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Nogueira RA, Lira MGS, Licá ICL, Frazão GCCG, Dos Santos VAF, Filho ACCM, Rodrigues JGM, Miranda GS, Carvalho RC, Nascimento FRF. Praziquantel: An update on the mechanism of its action against schistosomiasis and new therapeutic perspectives. Mol Biochem Parasitol 2022; 252:111531. [PMID: 36375598 DOI: 10.1016/j.molbiopara.2022.111531] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022]
Abstract
Praziquantel (PZQ) is the drug of choice for the treatment of all forms of schistosomiasis, although its mechanisms of action are not completely understood. PZQ acts largely on adult worms. This narrative literature review describes what is known about the mechanisms of action of PZQ against schistosomes from in vitro and in vivo studies and highlights the molecular targets in parasites and immune responses induced in definitive hosts by this drug. Moreover, new therapeutic uses of PZQ are discussed. Studies have demonstrated that in addition to impacting voltage-operated Ca2 + channels, PZQ may interact with other schistosome molecules, such as myosin regulatory light chain, glutathione S-transferase, and transient receptor potential channels. Following PZQ administration, increased T regulatory type 1 (Tr1) cell differentiation and decreased inflammation were observed, indicating that PZQ promotes immunoregulatory pathways. Although PZQ is widely used in mass drug administration schemes, the existence of resistant parasites has not been proven; however, it is a concern that should be constantly investigated in human populations. In addition, we discuss studies that evaluate health applications of PZQ (other than helminth infection), such as its effect in cancer therapy and its adjuvant action in vaccines against viruses.
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Affiliation(s)
- Ranielly Araujo Nogueira
- Graduate Program in Health Sciences, Center for Biological and Health Sciences, Federal University of Maranhão, São Luís, MA, Brazil
| | - Maria Gabriela Sampaio Lira
- Graduate Program in Health Sciences, Center for Biological and Health Sciences, Federal University of Maranhão, São Luís, MA, Brazil; Department of Education, Federal Institute of Education, Science and Technology of Maranhão, Zé Doca, MA, Brazil
| | - Irlla Correia Lima Licá
- Graduate Program in Health Sciences, Center for Biological and Health Sciences, Federal University of Maranhão, São Luís, MA, Brazil
| | | | - Vitor Augusto Ferreira Dos Santos
- Graduate Program in Health Sciences, Center for Biological and Health Sciences, Federal University of Maranhão, São Luís, MA, Brazil
| | | | - João Gustavo Mendes Rodrigues
- Department of Parasitology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Guilherme Silva Miranda
- Department of Education, Federal Institute of Education, Science and Technology of Maranhão, São Raimundo das Mangabeiras, MA, Brazil
| | - Rafael Cardoso Carvalho
- Graduate Program in Health Sciences, Center for Biological and Health Sciences, Federal University of Maranhão, São Luís, MA, Brazil
| | - Flávia Raquel Fernandes Nascimento
- Graduate Program in Health Sciences, Center for Biological and Health Sciences, Federal University of Maranhão, São Luís, MA, Brazil; Department of Pathology, Center for Biological and Health Sciences, Federal University of Maranhão, São Luís, MA, Brazil.
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Kim H, Ju J, Lee HN, Chun H, Seong J. Genetically Encoded Biosensors Based on Fluorescent Proteins. SENSORS (BASEL, SWITZERLAND) 2021; 21:795. [PMID: 33504068 PMCID: PMC7865379 DOI: 10.3390/s21030795] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023]
Abstract
Genetically encoded biosensors based on fluorescent proteins (FPs) allow for the real-time monitoring of molecular dynamics in space and time, which are crucial for the proper functioning and regulation of complex cellular processes. Depending on the types of molecular events to be monitored, different sensing strategies need to be applied for the best design of FP-based biosensors. Here, we review genetically encoded biosensors based on FPs with various sensing strategies, for example, translocation, fluorescence resonance energy transfer (FRET), reconstitution of split FP, pH sensitivity, maturation speed, and so on. We introduce general principles of each sensing strategy and discuss critical factors to be considered if available, then provide representative examples of these FP-based biosensors. These will help in designing the best sensing strategy for the successful development of new genetically encoded biosensors based on FPs.
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Affiliation(s)
- Hyunbin Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (H.K.); (J.J.); (H.N.L.); (H.C.)
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Jeongmin Ju
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (H.K.); (J.J.); (H.N.L.); (H.C.)
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Hae Nim Lee
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (H.K.); (J.J.); (H.N.L.); (H.C.)
- Department of Converging Science and Technology, Kyung Hee University, Seoul 02453, Korea
| | - Hyeyeon Chun
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (H.K.); (J.J.); (H.N.L.); (H.C.)
| | - Jihye Seong
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (H.K.); (J.J.); (H.N.L.); (H.C.)
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
- Department of Converging Science and Technology, Kyung Hee University, Seoul 02453, Korea
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3
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Fichtner M, Bozkurt E, Salvucci M, McCann C, McAllister KA, Halang L, Düssmann H, Kinsella S, Crawford N, Sessler T, Longley DB, Prehn JHM. Molecular subtype-specific responses of colon cancer cells to the SMAC mimetic Birinapant. Cell Death Dis 2020; 11:1020. [PMID: 33257690 PMCID: PMC7705699 DOI: 10.1038/s41419-020-03232-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/24/2022]
Abstract
Colorectal cancer is a molecularly heterogeneous disease. Responses to genotoxic chemotherapy in the adjuvant or palliative setting vary greatly between patients, and colorectal cancer cells often resist chemotherapy by evading apoptosis. Antagonists of an inhibitor of apoptosis proteins (IAPs) can restore defective apoptosis signaling by degrading cIAP1 and cIAP2 proteins and by inhibition of XIAP. Due to the multiple molecular mechanisms-of-action of these targets, responses to IAP antagonist may differ between molecularly distinct colon cancer cells. In this study, responses to the IAP antagonist Birinapant and oxaliplatin/5-fluorouracil (5-FU) were investigated in 14 colon cancer cell lines, representing the consensus molecular subtypes (CMS). Treatment with Birinapant alone did not result in a substantial increase in apoptotic cells in this cell line panel. Annexin-V/PI assays quantified by flow cytometry and high-content screening showed that Birinapant increased responses of CMS1 and partially CMS3 cell lines to oxaliplatin/5-FU, whereas CMS2 cells were not effectively sensitized. FRET-based imaging of caspase-8 and -3 activation validated these differences at the single-cell level, with CMS1 cells displaying sustained activation of caspase-8-like activity during Birinapant and oxaliplatin/5-FU co-treatment, ultimately activating the intrinsic mitochondrial apoptosis pathway. In CMS2 cell lines, Birinapant exhibited synergistic effects in combination with TNFα, suggesting that Birinapant can restore extrinsic apoptosis signaling in the context of inflammatory signals in this subtype. To explore this further, we co-cultured CMS2 and CMS1 colon cancer cells with peripheral blood mononuclear cells. We observed increased cell death during Birinapant single treatment in these co-cultures, which was abrogated by anti-TNFα-neutralizing antibodies. Collectively, our study demonstrates that IAP inhibition is a promising modulator of response to oxaliplatin/5-FU in colorectal cancers of the CMS1 subtype, and may show promise as in the CMS2 subtype, suggesting that molecular subtyping may aid as a patient stratification tool for IAP antagonists in this disease.
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Affiliation(s)
- Michael Fichtner
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Emir Bozkurt
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Balcova, Izmir, Turkey
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Christopher McCann
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | - Luise Halang
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Heiko Düssmann
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sinéad Kinsella
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland.,Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nyree Crawford
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Tamas Sessler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland.
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Kumar P, Bhadauria AS, Singh AK, Saha S. Betulinic acid as apoptosis activator: Molecular mechanisms, mathematical modeling and chemical modifications. Life Sci 2018; 209:24-33. [PMID: 30076920 DOI: 10.1016/j.lfs.2018.07.056] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/16/2018] [Accepted: 07/30/2018] [Indexed: 01/11/2023]
Abstract
A natural product betulinic acid (BA) has gained a huge significance in the recent years for its strong cytotoxicity. Surprisingly, in spite of being an interesting cancer protecting agent on a variety of tumor cells, the normal cells and tissues are rarely affected by BA. Betulinic acid and analogues (BAs) generally exert through the mechanisms that provokes an event of direct cell death and bypass the resistance to normal chemotherapeutics. Although the major mechanism associated with its ability to induce direct cell death is mitochondrial apoptosis, there are several other mechanisms explored recently. Importantly, mathematical modeling of apoptosis has been an important tool to explore the precise mechanism involved in mitochondrial apoptosis. Thus, this review is an endeavor to sum up the molecular mechanisms underlying the action of BA and future directions to apply mathematical modeling technique to better understand the precise mechanism of BA-induced apoptosis. The last section of the review encompasses the plausible structural modifications and formulations to enhance the therapeutic efficacy of BA.
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Affiliation(s)
- Pranesh Kumar
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, India
| | - Archana S Bhadauria
- Department of Mathematics and Statistics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur 273009, India
| | - Ashok K Singh
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, India
| | - Sudipta Saha
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, India.
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McCracken JM, Kinkead LC, McCaffrey RL, Allen LAH. Francisella tularensis Modulates a Distinct Subset of Regulatory Factors and Sustains Mitochondrial Integrity to Impair Human Neutrophil Apoptosis. J Innate Immun 2016; 8:299-313. [PMID: 26906922 DOI: 10.1159/000443882] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/09/2016] [Indexed: 12/13/2022] Open
Abstract
Tularemia is a disease characterized by profound neutrophil accumulation and tissue destruction. The causative organism, Francisella tularensis, is a facultative intracellular bacterium that replicates in neutrophil cytosol, inhibits caspase activation and profoundly prolongs cell lifespan. Here, we identify unique features of this infection and provide fundamental insight into the mechanisms of apoptosis inhibition. Mitochondria are critical regulators of neutrophil apoptosis. We demonstrate that F. tularensis significantly inhibits Bax translocation and Bid processing during 24-48 h of infection, and in this manner sustains mitochondrial integrity. Downstream of mitochondria, X-linked inhibitor of apoptosis protein (XIAP) and proliferating cell nuclear antigen (PCNA) inhibit caspase-9 and caspase-3 by direct binding. Notably, we find that PCNA disappeared rapidly and selectively from infected cells, thereby demonstrating that it is not essential for neutrophil survival, whereas upregulation of calpastatin correlated with diminished calpain activity and reduced XIAP degradation. In addition, R-roscovitine is a cyclin-dependent kinase inhibitor developed for the treatment of cancer; it also induces neutrophil apoptosis and can promote the resolution of several infectious and inflammatory disorders. We confirm the ability of R-roscovitine to induce neutrophil apoptosis, but also demonstrate that its efficacy is significantly impaired by F. tularensis. Collectively, our findings advance the understanding of neutrophil apoptosis and its capacity to be manipulated by pathogenic bacteria.
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Affiliation(s)
- Jenna M McCracken
- Inflammation Program, University of Iowa and VA Medical Center, Iowa City, Iowa, USA
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Rehm M, Parsons MJ, Bouchier-Hayes L. Measuring caspase activity by Förster resonance energy transfer. Cold Spring Harb Protoc 2015; 2015:pdb.prot082560. [PMID: 25561624 DOI: 10.1101/pdb.prot082560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Förster resonance energy transfer (FRET) occurs across very short distances (in the nanometer range) between donor and acceptor fluorophores that overlap in their emission and absorption spectra. FRET-compatible green fluorescent protein (GFP) variants that are fused to short peptide linkers containing caspase cleavage sites can be used to measure caspase activity. In the intact probes, the donor and acceptor fluorophores are in close proximity, and FRET is highly efficient. On caspase activation, proteolysis of the linker occurs, and the donor is separated from the acceptor. This results in a disruption of resonance energy transfer and an increase in donor fluorescence quantum yield; this event is typically referred to as sensitized emission or donor unquenching. A number of highly sensitive FRET probes based on the cyan fluorescent protein-yellow fluorescent protein (CFP-YFP) pair, or improved variants thereof, have been developed to detect intracellular caspase activities. In this protocol we describe how to use FRET-based caspase substrates and time-lapse imaging to measure caspase activity in cells undergoing apoptosis.
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Affiliation(s)
- Markus Rehm
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Melissa J Parsons
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030 Department of Pediatrics-Hematology, Baylor College of Medicine, Houston, Texas 77030
| | - Lisa Bouchier-Hayes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030 Department of Pediatrics-Hematology, Baylor College of Medicine, Houston, Texas 77030
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7
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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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Huber HJ, McKiernan RG, Prehn JHM. Harnessing system models of cell death signalling for cytotoxic chemotherapy: towards personalised medicine approaches? J Mol Med (Berl) 2014; 92:227-37. [PMID: 24477766 DOI: 10.1007/s00109-014-1126-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/09/2014] [Accepted: 01/14/2014] [Indexed: 12/27/2022]
Abstract
Most cytotoxic chemotherapeutics are believed to kill cancer cells by inducing apoptosis. Understanding the factors that contribute to impairment of apoptosis in cancer cells is therefore critical for the development of novel therapies that circumvent the widespread chemoresistance. Apoptosis, however, is a complex and tightly controlled process that can be induced by different classes of chemotherapeutics targeting different signalling nodes and pathways. Moreover, apoptosis initiation and apoptosis execution strongly depend on patient-specific, genomic and proteomic signatures. Here, we will review recent translational studies that suggest a critical link between the sensitivity of cancer cells to initiate apoptosis and clinical outcome. Next we will discuss recent advances in the field of system modelling of apoptosis pathways for the prediction of treatment responses. We propose that initiation of mitochondrial apoptosis, defined as the process of mitochondrial outer membrane permeabilisation (MOMP), is a dose-dependent decision process that allows for a prediction of individual therapy responses and therapeutic windows. We provide evidence in contrast that apoptosis execution post-MOMP may be a binary decision that dictates whether apoptosis is executed or not. We will discuss the implications of this concept for the future use of novel adjuvant therapeutics that specifically target apoptosis signalling pathways or which may be used to reduce the impact of cell-to-cell heterogeneity on therapy responses. Finally, we will discuss the technical and regulatory requirements surrounding the use and implications of system-based patient stratification tools for the future of personalised oncology.
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Affiliation(s)
- Heinrich J Huber
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland,
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Delgado ME, Olsson M, Lincoln FA, Zhivotovsky B, Rehm M. Determining the contributions of caspase-2, caspase-8 and effector caspases to intracellular VDVADase activities during apoptosis initiation and execution. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2279-92. [DOI: 10.1016/j.bbamcr.2013.05.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 05/15/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
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10
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Programming biological models in Python using PySB. Mol Syst Biol 2013; 9:646. [PMID: 23423320 PMCID: PMC3588907 DOI: 10.1038/msb.2013.1] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 01/07/2013] [Indexed: 12/19/2022] Open
Abstract
PySB is a framework for creating biological models as Python programs using a
high-level, action-oriented vocabulary that promotes transparency, extensibility and
reusability. PySB interoperates with many existing modeling tools and supports
distributed model development. ![]()
PySB models are programs and leverage existing programming tools for documentation, testing, and collaborative development. Reusable functions can encode common low-level biochemical processes as well as high-level modules, making models transparent and concise. Modeling workflow is accelerated through close integration with Python numerical tools and interoperability with existing modeling software. We demonstrate the use of PySB to encode 15 alternative hypotheses for the mitochondrial regulation of apoptosis, including a new ‘Embedded Together' model based on recent biochemical findings.
Mathematical equations are fundamental to modeling biological networks, but as
networks get large and revisions frequent, it becomes difficult to manage equations
directly or to combine previously developed models. Multiple simultaneous efforts to
create graphical standards, rule-based languages, and integrated software
workbenches aim to simplify biological modeling but none fully meets the need for
transparent, extensible, and reusable models. In this paper we describe PySB, an
approach in which models are not only created using programs, they are programs.
PySB draws on programmatic modeling concepts from little b and ProMot, the
rule-based languages BioNetGen and Kappa and the growing library of Python numerical
tools. Central to PySB is a library of macros encoding familiar biochemical actions
such as binding, catalysis, and polymerization, making it possible to use a
high-level, action-oriented vocabulary to construct detailed models. As Python
programs, PySB models leverage tools and practices from the open-source software
community, substantially advancing our ability to distribute and manage the work of
testing biochemical hypotheses. We illustrate these ideas using new and previously
published models of apoptosis.
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Activation of executioner caspases is a predictor of progression-free survival in glioblastoma patients: a systems medicine approach. Cell Death Dis 2013; 4:e629. [PMID: 23681224 PMCID: PMC3674364 DOI: 10.1038/cddis.2013.157] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Glioblastoma (GBM) is the most common and aggressive primary brain tumor in adults. GBM cells are highly resistant to apoptosis induced by antitumor drugs and radiotherapy resulting in cancer progression. We assessed whether a systems medicine approach, analysing the ability of tumor cells to execute apoptosis could be utilized to predict the response of GBM patients to treatment. Concentrations of the key proapoptotic proteins procaspase-3, procaspase-9, Smac and Apaf-1 and the antiapopotic protein XIAP were determined in a panel of GBM cell lines and GBM patient tumor resections. These values were used as input for APOPTO-CELL, a systems biological based mathematical model built to predict cellular susceptibility to undergo caspase activation. The modeling was capable of accurately distinguishing between GBM cells that die or survive in response to treatment with temozolomide in 10 of the 11 lines analysed. Importantly the results obtained using GBM patient samples show that APOPTO-CELL was capable of stratifying patients according to their progression-free survival times and predicted the ability of tumor cells to support caspase activation in 16 of the 21 GBM patients analysed. Calculating the susceptibility to apoptosis execution may be a potent tool in predicting GBM patient therapy responsiveness and may allow for the use of APOPTO-CELL in a clinical setting.
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Bagci EZ, Sen SM, Camurdan MC. Analysis of a mathematical model of apoptosis: individual differences and malfunction in programmed cell death. J Clin Monit Comput 2013; 27:465-79. [DOI: 10.1007/s10877-013-9468-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 04/02/2013] [Indexed: 12/13/2022]
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13
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Rehm M, Prehn JHM. Systems modelling methodology for the analysis of apoptosis signal transduction and cell death decisions. Methods 2013; 61:165-73. [PMID: 23607991 DOI: 10.1016/j.ymeth.2013.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 11/25/2022] Open
Abstract
Systems biology and systems medicine, i.e. the application of systems biology in a clinical context, is becoming of increasing importance in biology, drug discovery and health care. Systems biology incorporates knowledge and methods that are applied in mathematics, physics and engineering, but may not be part of classical training in biology. We here provide an introduction to basic concepts and methods relevant to the construction and application of systems models for apoptosis research. We present the key methods relevant to the representation of biochemical processes in signal transduction models, with a particular reference to apoptotic processes. We demonstrate how such models enable a quantitative and temporal analysis of changes in molecular entities in response to an apoptosis-inducing stimulus, and provide information on cell survival and cell death decisions. We introduce methods for analyzing the spatial propagation of cell death signals, and discuss the concepts of sensitivity analyses that enable a prediction of network responses to disturbances of single or multiple parameters.
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Affiliation(s)
- Markus Rehm
- Centre for Systems Medicine and Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
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14
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Equilibria and stability of a class of positive feedback loops. J Math Biol 2013; 68:609-45. [DOI: 10.1007/s00285-013-0644-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 01/05/2013] [Indexed: 01/08/2023]
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Wu ZH, Lu MK, Hu LY, Li X. Praziquantel synergistically enhances paclitaxel efficacy to inhibit cancer cell growth. PLoS One 2012; 7:e51721. [PMID: 23251610 PMCID: PMC3520897 DOI: 10.1371/journal.pone.0051721] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 11/05/2012] [Indexed: 12/21/2022] Open
Abstract
The major challenges we are facing in cancer therapy with paclitaxel (PTX) are the drug resistance and severe side effects. Massive efforts have been made to overcome these clinical challenges by combining PTX with other drugs. In this study, we reported the first preclinical data that praziquantel (PZQ), an anti-parasite agent, could greatly enhance the anticancer efficacy of PTX in various cancer cell lines, including PTX-resistant cell lines. Based on the combination index value, we demonstrated that PZQ synergistically enhanced PTX-induced cell growth inhibition. The co-treatment of PZQ and PTX also induced significant mitotic arrest and activated the apoptotic cascade. Moreover, PZQ combined with PTX resulted in a more pronounced inhibition of tumor growth compared with either drug alone in a mouse xenograft model. We tried to investigate the possible mechanisms of this synergistic efficacy induced by PZQ and PTX, and we found that the co-treatment of the two drugs could markedly decrease expression of X-linked inhibitor of apoptosis protein (XIAP), an anti-apoptotic protein. Our data further demonstrated that down-regulation of XIAP was required for the synergistic interaction between PZQ and PTX. Together, this study suggested that the combination of PZQ and PTX may represent a novel and effective anticancer strategy for optimizing PTX therapy.
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Affiliation(s)
- Zhen Hua Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Ming-ke Lu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Long Yu Hu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Xiaotong Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
- * E-mail:
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Kim SB, Ito Y, Torimura M. Bioluminescent Capsules for Live-Cell Imaging. Bioconjug Chem 2012; 23:2221-8. [DOI: 10.1021/bc300323x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sung Bae Kim
- Research Institute for Environmental Management Technology, National Institute
of Advanced Industrial Science and Technology (AIST), Onogawa 16-1,
Tsukuba, Ibaraki 305-8569, Japan
| | - Yuzuru Ito
- Research Center for Stem Cell Engineering, National Institute of Advanced
Industrial Science and Technology (AIST), Higashi 1-1-1, Tsukuba,
Ibaraki 305-8562, Japan
| | - Masaki Torimura
- Research Institute for Environmental Management Technology, National Institute
of Advanced Industrial Science and Technology (AIST), Onogawa 16-1,
Tsukuba, Ibaraki 305-8569, Japan
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17
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Longtine MS, Barton A, Chen B, Nelson DM. Live-cell imaging shows apoptosis initiates locally and propagates as a wave throughout syncytiotrophoblasts in primary cultures of human placental villous trophoblasts. Placenta 2012; 33:971-6. [PMID: 23102999 DOI: 10.1016/j.placenta.2012.09.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 08/24/2012] [Accepted: 09/24/2012] [Indexed: 12/20/2022]
Abstract
Human placental villi are surfaced by the syncytiotrophoblast, a multinucleated, epithelial-cell layer that functions in maternal-fetal exchange. Mononucleated cytotrophoblasts are subjacent to the syncytiotrophoblast. Using confocal fluorescence microscopy of third-trimester villi, we previously found that cytotrophoblasts are often interdigitated into the syncytiotrophoblast, that cytotrophoblasts undergo caspase-mediated apoptosis, and that apoptosis is much lower, and perhaps completely inhibited, in intact syncytiotrophoblast lacking fibrin-type fibrinoid. Previous analysis of primary cultures of human trophoblasts also indicated lower levels of apoptosis in syncytiotrophoblast compared to cytotrophoblasts. Here, using confocal microscopy we find that cultured cytotrophoblasts and syncytiotrophoblasts display complex structural relationships, as in vivo, and that apoptosis of a cytotrophoblast or syncytiotrophoblast does not induce apoptosis of adjacent trophoblasts. Using live-cell imaging of mitochondrial depolarization and nuclear condensation in cultured syncytiotrophoblasts, we show apoptosis initiates in a localized region and propagates radially at ∼5 μm/min with no loss of velocity until the entire syncytium has undergone apoptosis. The rate of propagation is similar in cases of spontaneous apoptosis and in apoptosis that occurs in the presence of cobalt chloride or rotenone, two inducers of apoptosis. We suggest that inhibition of syncytiotrophoblast apoptosis in vivo is important to prevent widespread syncytiotrophoblast death, which would result in placental dysfunction and contribute to poor pregnancy outcomes.
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Affiliation(s)
- M S Longtine
- Department of Obstetrics and Gynecology, Washington University, School of Medicine, St. Louis, MO 63110, USA.
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18
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Schmid J, Dussmann H, Boukes GJ, Flanagan L, Lindner AU, O'Connor CL, Rehm M, Prehn JHM, Huber HJ. Systems analysis of cancer cell heterogeneity in caspase-dependent apoptosis subsequent to mitochondrial outer membrane permeabilization. J Biol Chem 2012; 287:41546-59. [PMID: 23038270 DOI: 10.1074/jbc.m112.411827] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Deregulation of apoptosis is a hallmark of carcinogenesis. We here combine live cell imaging and systems modeling to investigate caspase-dependent apoptosis execution subsequent to mitochondrial outer membrane permeabilization (MOMP) in several cancer cell lines. We demonstrate that, although most cell lines that underwent MOMP also showed robust and fast activation of executioner caspases and apoptosis, the colorectal cancer cell lines LoVo and HCT-116 Smac(-/-), similar to X-linked inhibitor of apoptosis protein (XIAP)-overexpressing HeLa (HeLa XIAP(Adv)) cells, only showed delayed and often no caspase activation, suggesting apoptosis impairment subsequent to MOMP. Employing APOPTO-CELL, a recently established model of apoptosis subsequent to MOMP, this impairment could be understood by studying the systemic interaction of five proteins that are present in the apoptosis pathway subsequent to MOMP. Using APOPTO-CELL as a tool to study detailed molecular mechanisms during apoptosis execution in individual cell lines, we demonstrate that caspase-9 was the most important regulator in DLD-1, HCT-116, and HeLa cells and identified additional cell line-specific co-regulators. Developing and applying a computational workflow for parameter screening, systems modeling identified that apoptosis execution kinetics are more robust against changes in reaction kinetics in HCT-116 and HeLa than in DLD-1 cells. Our systems modeling study is the first to draw attention to the variability in cell specific protein levels and reaction rates and to the emergent effects of such variability on the efficiency of apoptosis execution and on apoptosis impairment subsequent to MOMP.
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Affiliation(s)
- Jasmin Schmid
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland
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19
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Birtwistle MR, von Kriegsheim A, Kida K, Schwarz JP, Anderson KI, Kolch W. Linear approaches to intramolecular Förster resonance energy transfer probe measurements for quantitative modeling. PLoS One 2011; 6:e27823. [PMID: 22114702 PMCID: PMC3218046 DOI: 10.1371/journal.pone.0027823] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Accepted: 10/26/2011] [Indexed: 11/19/2022] Open
Abstract
Numerous unimolecular, genetically-encoded Förster Resonance Energy Transfer (FRET) probes for monitoring biochemical activities in live cells have been developed over the past decade. As these probes allow for collection of high frequency, spatially resolved data on signaling events in live cells and tissues, they are an attractive technology for obtaining data to develop quantitative, mathematical models of spatiotemporal signaling dynamics. However, to be useful for such purposes the observed FRET from such probes should be related to a biological quantity of interest through a defined mathematical relationship, which is straightforward when this relationship is linear, and can be difficult otherwise. First, we show that only in rare circumstances is the observed FRET linearly proportional to a biochemical activity. Therefore in most cases FRET measurements should only be compared either to explicitly modeled probes or to concentrations of products of the biochemical activity, but not to activities themselves. Importantly, we find that FRET measured by standard intensity-based, ratiometric methods is inherently non-linear with respect to the fraction of probes undergoing FRET. Alternatively, we find that quantifying FRET either via (1) fluorescence lifetime imaging (FLIM) or (2) ratiometric methods where the donor emission intensity is divided by the directly-excited acceptor emission intensity (denoted R(alt)) is linear with respect to the fraction of probes undergoing FRET. This linearity property allows one to calculate the fraction of active probes based on the FRET measurement. Thus, our results suggest that either FLIM or ratiometric methods based on R(alt) are the preferred techniques for obtaining quantitative data from FRET probe experiments for mathematical modeling purposes.
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Affiliation(s)
- Marc R Birtwistle
- Systems Biology Ireland, University College Dublin, Belfield, Republic of Ireland.
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20
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Huber HJ, Duessmann H, Wenus J, Kilbride SM, Prehn JHM. Mathematical modelling of the mitochondrial apoptosis pathway. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1813:608-15. [PMID: 20950651 DOI: 10.1016/j.bbamcr.2010.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 09/29/2010] [Accepted: 10/04/2010] [Indexed: 12/23/2022]
Abstract
Mitochondria are pivotal for cellular bioenergetics, but are also a core component of the cell death machinery. Hypothesis-driven research approaches have greatly advanced our understanding of the role of mitochondria in cell death and cell survival, but traditionally focus on a single gene or specific signalling pathway at a time. Predictions originating from these approaches become limited when signalling pathways show increased complexity and invariably include redundancies, feedback loops, anisotropies or compartmentalisation. By introducing methods from theoretical chemistry, control theory, and biophysics, computational models have provided new quantitative insights into cell decision processes and have led to an increased understanding of the key regulatory principles of apoptosis. In this review, we describe the currently applied modelling approaches, discuss the suitability of different modelling techniques, and evaluate their contribution to the understanding of the mitochondrial apoptosis pathway. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.
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Affiliation(s)
- Heinrich J Huber
- Department of Physiology and Mental Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
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21
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Würstle ML, Laussmann MA, Rehm M. The caspase-8 dimerization/dissociation balance is a highly potent regulator of caspase-8, -3, -6 signaling. J Biol Chem 2010; 285:33209-33218. [PMID: 20702410 DOI: 10.1074/jbc.m110.113860] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apoptosis is driven by positive feedback activation between aspartate-specific cysteinyl proteases (caspases). These feedback loops ensure the swift and efficient elimination of cells upon initiation of apoptosis execution. At the same time, the signaling network must be insensitive to erroneous, mild caspase activation to avoid unwanted, excessive cell death. Sublethal caspase activation in fact was shown to be a requirement for the differentiation of multiple cell types but might also occur accidentally during short, transient cellular stress conditions. Here we carried out an in silico comparison of the molecular mechanisms that so far have been identified to impair the amplification of caspase activities via the caspase-8, -3, -6 loop. In a systems model resembling HeLa cervical cancer cells, the dimerization/dissociation balance of caspase-8 potently suppressed the amplification of caspase responses, surprisingly outperforming or matching known caspase-8 and -3 inhibitors such as bifunctional apoptosis repressor or x-linked inhibitor of apoptosis protein. These findings were further substantiated in global sensitivity analyses based on combinations of protein concentrations from the sub- to superphysiological range to screen the full spectrum of biological variability that can be expected within cell populations and between distinct cell types. Additional modeling showed that the combined effects of x-linked inhibitor of apoptosis protein and caspase-8 dimerization/dissociation processes can also provide resistance to larger inputs of active caspases. Our study therefore highlights a central and so far underappreciated role of caspase-8 dimerization/dissociation in avoiding unwanted cell death by lethal amplification of caspase responses via the caspase-8, -3, -6 loop.
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Affiliation(s)
- Maximilian L Würstle
- From the Department of Physiology and Medical Physics, Dublin 2, Ireland; Systems Biology Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Maike A Laussmann
- From the Department of Physiology and Medical Physics, Dublin 2, Ireland; Systems Biology Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Markus Rehm
- From the Department of Physiology and Medical Physics, Dublin 2, Ireland; Systems Biology Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
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22
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Abstract
X-linked inhibitor of apoptosis protein (XIAP) is a potent inhibitor of caspases 3, 7 and 9, and mitochondrial Smac (second mitochondria-derived activator of caspase) release during apoptosis inhibits the activity of XIAP. In this study we show that cytosolic XIAP also feeds back to mitochondria to impair Smac release. We constructed a fluorescent XIAP-fusion protein by labelling NH2- and COOH-termini with Cerulean fluorescent protein (C-XIAP-C). Immunoprecipitation confirmed that C-XIAP-C retained the ability to interact with Smac and impaired extrinsically and intrinsically activated apoptosis in response to tumour necrosis factor-related apoptosis-inducing ligand/cycloheximide and staurosporine. In C-XIAP-C-expressing cells, cytochrome c release from mitochondria proceeded normally, whereas Smac release was significantly prolonged and incomplete. In addition, physiological expression of native XIAP prolonged or limited Smac release in HCT-116 colon cancer cells and primary mouse cortical neurons. The Smac-binding capacity of XIAP, but not caspase inhibition, was central for mitochondrial Smac retention, as evidenced in experiments using XIAP mutants that cannot bind to Smac or effector caspases. Similarly, the release of a Smac mutant that cannot bind to XIAP was not impaired by C-XIAP-C expression. Full Smac release could however be provoked by rapid cytosolic C-XIAP-C depletion upon digitonin-induced plasma membrane permeabilization. Our findings suggest that although mitochondria may already contain pores sufficient for cytochrome c release, elevated amounts of XIAP can selectively impair and limit the release of Smac.
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Pace V, Bellizzi D, Giordano F, Panno ML, De Benedictis G. Experimental testing of a mathematical model relevant to the extrinsic pathway of apoptosis. Cell Stress Chaperones 2010; 15:13-23. [PMID: 19455405 PMCID: PMC2866975 DOI: 10.1007/s12192-009-0118-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 04/15/2009] [Accepted: 04/19/2009] [Indexed: 12/28/2022] Open
Abstract
Apoptosis is a programmed cell death process, whose complexity led researchers to build mathematical models that could help to identify its crucial steps. In previous works, we theoretically analyzed and numerically simulated a model that describes a pathway from an external stimulus to caspase-3 activation. Here, the results of experiments performed on populations of synchronized cells treated with the inducer Apo2L/TRAIL are reported and are compared with model predictions. In particular, we have compared in vitro and in silico results relevant to the time evolutions of caspase-3 and caspase-8 activities, as well as of the dead cells fractions. In addition, the effect of the BAR gene silencing was evaluated. Caspase-3 activation and cell death is faster in silenced than in nonsilenced cells, thus confirming previous simulation results. Interestingly, Apo2L/TRAIL treatment in itself reduces the BAR gene expression. The qualitative agreement between model predictions and cell cultures behavior suggests that the model captures the essential features of the biological process and could be a tool in further studies of caspases activation. In this manuscript, we report the results of in vitro experiments aimed at revealing the dynamics of caspase activation in a cell population. A qualitative agreement between these results and a mathematical model describing a pathway from an external stimulus to caspase-3 activation was obtained, thus showing that the model captures the essential features of the biological process and may be a reliable tool in further studies of caspase activation.
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Affiliation(s)
- Vincenza Pace
- Department of Cell Biology, University of Calabria, 87036 Rende, Italy
| | - Dina Bellizzi
- Department of Cell Biology, University of Calabria, 87036 Rende, Italy
| | | | - Maria Luisa Panno
- Department of Cell Biology, University of Calabria, 87036 Rende, Italy
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