliation(s)
- I N Lavrik
- Department of Translational Inflammation Research, Institute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany
- Faculty of Fundamental Medicine, MV Lomonosov Moscow State University, Moscow, Russia
- Department of Translational Inflammation Research, Institute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany. Tel: +49 3916724767; Fax: +49 3916724769; E-mail:
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