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Duan P, Li B, Zhou Y, Cao H, Chen S, Xing Y. ZBTB20 suppresses tumor growth in glioblastoma through activating the TET1/FAS/caspase‑3 pathway. Oncol Lett 2024; 28:358. [PMID: 38881713 PMCID: PMC11176889 DOI: 10.3892/ol.2024.14491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/16/2024] [Indexed: 06/18/2024] Open
Abstract
Zinc finger and BTB domain containing 20 (ZBTB20) is a key transcription repressor that regulates multiple physiological and pathophysiological processes. Thus far, the role of ZBTB20 in glioblastoma (GBM), a World Health Organization grade IV glioma, remains unclear. In the present study, the expression profile data of ZBTB20 in GBM tissues from public databases was analyzed. It was found that ZBTB20 expression in GBM tissues was significantly lower than that measured in lower grade glioma tissues. Furthermore, patients with GBM with lower ZBTB20 expression were associated with a shorter overall survival time. Gain- and loss-of-function experiments in GBM cells were also performed. The results demonstrated that ZBTB20 overexpression decreased GBM cell proliferation, while ZBTB20 knockdown significantly enhanced it. Cell cycle analysis showed the ZBTB20 overexpression may have inhibited proliferation through cell cycle arrest at the G2/M phase, while ZBTB20 knockdown increased the percentages of cells in both the S phase and G2/M phase. Ten-eleven translocation 1 (TET1) is an important tumor suppressor involved in the formation of various types of tumor, and it was upregulated in ZBTB20-overexpressing GBM cells. It was further demonstrated that ZBTB20 activated the TET1/FAS/caspase-3 pathway. The results of the present study therefore indicated the potential role of ZBTB20 as a tumor suppressor and therapeutic target for GBM.
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Affiliation(s)
- Ping Duan
- Department of Physiology and Neurobiology, College of Medicine, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Bo Li
- Department of Physiology and Neurobiology, College of Medicine, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Yifan Zhou
- Department of Physiology and Neurobiology, College of Medicine, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Huanhuan Cao
- Department of Physiology and Neurobiology, College of Medicine, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Shiyue Chen
- Department of Physiology and Neurobiology, College of Medicine, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Ying Xing
- Department of Physiology and Neurobiology, College of Medicine, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
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2
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König C, Ivanisenko NV, Hillert-Richter LK, Namjoshi D, Natu K, Espe J, Reinhold D, Kolchanov NA, Ivanisenko VA, Kähne T, Bose K, Lavrik IN. Targeting type I DED interactions at the DED filament serves as a sensitive switch for cell fate decisions. Cell Chem Biol 2024:S2451-9456(24)00274-5. [PMID: 39053461 DOI: 10.1016/j.chembiol.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/22/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024]
Abstract
Activation of procaspase-8 in the death effector domain (DED) filaments of the death-inducing signaling complex (DISC) is a key step in apoptosis. In this study, a rationally designed cell-penetrating peptide, DEDid, was engineered to mimic the h2b helical region of procaspase-8-DED2 containing a highly conservative FL motif. Furthermore, mutations were introduced into the DEDid binding site of the procaspase-8 type I interface. Additionally, our data suggest that DEDid targets other type I DED interactions such as those of FADD. Both approaches of blocking type I DED interactions inhibited CD95L-induced DISC assembly, caspase activation and apoptosis. We showed that inhibition of procaspase-8 type I interactions by mutations not only diminished procaspase-8 recruitment to the DISC but also destabilized the FADD core of DED filaments. Taken together, this study offers insights to develop strategies to target DED proteins, which may be considered in diseases associated with cell death and inflammation.
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Affiliation(s)
- Corinna König
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, Magdeburg, Germany
| | - Nikita V Ivanisenko
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, Magdeburg, Germany
| | - Laura K Hillert-Richter
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, Magdeburg, Germany
| | - Deepti Namjoshi
- Integrated Biophysics and Structural Biology Lab, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India
| | - Kalyani Natu
- Integrated Biophysics and Structural Biology Lab, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India; Homi Bhabha National Institute, BARC Training School Complex, Mumbai, India
| | - Johannes Espe
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, Magdeburg, Germany
| | - Dirk Reinhold
- Institute of Molecular and Clinical immunology, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Nikolai A Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia; Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Vladimir A Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia; Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia; State Novosibirsk University, Novosibirsk, Russia
| | - Thilo Kähne
- Institute of Experimental and Internal Medicine (iEIM), Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Kakoli Bose
- Integrated Biophysics and Structural Biology Lab, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India; Homi Bhabha National Institute, BARC Training School Complex, Mumbai, India
| | - Inna N Lavrik
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, Magdeburg, Germany.
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Wohlfromm F, Ivanisenko NV, Pietkiewicz S, König C, Seyrek K, Kähne T, Lavrik IN. Arginine methylation of caspase-8 controls life/death decisions in extrinsic apoptotic networks. Oncogene 2024; 43:1955-1971. [PMID: 38730267 PMCID: PMC11178496 DOI: 10.1038/s41388-024-03049-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/26/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024]
Abstract
Procaspase-8 is a key mediator of death receptor (DR)-mediated pathways. Recently, the role of post-translational modifications (PTMs) of procaspase-8 in controlling cell death has received increasing attention. Here, using mass spectrometry screening, pharmacological inhibition and biochemical assays, we show that procaspase-8 can be targeted by the PRMT5/RIOK1/WD45 methylosome complex. Furthermore, two potential methylation sites of PRMT5 on procaspase-8, R233 and R435, were identified in silico. R233 and R435 are highly conserved in mammals and their point mutations are among the most common mutations of caspase-8 in cancer. The introduction of mutations at these positions resulted in inhibitory effects on CD95L-induced caspase-8 activity, effector caspase activation and apoptosis. In addition, we show that procaspase-8 can undergo symmetric di-methylation. Finally, the pharmacological inhibition of PRMT5 resulted in the inhibitory effects on caspase activity and apoptotic cell death. Taken together, we have unraveled the additional control checkpoint in procaspase-8 activation and the arginine methylation network in the extrinsic apoptosis pathway.
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Affiliation(s)
- Fabian Wohlfromm
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems (CDS), Otto von Guericke University, 39106, Magdeburg, Germany
| | - Nikita V Ivanisenko
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems (CDS), Otto von Guericke University, 39106, Magdeburg, Germany
| | - Sabine Pietkiewicz
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems (CDS), Otto von Guericke University, 39106, Magdeburg, Germany
| | - Corinna König
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems (CDS), Otto von Guericke University, 39106, Magdeburg, Germany
| | - Kamil Seyrek
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems (CDS), Otto von Guericke University, 39106, Magdeburg, Germany
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120, Magdeburg, Germany
| | - Inna N Lavrik
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems (CDS), Otto von Guericke University, 39106, Magdeburg, Germany.
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4
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Michalski M, Bauer M, Walz F, Tümen D, Heumann P, Stöckert P, Gunckel M, Kunst C, Kandulski A, Schmid S, Müller M, Gülow K. Simultaneous Inhibition of Mcl-1 and Bcl-2 Induces Synergistic Cell Death in Hepatocellular Carcinoma. Biomedicines 2023; 11:1666. [PMID: 37371761 DOI: 10.3390/biomedicines11061666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Despite the recent approval of new therapies, the prognosis for patients with hepatocellular carcinoma (HCC) remains poor. There is a clinical need for new highly effective therapeutic options. Here, we present a combined application of BH3-mimetics as a potential new treatment option for HCC. BH3-mimetics inhibit anti-apoptotic proteins of the BCL-2 family and, thus, trigger the intrinsic apoptosis pathway. Anti-apoptotic BCL-2 proteins such as Bcl-2 and Mcl-1 are frequently overexpressed in HCC. Therefore, we analyzed the efficacy of the two BH3-mimetics ABT-199 (Bcl-2 inhibitor) and MIK665 (Mcl-1 inhibitor) in HCC cell lines with differential expression levels of endogenous Bcl-2 and Mcl-1. While administration of one BH3-mimetic alone did not substantially trigger cell death, the combination of two inhibitors enhanced induction of the intrinsic apoptosis pathway. Both drugs acted synergistically, highlighting the effectivity of this specific BH3-mimetic combination, particularly in HCC cell lines. These results indicate the potential of combining inhibitors of the BCL-2 family as new therapeutic options in HCC.
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Affiliation(s)
- Marlen Michalski
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Magdalena Bauer
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Franziska Walz
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Deniz Tümen
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Philipp Heumann
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Petra Stöckert
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Manuela Gunckel
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Claudia Kunst
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Arne Kandulski
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Stephan Schmid
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Martina Müller
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Karsten Gülow
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
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5
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Triptolide-mediated downregulation of FLIP S in hepatoma cells occurs at the post-transcriptional level independently of proteasome-mediated pathways. Med Oncol 2023; 40:7. [PMID: 36308574 PMCID: PMC9617966 DOI: 10.1007/s12032-022-01857-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/20/2022] [Indexed: 01/17/2023]
Abstract
Cellular c-FLIP prevents apoptosis mediated by death receptor through inhibiting activation of caspase-8. Therefore, when c-FLIP is downregulated or eliminated, caspase-8 activation is promoted, and death receptor ligand-induced apoptosis is activated. It was reported that triptolide (TPL) sensitized tumor cells to TNF-α-induced apoptosis by blocking TNF-α-induced activation of NF-κB and transcription of c-IAP1 and c-IAP2. However, the effect of TPL on basal c-FLIP expression was not understood. In this study, we found that the combination of TNF-α and TPL accelerated apoptosis in human hepatocellular carcinoma cells and TNF-α-induced elevated as well as basal level of FLIPS protein were downregulated by TPL. Additionally, we demonstrated that the basal level of FLIPS in Huh7 cells was continuously downregulated following the incubation of TPL and downregulated more when dosage of TPL for treatment was increased. Subsequently, we showed that TPL reduced FLIPS level in a transcription- and degradation-independent mechanism. Our findings suggest that TPL induces loss of FLIPS at the post-transcriptional level independently of proteasome-mediated pathway, an additional mechanism of TPL sensitizing cancer cells to TNF-α-induced apoptosis.
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Srinivasan M, Clarke R, Kraikivski P. Mathematical Models of Death Signaling Networks. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1402. [PMID: 37420422 PMCID: PMC9602293 DOI: 10.3390/e24101402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 07/09/2023]
Abstract
This review provides an overview of the progress made by computational and systems biologists in characterizing different cell death regulatory mechanisms that constitute the cell death network. We define the cell death network as a comprehensive decision-making mechanism that controls multiple death execution molecular circuits. This network involves multiple feedback and feed-forward loops and crosstalk among different cell death-regulating pathways. While substantial progress has been made in characterizing individual cell death execution pathways, the cell death decision network is poorly defined and understood. Certainly, understanding the dynamic behavior of such complex regulatory mechanisms can be only achieved by applying mathematical modeling and system-oriented approaches. Here, we provide an overview of mathematical models that have been developed to characterize different cell death mechanisms and intend to identify future research directions in this field.
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Affiliation(s)
- Madhumita Srinivasan
- College of Architecture, Arts, and Design, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Robert Clarke
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Pavel Kraikivski
- Academy of Integrated Science, Division of Systems Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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7
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Risso V, Lafont E, Le Gallo M. Therapeutic approaches targeting CD95L/CD95 signaling in cancer and autoimmune diseases. Cell Death Dis 2022; 13:248. [PMID: 35301281 PMCID: PMC8931059 DOI: 10.1038/s41419-022-04688-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 02/09/2022] [Accepted: 02/24/2022] [Indexed: 12/14/2022]
Abstract
Cell death plays a pivotal role in the maintenance of tissue homeostasis. Key players in the controlled induction of cell death are the Death Receptors (DR). CD95 is a prototypic DR activated by its cognate ligand CD95L triggering programmed cell death. As a consequence, alterations in the CD95/CD95L pathway have been involved in several disease conditions ranging from autoimmune diseases to inflammation and cancer. CD95L-induced cell death has multiple roles in the immune response since it constitutes one of the mechanisms by which cytotoxic lymphocytes kill their targets, but it is also involved in the process of turning off the immune response. Furthermore, beyond the canonical pro-death signals, CD95L, which can be membrane-bound or soluble, also induces non-apoptotic signaling that contributes to its tumor-promoting and pro-inflammatory roles. The intent of this review is to describe the role of CD95/CD95L in the pathophysiology of cancers, autoimmune diseases and chronic inflammation and to discuss recently patented and emerging therapeutic strategies that exploit/block the CD95/CD95L system in these diseases.
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Affiliation(s)
- Vesna Risso
- INSERM U1242, Oncogenesis Stress Signaling, University of Rennes, Rennes, France
- Centre de lutte contre le cancer Eugène Marquis, Rennes, France
| | - Elodie Lafont
- INSERM U1242, Oncogenesis Stress Signaling, University of Rennes, Rennes, France
- Centre de lutte contre le cancer Eugène Marquis, Rennes, France
| | - Matthieu Le Gallo
- INSERM U1242, Oncogenesis Stress Signaling, University of Rennes, Rennes, France.
- Centre de lutte contre le cancer Eugène Marquis, Rennes, France.
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8
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Ivanisenko NV, Seyrek K, Hillert-Richter LK, König C, Espe J, Bose K, Lavrik IN. Regulation of extrinsic apoptotic signaling by c-FLIP: towards targeting cancer networks. Trends Cancer 2021; 8:190-209. [PMID: 34973957 DOI: 10.1016/j.trecan.2021.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023]
Abstract
The extrinsic pathway is mediated by death receptors (DRs), including CD95 (APO-1/Fas) or TRAILR-1/2. Defects in apoptosis regulation lead to cancer and other malignancies. The master regulator of the DR networks is the cellular FLICE inhibitory protein (c-FLIP). In addition to its key role in apoptosis, c-FLIP may exert other cellular functions, including control of necroptosis, pyroptosis, nuclear factor κB (NF-κB) activation, and tumorigenesis. To gain further insight into the molecular mechanisms of c-FLIP action in cancer networks, we focus on the structure, isoforms, interactions, and post-translational modifications of c-FLIP. We also discuss various avenues to target c-FLIP in cancer cells for therapeutic benefit.
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Affiliation(s)
- Nikita V Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; Artificial Intelligence Research Institute, Moscow, Russia
| | - Kamil Seyrek
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Laura K Hillert-Richter
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Corinna König
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Johannes Espe
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Kakoli Bose
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Inna N Lavrik
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany.
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9
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Chaves M, Gomes-Pereira LC, Roux J. Two-level modeling approach to identify the regulatory dynamics capturing drug response heterogeneity in single-cells. Sci Rep 2021; 11:20809. [PMID: 34675364 PMCID: PMC8531316 DOI: 10.1038/s41598-021-99943-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/27/2021] [Indexed: 11/09/2022] Open
Abstract
Single-cell multimodal technologies reveal the scales of cellular heterogeneity impairing cancer treatment, yet cell response dynamics remain largely underused to decipher the mechanisms of drug resistance they take part in. As the phenotypic heterogeneity of a clonal cell population informs on the capacity of each single-cell to recapitulate the whole range of observed behaviors, we developed a modeling approach utilizing single-cell response data to identify regulatory reactions driving population heterogeneity in drug response. Dynamic data of hundreds of HeLa cells treated with TNF-related apoptosis-inducing ligand (TRAIL) were used to characterize the fate-determining kinetic parameters of an apoptosis receptor reaction model. Selected reactions sets were augmented to incorporate a mechanism that leads to the separation of the opposing response phenotypes. Using a positive feedback loop motif to identify the reaction set, we show that caspase-8 is able to encapsulate high levels of heterogeneity by introducing a response delay and amplifying the initial differences arising from natural protein expression variability. Our approach enables the identification of fate-determining reactions that drive the population response heterogeneity, providing regulatory targets to curb the cell dynamics of drug resistance.
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Affiliation(s)
- Madalena Chaves
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore Team, Sophia Antipolis, France
| | - Luis C Gomes-Pereira
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore Team, Sophia Antipolis, France.,Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107, Nice, France
| | - Jérémie Roux
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107, Nice, France.
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10
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Zhang J, Sun H, Jiang K, Song X, Wang X, Yang Y, Liu H, Ji Q, Yu X, Liu Y, Han J, Wang W. Cudraxanthone L inhibits gastric cancer by regulating the MAPK signalling and promoting FAS-mediated pathway. Biomed Pharmacother 2021; 141:111876. [PMID: 34328085 DOI: 10.1016/j.biopha.2021.111876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 02/09/2023] Open
Abstract
Gastric cancer (GC) is one of the most common malignancies and has the second highest lethal rate in the world; thus, finding new medicines with high potency and low toxicity is urgent. Cudrania tricuspidata (Carr.) Bur. ex Lavallee (Moraceae) is a traditional medicinal herb that is considered to have antitumour efficacy. We extracted and isolated cudraxanthone L (CXL) from Cudrania tricuspidata and evaluated its anti-cancer efficacy. CXL treatment inhibited angiogenesis of chorioallantoic membrane (CAM) and repressed the cell viability of various human cancer cells, indicating it presented the antitumour potential. Among them, CXL presented the best inhibitory effects on MGC803 cells. In addition, the invasion, migration and clonogenicity were significantly repressed, S phase of the cell cycle was arrested, and apoptosis was induced when MGC803 cells were treated with CXL. The results of RNA sequencing, qRT-PCR and western blotting verified that CXL regulated the MAPK signalling pathway and induced apoptosis by FAS-mediated pathway. The in vivo data revealed that CXL arrested tumour growth without toxic effects and upregulated the protein levels in FAS-mediated pathway in MGC803 gastric cancer-bearing mice. In summary, we demonstrate CXL presents impactful anti-GC efficacy by regulating the MAPK signalling pathway and promoting the FAS-mediated pathway.
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Affiliation(s)
- Jiamei Zhang
- College of Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China
| | - Huihui Sun
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China
| | - KunXiu Jiang
- College of Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China
| | - Xingzhuo Song
- College of Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China
| | - Xirui Wang
- College of Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China
| | - Yuqian Yang
- College of Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China
| | - Hanying Liu
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China
| | - Qingxuan Ji
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China
| | - Xue Yu
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China
| | - Yonggang Liu
- College of Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China.
| | - Jing Han
- Institute of traditional Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China.
| | - Wei Wang
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, 100029, Beijing, China.
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11
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Zhou J, Ramanathan R, Wong WF. Synthesis of the Dynamical Properties of Feedback Loops in Bio-Pathways. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1217-1226. [PMID: 31443044 DOI: 10.1109/tcbb.2019.2936200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Feedback loops regulate various biological functions such as oscillations, bistability, and robustness. They play a significant role in developmental signalling and failure of feedback can lead to disease. Systematic analysis of feedback loops could be useful in understanding their properties and biological effects. We propose here a method to automatically analyze feedback loops in bio-pathways and synthesize temporal logic properties which describe their dynamics. Starting with an ordinary differential equations (ODEs) based model of a bio-pathway, for a chosen feedback loop present in the pathway, we use a convolutional neural network to classify the behaviours of the key components of the feedback according to templates specified in bounded linear temporal logic (BLTL). Once a template has been identified, we instantiate the symbolic variables appearing in the template and synthesize properties using a parameter estimation procedure based on sequential hypothesis testing. We have applied this framework to a number of bio-pathway models and validated that the synthesized properties faithfully describe the behaviours of the feedback loops.
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12
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Adamo A, Frusteri C, Pallotta MT, Pirali T, Sartoris S, Ugel S. Moonlighting Proteins Are Important Players in Cancer Immunology. Front Immunol 2021; 11:613069. [PMID: 33584695 PMCID: PMC7873856 DOI: 10.3389/fimmu.2020.613069] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/30/2020] [Indexed: 12/21/2022] Open
Abstract
Plasticity and adaptation to environmental stress are the main features that tumor and immune system share. Except for intrinsic and high-defined properties, cancer and immune cells need to overcome the opponent's defenses by activating more effective signaling networks, based on common elements such as transcriptional factors, protein-based complexes and receptors. Interestingly, growing evidence point to an increasing number of proteins capable of performing diverse and unpredictable functions. These multifunctional proteins are defined as moonlighting proteins. During cancer progression, several moonlighting proteins are involved in promoting an immunosuppressive microenvironment by reprogramming immune cells to support tumor growth and metastatic spread. Conversely, other moonlighting proteins support tumor antigen presentation and lymphocytes activation, leading to several anti-cancer immunological responses. In this light, moonlighting proteins could be used as promising new potential targets for improving current cancer therapies. In this review, we describe in details 12 unprecedented moonlighting proteins that during cancer progression play a decisive role in guiding cancer-associated immunomodulation by shaping innate or adaptive immune response.
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Affiliation(s)
- Annalisa Adamo
- Section of Immunology, Department of Medicine, University of Verona, Verona, Italy
| | - Cristina Frusteri
- Section of Immunology, Department of Medicine, University of Verona, Verona, Italy
| | | | - Tracey Pirali
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Silvia Sartoris
- Section of Immunology, Department of Medicine, University of Verona, Verona, Italy
| | - Stefano Ugel
- Section of Immunology, Department of Medicine, University of Verona, Verona, Italy
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13
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Ivanisenko NV, Lavrik IN. Mathematical Modeling Reveals the Importance of the DED Filament Composition in the Effects of Small Molecules Targeting Caspase-8/c-FLIP L Heterodimer. BIOCHEMISTRY (MOSCOW) 2020; 85:1134-1144. [PMID: 33202199 DOI: 10.1134/s0006297920100028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Procaspase-8 activation at the death-inducing signaling complex (DISC) triggers extrinsic apoptotic pathway. Procaspase-8 activation takes place in the death effector domain (DED) filaments and is regulated by c-FLIP proteins, in particular, by the long isoform c-FLIPL. Recently, the first-in-class chemical probe targeting the caspase-8/c-FLIPL heterodimer was reported. This rationally designed small molecule, FLIPin, enhances caspase-8 activity after initial heterodimer processing. Here, we used a kinetic mathematical model to gain an insight into the mechanisms of FLIPin action in a complex with DISC, in particular, to unravel the effects of FLIPin at different stoichiometry and composition of the DED filament. Analysis of this model has identified the optimal c-FLIPL to procaspase-8 ratios in different cellular landscapes favoring the activity of FLIPin. We predicted that the activity FLIPin is regulated via different mechanisms upon c-FLIPL downregulation or upregulation. Our study demonstrates that a combination of mathematical modeling with system pharmacology allows development of more efficient therapeutic approaches and prediction of optimal treatment strategies.
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Affiliation(s)
- N V Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - I N Lavrik
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, 39106, Germany
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14
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Ivanisenko NV, Seyrek K, Kolchanov NA, Ivanisenko VA, Lavrik IN. The role of death domain proteins in host response upon SARS-CoV-2 infection: modulation of programmed cell death and translational applications. Cell Death Discov 2020; 6:101. [PMID: 33072409 PMCID: PMC7547561 DOI: 10.1038/s41420-020-00331-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/17/2020] [Indexed: 02/08/2023] Open
Abstract
The current pandemic of novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) poses a significant global public health threat. While urgent regulatory measures in control of the rapid spread of this virus are essential, scientists around the world have quickly engaged in this battle by studying the molecular mechanisms and searching for effective therapeutic strategies against this deadly disease. At present, the exact mechanisms of programmed cell death upon SARS-CoV-2 infection remain to be elucidated, though there is increasing evidence suggesting that cell death pathways play a key role in SARS-CoV-2 infection. There are several types of programmed cell death, including apoptosis, pyroptosis, and necroptosis. These distinct programs are largely controlled by the proteins of the death domain (DD) superfamily, which play an important role in viral pathogenesis and host antiviral response. Many viruses have acquired the capability to subvert the program of cell death and evade the host immune response, mainly by virally encoded gene products that control cell signaling networks. In this mini-review, we will focus on SARS-CoV-2, and discuss the implication of restraining the DD-mediated signaling network to potentially suppress viral replication and reduce tissue damage.
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Affiliation(s)
- Nikita V. Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Kamil Seyrek
- Translational Inflammation Research, CDS, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Nikolay A. Kolchanov
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Vladimir A. Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Inna N. Lavrik
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Translational Inflammation Research, CDS, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
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15
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Vigneswara V, Ahmed Z. The Role of Caspase-2 in Regulating Cell Fate. Cells 2020; 9:cells9051259. [PMID: 32438737 PMCID: PMC7290664 DOI: 10.3390/cells9051259] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Caspase-2 is the most evolutionarily conserved member of the mammalian caspase family and has been implicated in both apoptotic and non-apoptotic signaling pathways, including tumor suppression, cell cycle regulation, and DNA repair. A myriad of signaling molecules is associated with the tight regulation of caspase-2 to mediate multiple cellular processes far beyond apoptotic cell death. This review provides a comprehensive overview of the literature pertaining to possible sophisticated molecular mechanisms underlying the multifaceted process of caspase-2 activation and to highlight its interplay between factors that promote or suppress apoptosis in a complicated regulatory network that determines the fate of a cell from its birth and throughout its life.
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16
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Seyrek K, Lavrik IN. Modulation of CD95-mediated signaling by post-translational modifications: towards understanding CD95 signaling networks. Apoptosis 2020; 24:385-394. [PMID: 31069559 DOI: 10.1007/s10495-019-01540-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
CD95 is a member of the death receptor family and is well-known to promote apoptosis. However, accumulating evidence indicates that in some context CD95 has not only the potential to induce apoptosis but also can trigger non-apoptotic signal leading to cell survival, proliferation, cancer growth and metastasis. Despite extensive investigations focused on alterations in the expression level of CD95 and associated signal molecules, very few studies, however, have investigated the effects of post-translational modifications such as glycosylation, phosphorylation, palmitoylation, nitrosylation and glutathionylation on CD95 function. Post-translational modifications of CD95 in mammalian systems are likely to play a more prominent role than anticipated in CD95 induced cell death. In this review we will focus on the alterations in CD95-mediated signaling caused by post-translational modifications of CD95.
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Affiliation(s)
- Kamil Seyrek
- Translational Inflammation Research, Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Inna N Lavrik
- Translational Inflammation Research, Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, Magdeburg, Germany.
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17
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Data-Driven Modeling Identifies TIRAP-Independent MyD88 Activation Complex and Myddosome Assembly Strategy in LPS/TLR4 Signaling. Int J Mol Sci 2020; 21:ijms21093061. [PMID: 32357531 PMCID: PMC7246728 DOI: 10.3390/ijms21093061] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/24/2020] [Accepted: 04/25/2020] [Indexed: 02/06/2023] Open
Abstract
TLR4 complexes are essential for the initiation of the LPS-induced innate immune response. The Myddosome, which mainly contains TLR4, TIRAP, MyD88, IRAK1/4 and TRAF6 proteins, is regarded as a major complex of TLR4. Although the Myddosome has been well studied, a quantitative description of the Myddosome assembly dynamics is still lacking. Furthermore, whether some unknown TLR4 complexes exist remains unclear. In this study, we constructed a SWATH-MS data-based mathematical model that describes the component assembly dynamics of TLR4 complexes. In addition to Myddosome, we suggest that a TIRAP-independent MyD88 activation complex is formed upon LPS stimulation, in which TRAF6 is not included. Furthermore, quantitative analysis reveals that the distribution of components in TIRAP-dependent and -independent MyD88 activation complexes are LPS stimulation-dependent. The two complexes compete for recruiting IRAK1/4 proteins. MyD88 forms higher-order assembly in the Myddosome and we show that the strategy to form higher-order assembly is also LPS stimulation-dependent. MyD88 forms a long chain upon weak stimulation, but forms a short chain upon strong stimulation. Higher-order assembly of MyD88 is directly determined by the level of TIRAP in the Myddosome, providing a formation mechanism for efficient signaling transduction. Taken together, our study provides an enhanced understanding of component assembly dynamics and strategies in TLR4 complexes.
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18
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Hillert LK, Ivanisenko NV, Busse D, Espe J, König C, Peltek SE, Kolchanov NA, Ivanisenko VA, Lavrik IN. Dissecting DISC regulation via pharmacological targeting of caspase-8/c-FLIP L heterodimer. Cell Death Differ 2020; 27:2117-2130. [PMID: 31959913 DOI: 10.1038/s41418-020-0489-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/18/2019] [Accepted: 12/27/2019] [Indexed: 11/09/2022] Open
Abstract
Pharmacological targeting via small molecule-based chemical probes has recently acquired an emerging importance as a valuable tool to delineate molecular mechanisms. Induction of apoptosis via CD95/Fas and TRAIL-R1/2 is triggered by the formation of the death-inducing signaling complex (DISC). Caspase-8 activation at the DISC is largely controlled by c-FLIP proteins. However molecular mechanisms of this control have just started to be uncovered. In this study we report the first-in-class chemical probe targeting c-FLIPL in the heterodimer caspase-8/c-FLIPL. This rationally designed small molecule was aimed to imitate the closed conformation of the caspase-8 L2' loop and thereby increase caspase-8 activity after initial processing of the heterodimer. In accordance with in silico predictions, this small molecule enhanced caspase-8 activity at the DISC, CD95L/TRAIL-induced caspase activation, and subsequent apoptosis. The generated computational model provided further evidence for the proposed effects of the small molecule on the heterodimer caspase-8/c-FLIPL. In particular, the model has demonstrated that boosting caspase-8 activity by the small molecule at the early time points after DISC assembly is crucial for promoting apoptosis induction. Taken together, our study allowed to target the heterodimer caspase-8/c-FLIPL and get new insights into molecular mechanisms of its activation.
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Affiliation(s)
- Laura K Hillert
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University Magdeburg, Geb.28. 1 OG/R. 111, Pfälzer Platz 2, 39106, Magdeburg, Germany
| | - Nikita V Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Denise Busse
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University Magdeburg, Geb.28. 1 OG/R. 111, Pfälzer Platz 2, 39106, Magdeburg, Germany
| | - Johannes Espe
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University Magdeburg, Geb.28. 1 OG/R. 111, Pfälzer Platz 2, 39106, Magdeburg, Germany
| | - Corinna König
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University Magdeburg, Geb.28. 1 OG/R. 111, Pfälzer Platz 2, 39106, Magdeburg, Germany
| | - Sergey E Peltek
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Nikolai A Kolchanov
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Vladimir A Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Inna N Lavrik
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University Magdeburg, Geb.28. 1 OG/R. 111, Pfälzer Platz 2, 39106, Magdeburg, Germany.
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19
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Long and short isoforms of c-FLIP act as control checkpoints of DED filament assembly. Oncogene 2019; 39:1756-1772. [PMID: 31740779 DOI: 10.1038/s41388-019-1100-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022]
Abstract
The assembly of the death-inducing signaling complex (DISC) and death effector domain (DED) filaments at CD95/Fas initiates extrinsic apoptosis. Procaspase-8 activation at the DED filaments is controlled by short and long c-FLIP isoforms. Despite apparent progress in understanding the assembly of CD95-activated platforms and DED filaments, the detailed molecular mechanism of c-FLIP action remains elusive. Here, we further addressed the mechanisms of c-FLIP action at the DISC using biochemical assays, quantitative mass spectrometry, and structural modeling. Our data strongly indicate that c-FLIP can bind to both FADD and procaspase-8 at the DED filament. Moreover, the constructed in silico model shows that c-FLIP proteins can lead to the formation of the DISCs comprising short DED filaments as well as serve as bridging motifs for building a cooperative DISC network, in which adjacent CD95 DISCs are connected by DED filaments. This network is based on selective interactions of FADD with both c-FLIP and procaspase-8. Hence, c-FLIP proteins at the DISC control initiation, elongation, and composition of DED filaments, playing the role of control checkpoints. These findings provide new insights into DISC and DED filament regulation and open innovative possibilities for targeting the extrinsic apoptosis pathway.
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20
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Athari SS. Targeting cell signaling in allergic asthma. Signal Transduct Target Ther 2019; 4:45. [PMID: 31637021 PMCID: PMC6799822 DOI: 10.1038/s41392-019-0079-0] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/03/2019] [Accepted: 09/15/2019] [Indexed: 02/08/2023] Open
Abstract
Asthma is chronic inflammation of the airways characterized by airway hyper-responsiveness, wheezing, cough, and dyspnea. Asthma affects >350 million people worldwide. The Th2 immune response is a major contributor to the pathophysiology of asthma. Targeted therapy modulating cell signaling pathways can be a powerful strategy to design new drugs to treat asthma. The potential molecular pathways that can be targeted include IL-4-IL-13-JAK-STAT-MAP kinases, adiponectin-iNOS-NF-κB, PGD2-CRTH2, IFNs-RIG, Wnt/β-catenin-FAM13A, FOXC1-miR-PI3K/AKT, JNK-Gal-7, Nrf2-ROS, Foxp3-RORγt, CysLTR, AMP, Fas-FasL, PTHrP/PPARγ, PAI-1, FcɛRI-LAT-SLP-76, Tim-3-Gal-9, TLRs-MyD88, PAR2, and Keap1/Nrf2/ARE. Therapeutic drugs can be designed to target one or more of these pathways to treat asthma.
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Affiliation(s)
- Seyyed Shamsadin Athari
- Department of Immunology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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21
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Quantitative Analysis of the Rewiring of Signaling Pathways to Alter Cancer Cell Fate. J Med Biol Eng 2019. [DOI: 10.1007/s40846-019-00489-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Ivanisenko NV, Buchbinder JH, Espe J, Richter M, Bollmann M, Hillert LK, Ivanisenko VA, Lavrik IN. Delineating the role of c-FLIP/NEMO interaction in the CD95 network via rational design of molecular probes. BMC Genomics 2019; 20:293. [PMID: 31815628 PMCID: PMC6900753 DOI: 10.1186/s12864-019-5539-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Structural homology modeling supported by bioinformatics analysis plays a key role in uncovering new molecular interactions within gene regulatory networks. Here, we have applied this powerful approach to analyze the molecular interactions orchestrating death receptor signaling networks. In particular, we focused on the molecular mechanisms of CD95-mediated NF-κB activation and the role of c-FLIP/NEMO interaction in the induction of this pathway. RESULTS To this end, we have created the homology model of the c-FLIP/NEMO complex using the reported structure of the v-FLIP/NEMO complex, and rationally designed peptides targeting this complex. The designed peptides were based on the NEMO structure. Strikingly, the experimental in vitro validation demonstrated that the best inhibitory effects on CD95-mediated NF-κB activation are exhibited by the NEMO-derived peptides with the substitution D242Y of NEMO. Furthermore, we have assumed that the c-FLIP/NEMO complex is recruited to the DED filaments formed upon CD95 activation and validated this assumption in silico. Further insight into the function of c-FLIP/NEMO complex was provided by the analysis of evolutionary conservation of interacting regions which demonstrated that this interaction is common in distinct mammalian species. CONCLUSIONS Taken together, using a combination of bioinformatics and experimental approaches we obtained new insights into CD95-mediated NF-κB activation, providing manifold possibilities for targeting the death receptor network.
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Affiliation(s)
- Nikita V Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Jörn H Buchbinder
- Translational Inflammation research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Johannes Espe
- Translational Inflammation research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Max Richter
- Translational Inflammation research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Miriam Bollmann
- Translational Inflammation research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Laura K Hillert
- Translational Inflammation research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Vladimir A Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Inna N Lavrik
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia. .,Translational Inflammation research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany.
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23
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Shockley EM, Vrugt JA, Lopez CF. PyDREAM: high-dimensional parameter inference for biological models in python. Bioinformatics 2019; 34:695-697. [PMID: 29028896 PMCID: PMC5860607 DOI: 10.1093/bioinformatics/btx626] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/03/2017] [Indexed: 11/22/2022] Open
Abstract
Summary Biological models contain many parameters whose values are difficult to measure directly via experimentation and therefore require calibration against experimental data. Markov chain Monte Carlo (MCMC) methods are suitable to estimate multivariate posterior model parameter distributions, but these methods may exhibit slow or premature convergence in high-dimensional search spaces. Here, we present PyDREAM, a Python implementation of the (Multiple-Try) Differential Evolution Adaptive Metropolis [DREAM(ZS)] algorithm developed by Vrugt and ter Braak (2008) and Laloy and Vrugt (2012). PyDREAM achieves excellent performance for complex, parameter-rich models and takes full advantage of distributed computing resources, facilitating parameter inference and uncertainty estimation of CPU-intensive biological models. Availability and implementation PyDREAM is freely available under the GNU GPLv3 license from the Lopez lab GitHub repository at http://github.com/LoLab-VU/PyDREAM. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Erin M Shockley
- Department of Biochemistry, Vanderbilt University, 2215 Garland Avenue, Nashville, TN 37212, USA
| | - Jasper A Vrugt
- Department of Civil and Environmental Engineering, University of California Irvine, 4130 Engineering Gateway, Irvine, CA 92697-2175, USA.,Department of Earth System Science, University of California Irvine, 3200 Croul Hall St, Irvine, CA 92697-2175, USA
| | - Carlos F Lopez
- Department of Biochemistry, Vanderbilt University, 2215 Garland Avenue, Nashville, TN 37212, USA
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24
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Delgado ME, Brunner T. The many faces of tumor necrosis factor signaling in the intestinal epithelium. Genes Immun 2019; 20:609-626. [DOI: 10.1038/s41435-019-0057-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/26/2018] [Indexed: 01/15/2023]
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25
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Valentinuzzi D, Simončič U, Uršič K, Vrankar M, Turk M, Jeraj R. Predicting tumour response to anti-PD-1 immunotherapy with computational modelling. ACTA ACUST UNITED AC 2019; 64:025017. [DOI: 10.1088/1361-6560/aaf96c] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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26
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Williams JW, Ferreira CM, Blaine KM, Rayon C, Velázquez F, Tong J, Peter ME, Sperling AI. Non-apoptotic Fas (CD95) Signaling on T Cells Regulates the Resolution of Th2-Mediated Inflammation. Front Immunol 2018; 9:2521. [PMID: 30443253 PMCID: PMC6221963 DOI: 10.3389/fimmu.2018.02521] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/12/2018] [Indexed: 02/05/2023] Open
Abstract
Fas (CD95/APO-1) and its ligand (FasL/CD95L) promote the resolution of type 2 lung inflammation and eosinophilia. We previously found that Fas-deficiency on T cells, but not eosinophils, delayed resolution of inflammation. However, Fas can signal both cell death and have a positive signaling function that can actually activate cells. In this study, we investigated whether Fas-induced death or Fas-activated signaling pathways promote resolution of allergic lung inflammation. By increasing T cell survival through two Fas-independent pathways, using Bim-deficient T cells or Bcl-xL overexpressing T cells, no differences in resolution of Th2-mediated inflammation was observed. Furthermore, Th2 cells were inherently resistant to Fas-mediated apoptosis and preferentially signaled through non-apoptotic pathways following FasL treatment. Utilizing Fas-mutant mice deficient in apoptotic but sufficient for non-apoptotic Fas signaling pathways, we demonstrate that non-apoptotic Fas signaling in T cells drives resolution of Th2-mediated airway inflammation. Our findings reveal a previously unknown role for non-apoptotic Fas signaling on Th2 cells in the induction of resolution of type 2 inflammation.
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Affiliation(s)
- Jesse W Williams
- Committee on Molecular Pathology and Molecular Medicine, Chicago, IL, United States
| | - Caroline M Ferreira
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, Chicago, IL, United States
| | - Kelly M Blaine
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, Chicago, IL, United States
| | - Crystal Rayon
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, Chicago, IL, United States
| | - Francisco Velázquez
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, Chicago, IL, United States
| | - Jiankun Tong
- Department of Pathology, University of Chicago, Chicago, IL, United States
| | - Marcus E Peter
- Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Anne I Sperling
- Committee on Molecular Pathology and Molecular Medicine, Chicago, IL, United States.,Department of Medicine, Section of Pulmonary and Critical Care Medicine, Chicago, IL, United States.,Department of Pathology, University of Chicago, Chicago, IL, United States
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27
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Quantitative single cell analysis uncovers the life/death decision in CD95 network. PLoS Comput Biol 2018; 14:e1006368. [PMID: 30256782 PMCID: PMC6175528 DOI: 10.1371/journal.pcbi.1006368] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 10/08/2018] [Accepted: 07/16/2018] [Indexed: 11/20/2022] Open
Abstract
CD95/Fas/APO-1 is a member of the death receptor family that triggers apoptotic and anti-apoptotic responses in particular, NF-κB. These responses are characterized by a strong heterogeneity within a population of cells. To determine how the cell decides between life and death we developed a computational model supported by imaging flow cytometry analysis of CD95 signaling. Here we show that CD95 stimulation leads to the induction of caspase and NF-κB pathways simultaneously in one cell. The related life/death decision strictly depends on cell-to-cell variability in the formation of the death-inducing complex (DISC) on one side (extrinsic noise) vs. stochastic gene expression of the NF-κB pathway on the other side (intrinsic noise). Moreover, our analysis has uncovered that the stochasticity in apoptosis and NF-kB pathways leads not only to survival or death of a cell, but also causes a third type of response to CD95 stimulation that we termed ambivalent response. Cells in the ambivalent state can undergo cell death or survive which was subsequently validated by experiments. Taken together, we have uncovered how these two competing pathways control the fate of a cell, which in turn plays an important role for development of anti-cancer therapies. Activation of death receptor (DR) family has been reported to activate both apoptotic as well as anti-apoptotic responses. Molecular mechanisms underlying the intricate details of this crosstalk have not been established yet. Here we show that these pathways are triggered simultaneously in one cell. Furthermore, using stochastic computational modeling we uncovered how an individual cell undergoes apoptosis, while other cells survive upon the same DR activation conditions. This was only possible by combination of computational modeling supported by experimental validation based on the state of the art single cell analysis. The latter included cutting edge technology of imaging flow cytometry, which combines microscopy and flow cytometry in one measurement circuit enabling quantitative analysis of endogenous cellular protein levels estimated from a large number of cells simultaneously. This allowed to shed the light on the question how a single cell possibly avoids apoptosis, which is a highly actual topic in the field of cancer research and development of efficient anti-cancer therapies.
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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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29
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Hang X, Li D, Wang J, Wang G. Prognostic significance of microsatellite instability‑associated pathways and genes in gastric cancer. Int J Mol Med 2018; 42:149-160. [PMID: 29717769 PMCID: PMC5979886 DOI: 10.3892/ijmm.2018.3643] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 04/04/2018] [Indexed: 12/20/2022] Open
Abstract
The aim of the present study was to reveal the potential molecular mechanisms of microsatellite instability (MSI) on the prognosis of gastric cancer (GC). The investigation was performed based on an RNAseq expression profiling dataset downloaded from The Cancer Genome Atlas, including 64 high‑level MSI (MSI‑H) GC samples, 44 low‑level MSI (MSI‑L) GC samples and 187 stable microsatellite (MSI‑S) GC samples. Differentially expressed genes (DEGs) were identified between the MSI‑H, MSI‑L and MSI‑S samples. Pathway enrichment analysis was performed for the identified DEGs and the pathway deviation scores of the significant enrichment pathways were calculated. A Multi‑Layer Perceptron (MLP) classifier, based on the different pathways associated with the MSI statuses was constructed for predicting the outcome of patients with GC, which was validated in another independent dataset. A total of 190 DEGs were selected between the MSI‑H, MSI‑L and MSI‑S samples. The MLP classifier was established based on the deviation scores of 10 significant pathways, among which antigen processing and presentation, and inflammatory bowel disease pathways were significantly enriched with HLA‑DRB5, HLA‑DMA, HLA‑DQA1 and HLA‑DRA; the measles, toxoplasmosis and herpes simplex infection pathways were significantly enriched with Janus kinase 2 (JAK2), caspase‑8 (CASP8) and Fas. The classifier performed well on an independent validation set with 100 GC samples. Taken together, the results indicated that MSI status may affect GC prognosis, partly through the antigen processing and presentation, inflammatory bowel disease, measles, toxoplasmosis and herpes simplex infection pathways. HLA‑DRB5, HLA‑DMA, HLA‑DQA1, HLA‑DRA, JAK2, CASP8 and Fas may be predictive factors for prognosis in GC.
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Affiliation(s)
- Xiaosheng Hang
- Department of Medical Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062
| | | | - Jianping Wang
- Department of Radiation, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215008
| | - Ge Wang
- Cancer Center, Changzhou No. 2 People's Hospital, Changzhou, Jiangsu 213002, P.R. China
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30
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Chen X, Li X, Zhao W, Li T, Ouyang Q. Parameter sensitivity analysis for a stochastic model of mitochondrial apoptosis pathway. PLoS One 2018; 13:e0198579. [PMID: 29912904 PMCID: PMC6005494 DOI: 10.1371/journal.pone.0198579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/22/2018] [Indexed: 11/18/2022] Open
Abstract
Understanding how gene alterations induce oncogenesis plays an important role in cancer research and may be instructive for cancer prevention and treatment. We conducted a parameter sensitivity analysis to the mitochondrial apoptosis model. Both a nonlinear bifurcation analysis of the deterministic dynamics and energy barrier analysis of the corresponding stochastic models were performed. We found that the parameter sensitivity ranking according to the change of the bifurcation-point locations in deterministic models and the change of the barrier heights from a living to death state of the cell in stochastic models are highly correlated. For the model we considered, in combination with previous knowledge that the parameters significantly affecting the system’s bifurcation point are strongly associated with frequently mutated oncogenic genes, we conclude that the energy barrier height can be used as indicator of oncogenesis as well as bifurcation point. We provide a possible mechanism that may help elucidate the logic of cancer initiation from the view of stochastic dynamics and energy landscape. And we show the equivalence of energy barrier height and bifurcation-point location in determining the parameter sensitivity spectrum for the first time.
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Affiliation(s)
- Xianli Chen
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Department of Physics, Peking University, Beijing, China
| | - Xiaoguang Li
- College of Mathematics and Compute Science, Hunan Normal University, Changsha, China
- Beijing Computational Science Research Center, Beijing, China
| | - Wei Zhao
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Tiejun Li
- LMAM and School of Mathematical Sciences, Peking University, Beijing, China
- * E-mail: (TL); (QO)
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Department of Physics, Peking University, Beijing, China
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- * E-mail: (TL); (QO)
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31
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Effects of Periostracum Cicadae on Cytokines and Apoptosis Regulatory Proteins in an IgA Nephropathy Rat Model. Int J Mol Sci 2018; 19:ijms19061599. [PMID: 29844269 PMCID: PMC6032130 DOI: 10.3390/ijms19061599] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/04/2018] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Periostracum cicadae, the cast-off shell of the cicada Cryptotympana pustulata Fabricius, is used in traditional Chinese medicine for its diaphoretic, anticonvulsive, sedative, antipyretic, and antiallergic effects. However, the exact pathogenesis of immunoglobulin A nephropathy (IgAN) remains unclear, thereby hindering investigations to identify novel therapeutic agents. A rat IgAN model was established by administration of bovine serum albumin, lipopolysaccharide, and carbon tetrachloride, which simultaneously established blood stasis and a heat syndrome model. The animals were sacrificed to detect changes in protein levels in urine and blood. Immunofluorescence was performed to assess IgA deposition in the glomeruli. Tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin 6 (IL-6) levels were measured in bronchoalveolar lavage fluid (BALF) by enzyme-linked immunosorbent assay. Hematology and eosin, periodic acid-Schiff, TUNEL (TdT-mediated dUTP Nick-End Labeling), and immunohistochemical staining were performed to evaluate histopathological changes in kidney tissues. Additionally, target-related proteins were measured by Western blotting. Periostracum cicadae resulted in a reduction in blood and urine protein levels. Serum TNF-α, IL-1β, and IL-6 levels significantly decreased in the periostracum cicadae-treated groups compared to the IgAN group. Furthermore, a reduction in MCP-1 (Monocyte Chemotactic Protein-1), TLR4 ((Toll-Like Receptor 4)), and IgA expression levels and a dose-dependent increase in caspase 3 expression were observed in response to periostracum cicadae treatment. TGF-β1(Transforming Growth Factor-β) levels decreased, whereas that of Fas increased in the kidney tissues of the periostracum cicadae-treated groups. The findings of the present study indicate that periostracum cicadae induces apoptosis and improves kidney inflammation and fibrosis in IgA nephropathy rat models.
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Pischel D, Buchbinder JH, Sundmacher K, Lavrik IN, Flassig RJ. A guide to automated apoptosis detection: How to make sense of imaging flow cytometry data. PLoS One 2018; 13:e0197208. [PMID: 29768460 PMCID: PMC5955558 DOI: 10.1371/journal.pone.0197208] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/27/2018] [Indexed: 11/24/2022] Open
Abstract
Imaging flow cytometry is a powerful experimental technique combining the strength of microscopy and flow cytometry to enable high-throughput characterization of cell populations on a detailed microscopic scale. This approach has an increasing importance for distinguishing between different cellular phenotypes such as proliferation, cell division and cell death. In the course of undergoing these different pathways, each cell is characterized by a high amount of properties. This makes it hard to filter the most relevant information for cell state discrimination. The traditional methods for cell state discrimination rely on dye based two-dimensional gating strategies ignoring information that is hidden in the high-dimensional property space. In order to make use of the information ignored by the traditional methods, we present a simple and efficient approach to distinguish biological states within a cell population based on machine learning techniques. We demonstrate the advantages and drawbacks of filter techniques combined with different classification schemes. These techniques are illustrated with two case studies of apoptosis detection in HeLa cells. Thereby we highlight (i) the aptitude of imaging flow cytometry regarding automated, label-free cell state discrimination and (ii) pitfalls that are frequently encountered. Additionally a MATLAB script is provided, which gives further insight regarding the computational work presented in this study.
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Affiliation(s)
- Dennis Pischel
- Process Systems Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Jörn H. Buchbinder
- Translational Inflammation Research, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Kai Sundmacher
- Process Systems Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Inna N. Lavrik
- Translational Inflammation Research, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Robert J. Flassig
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- * E-mail:
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Gates-Tanzer LT, Shisler JL. Cellular FLIP long isoform (cFLIP L)-IKKα interactions inhibit IRF7 activation, representing a new cellular strategy to inhibit IFNα expression. J Biol Chem 2018; 293:1745-1755. [PMID: 29222334 PMCID: PMC5798304 DOI: 10.1074/jbc.ra117.000541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/16/2017] [Indexed: 01/01/2023] Open
Abstract
Interferon α (IFNα) is important for antiviral and anticancer defenses. However, overproduction is associated with autoimmune disorders. Thus, the cell must precisely up- and down-regulate IFNα to achieve immune system homeostasis. The cellular FLICE-like inhibitory protein (cFLIP) is reported to inhibit IFNα production. However, the mechanism for this antagonism remained unknown. The goal here was to identify this mechanism. Here we examined the signal transduction events that occur during TLR9-induced IRF7 activation. The cFLIP long isoform (cFLIPL) inhibited the expression of IRF7-controlled natural or synthetic genes in several cell lines, including those with abundant IRF7 protein levels (e.g. dendritic cells). cFLIPL inhibited IRF7 phosphorylation; however, cFLIPL-IRF7 interactions were not detectable, implying that cFLIPL acted upstream of IRF7 dimerization. Interestingly, cFLIPL co-immunoprecipitated with IKKα, and these interactions correlated with a loss of IKKα-IRF7 interactions. Thus, cFLIP appears to bind to IKKα to prevent IKKα from phosphorylating and activating IRF7. To the best of our knowledge, this is the first report of a cellular protein that uses this approach to inhibit IRF7 activation. Perhaps this cFLIP property could be engineered to minimize the deleterious effects of IFNα expression that occur during certain autoimmune disorders.
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Affiliation(s)
| | - Joanna L Shisler
- From the Department of Microbiology, University of Illinois, Urbana, Illinois 61801
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34
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Synonymous mutations in oncogenesis and apoptosis versus survival unveiled by network modeling. Oncotarget 2017; 7:34599-616. [PMID: 27129147 PMCID: PMC5085179 DOI: 10.18632/oncotarget.8963] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/11/2016] [Indexed: 12/11/2022] Open
Abstract
Synonymous mutations, which do not alter the encoded amino acid, have been routinely assumed to be ‘neutral’ and would have no effect on phenotype or fitness. Yet increasing observations have emerged to overturn this conventional concept. However, convicted elucidation of how synonymous mutations exert biological consequences in oncogenesis is still lacking. By performing systematic analysis of the TNF-α signaling network model, we identify the critical dose which separates the cell survival and apoptosis regions and define the sensitive parameters with single-parameter sensitivity analysis. Combining with the cancer-related mutation spectra obtained from 9 cancers, our results hint that, similar as missense and nonsense mutations, synonymous mutations are also strongly correlated with the parameter sensitivity of the critical dose, providing possible causal mechanism of the mutations in cancer development. Based on such a correlation, we furthermore dissect that members of caspases family proteases (caspase3, 6, 8) could jointly inhibit NFκB activation, providing efficient pro-apoptotic behavior. Thus, we argue that apoptosis module could suppress survival module through negative feedback of caspases family on NFκB.
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35
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Wu Q, Finley SD. Predictive model identifies strategies to enhance TSP1-mediated apoptosis signaling. Cell Commun Signal 2017; 15:53. [PMID: 29258506 PMCID: PMC5735807 DOI: 10.1186/s12964-017-0207-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 12/07/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Thrombospondin-1 (TSP1) is a matricellular protein that functions to inhibit angiogenesis. An important pathway that contributes to this inhibitory effect is triggered by TSP1 binding to the CD36 receptor, inducing endothelial cell apoptosis. However, therapies that mimic this function have not demonstrated clear clinical efficacy. This study explores strategies to enhance TSP1-induced apoptosis in endothelial cells. In particular, we focus on establishing a computational model to describe the signaling pathway, and using this model to investigate the effects of several approaches to perturb the TSP1-CD36 signaling network. METHODS We constructed a molecularly-detailed mathematical model of TSP1-mediated intracellular signaling via the CD36 receptor based on literature evidence. We employed systems biology tools to train and validate the model and further expanded the model by accounting for the heterogeneity within the cell population. The initial concentrations of signaling species or kinetic rates were altered to simulate the effects of perturbations to the signaling network. RESULTS Model simulations predict the population-based response to strategies to enhance TSP1-mediated apoptosis, such as downregulating the apoptosis inhibitor XIAP and inhibiting phosphatase activity. The model also postulates a new mechanism of low dosage doxorubicin treatment in combination with TSP1 stimulation. Using computational analysis, we predict which cells will undergo apoptosis, based on the initial intracellular concentrations of particular signaling species. CONCLUSIONS This new mathematical model recapitulates the intracellular dynamics of the TSP1-induced apoptosis signaling pathway. Overall, the modeling framework predicts molecular strategies that increase TSP1-mediated apoptosis, which is useful in many disease settings.
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Affiliation(s)
- Qianhui Wu
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, USA
| | - Stacey D Finley
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, USA.
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, USA.
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36
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Pevonedistat, a Nedd8-activating enzyme inhibitor, sensitizes neoplastic B-cells to death receptor-mediated apoptosis. Oncotarget 2017; 8:21128-21139. [PMID: 28177892 PMCID: PMC5400571 DOI: 10.18632/oncotarget.15050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/07/2017] [Indexed: 12/14/2022] Open
Abstract
While death receptor ligands (Fas and TRAIL) kill chemoresistant tumor cell lines, related therapies have limited clinical efficacy as single agents. Death receptor signaling is modulated by nuclear factor-κB (NFκB), a family of transcription factors which are constitutively active in B-cell malignancies. We and others have shown that pevonedistat, an investigational inhibitor of the NEDD8-activating enzyme, abrogates NFκB activity in B-cell neoplasia. Here we demonstrate that diffuse large B-cell lymphoma, particularly activated B-cell type, and primary chronic lymphocytic leukemia cells are re-sensitized to extrinsic apoptosis by pevonedistat. Pevonedistat enhanced caspase-8 processing following death receptor ligation, and downmodulated cFLIP, a NFκB-regulated protease-deficient caspase homolog. However, treatment with pevonedistat did not modulate death-inducing signaling complex in neoplastic B-cells, suggesting that they were sensitized to death ligands through the mitochondrial pathway. Our data provide rationale for further development of pharmacologic agents including pevonedistat in strategies which enhance death receptor signaling in lymphoid malignancies.
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37
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Pietkiewicz S, Wolfe C, Buchbinder JH, Lavrik IN. Measuring Procaspase-8 and -10 Processing upon Apoptosis Induction. Bio Protoc 2017; 7:e2081. [PMID: 34458412 DOI: 10.21769/bioprotoc.2081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/07/2016] [Accepted: 12/06/2016] [Indexed: 11/02/2022] Open
Abstract
Apoptosis or programmed cell death is important for multicellular organisms to keep cell homeostasis and for the clearance of mutated or infected cells. Apoptosis can be induced by intrinsic or extrinsic stimuli. The first event in extrinsic apoptosis is the formation of the Death-Inducing Signalling Complex (DISC), where the initiator caspases-8 and -10 are fully activated by several proteolytic cleavage steps and induce the caspase cascade leading to apoptotic cell death. Analysing the processing of procaspases-8 and -10 by Western blot is a commonly used method to study the induction of apoptosis by death receptor stimulation. To analyse procaspase-8 and -10 cleavage, cells are stimulated with a death ligand for different time intervals, lysed and subjected to Western blot analysis using anti-caspase-8 and anti-caspase-10 antibodies. This allows monitoring the caspase cleavage products and thereby induction of apoptosis.
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Affiliation(s)
- Sabine Pietkiewicz
- Translational Inflammation Research, Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, Medical Faculty, Magdeburg, Germany.,Current address: Medical advisory service of social health insurance, Essen, Germany
| | - Clara Wolfe
- Translational Inflammation Research, Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, Medical Faculty, Magdeburg, Germany
| | - Jörn H Buchbinder
- Translational Inflammation Research, Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, Medical Faculty, Magdeburg, Germany
| | - Inna N Lavrik
- Translational Inflammation Research, Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, Medical Faculty, Magdeburg, Germany.,Federal research center Institute of Cytology and Genetics, Novosibirsk, Russia
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Zhang F, Liu R, Zheng J. Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation. BMC SYSTEMS BIOLOGY 2016; 10:123. [PMID: 28155685 PMCID: PMC5259907 DOI: 10.1186/s12918-016-0365-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Background Linking computational models of signaling pathways to predicted cellular responses such as gene expression regulation is a major challenge in computational systems biology. In this work, we present Sig2GRN, a Cytoscape plugin that is able to simulate time-course gene expression data given the user-defined external stimuli to the signaling pathways. Methods A generalized logical model is used in modeling the upstream signaling pathways. Then a Boolean model and a thermodynamics-based model are employed to predict the downstream changes in gene expression based on the simulated dynamics of transcription factors in signaling pathways. Results Our empirical case studies show that the simulation of Sig2GRN can predict changes in gene expression patterns induced by DNA damage signals and drug treatments. Conclusions As a software tool for modeling cellular dynamics, Sig2GRN can facilitate studies in systems biology by hypotheses generation and wet-lab experimental design. Availability: http://histone.scse.ntu.edu.sg/Sig2GRN/
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Affiliation(s)
- Fan Zhang
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Runsheng Liu
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Jie Zheng
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore. .,Complexity Institute, Nanyang Technological University, Singapore, 637723, Singapore. .,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore.
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Wang X, Fu Z, Chen Y, Liu L. Fas expression is downregulated in gastric cancer. Mol Med Rep 2016; 15:627-634. [PMID: 28000850 PMCID: PMC5364875 DOI: 10.3892/mmr.2016.6037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 11/10/2016] [Indexed: 01/09/2023] Open
Abstract
The aim of the present study was to investigate Fas expression in tumor samples from patients with gastric cancer, in order to determine the involvement of the Fas signaling pathway. The protein expression levels of Fas, caspase-8, caspase-3 and poly (adenosine diphosphate-ribose) polymerase 1 (PARP1) were examined in gastric cancer specimens and their associations with clinical pathological parameters were analyzed with immunohistochemical staining and western blot analysis. The mRNA expression was quantified with quantitative PCR and apoptosis was examined with a FACScan flow cytometer. The results demonstrated that the downregulation of Fas expression was correlated with less histological differentiation, gender (male), and increased lymph node and distant metastases (P<0.05). In the AGS established gastric cancer cell line, upregulation of the Fas signaling pathway promoted the apoptosis of gastric cancer cells by upregulating the expression of caspase-8 and caspase-3, and downregulating the expression of PARP1. The present study demonstrated that Fas was associated with gastric cancer and promoted the apoptosis of gastric cancer cells via caspase-8, caspase-3 and PARP1. These results suggested that caspase-8, caspase-3 and PARP1 may be triggers of gastric cancer, and upregulation of caspase-8 and caspase-3 expression, or inhibition of PARP1 expression may improve the therapeutic outcome in patients with gastric cancer.
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Affiliation(s)
- Xuming Wang
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, Hubei 430056, P.R. China
| | - Zhengqi Fu
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, Hubei 430056, P.R. China
| | - Ying Chen
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, Hubei 430056, P.R. China
| | - Lijiang Liu
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, Hubei 430056, P.R. China
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Kondofersky I, Theis FJ, Fuchs C. Inferring catalysis in biological systems. IET Syst Biol 2016; 10:210-218. [PMID: 27879475 PMCID: PMC8687166 DOI: 10.1049/iet-syb.2015.0087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/24/2016] [Accepted: 04/06/2016] [Indexed: 09/22/2023] Open
Abstract
In systems biology, one is often interested in the communication patterns between several species, such as genes, enzymes or proteins. These patterns become more recognisable when temporal experiments are performed. This temporal communication can be structured by reaction networks such as gene regulatory networks or signalling pathways. Mathematical modelling of data arising from such networks can reveal important details, thus helping to understand the studied system. In many cases, however, corresponding models still deviate from the observed data. This may be due to unknown but present catalytic reactions. From a modelling perspective, the question of whether a certain reaction is catalysed leads to a large increase of model candidates. For large networks the calibration of all possible models becomes computationally infeasible. We propose a method which determines a substantially reduced set of appropriate model candidates and identifies the catalyst of each reaction at the same time. This is incorporated in a multiple-step procedure which first extends the network by additional latent variables and subsequently identifies catalyst candidates using similarity analysis methods. Results from synthetic data examples suggest a good performance even for non-informative data with few observations. Applied on CD95 apoptotic pathway our method provides new insights into apoptosis regulation.
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Affiliation(s)
- Ivan Kondofersky
- Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Boltzmannstr. 3, 85748 Garching, Germany
| | - Fabian J Theis
- Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Boltzmannstr. 3, 85748 Garching, Germany
| | - Christiane Fuchs
- Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Boltzmannstr. 3, 85748 Garching, Germany.
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41
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Peng H, Zhao W, Tan H, Ji Z, Li J, Li K, Zhou X. Prediction of treatment efficacy for prostate cancer using a mathematical model. Sci Rep 2016; 6:21599. [PMID: 26868634 PMCID: PMC4751505 DOI: 10.1038/srep21599] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/27/2016] [Indexed: 12/23/2022] Open
Abstract
Prostate immune system plays a critical role in the regulation of prostate cancer development regarding androgen-deprivation therapy (ADT) and/or immunotherapy (vaccination). In this study, we developed a mathematical model to explore the interactions between prostate tumor and immune microenvironment. This model was used to predict treatment outcomes for prostate cancer with ADT, vaccination, Treg depletion and/or IL-2 neutralization. Animal data were used to guide construction, parameter selection, and validation of our model. Our analysis shows that Treg depletion and/or IL-2 neutralization can effectively improve the treatment efficacy of combined therapy with ADT and vaccination. Treg depletion has a higher synergetic effect than that from IL-2 neutralization. This study highlights a potential therapeutic strategy in effectively managing prostate tumor growth and provides a framework of systems biology approach in studying tumor-related immune mechanism and consequent selection of therapeutic regimens.
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Affiliation(s)
- Huiming Peng
- Division of Radiologic Sciences – Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Weiling Zhao
- Division of Radiologic Sciences – Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Hua Tan
- Division of Radiologic Sciences – Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Zhiwei Ji
- Division of Radiologic Sciences – Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Jingsong Li
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - King Li
- Division of Radiologic Sciences – Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Xiaobo Zhou
- Division of Radiologic Sciences – Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
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Baratchian M, Davis CA, Shimizu A, Escors D, Bagnéris C, Barrett T, Collins MK. Distinct Activation Mechanisms of NF-κB Regulator Inhibitor of NF-κB Kinase (IKK) by Isoforms of the Cell Death Regulator Cellular FLICE-like Inhibitory Protein (cFLIP). J Biol Chem 2016; 291:7608-20. [PMID: 26865630 PMCID: PMC4817188 DOI: 10.1074/jbc.m116.718122] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 11/06/2022] Open
Abstract
The viral FLICE-like inhibitory protein (FLIP) protein from Kaposi sarcoma-associated herpesvirus activates the NF-κB pathway by forming a stable complex with a central region (amino acids 150-272) of the inhibitor of NF-κB kinase (IKK) γ subunits, thereby activating IKK. Cellular FLIP (cFLIP) forms are also known to activate the NF-κB pathway via IKK activation. Here we demonstrate that cFLIPL, cFLIPS, and their proteolytic product p22-FLIP all require the C-terminal region of NEMO/IKKγ (amino acids 272-419) and its ubiquitin binding function for activation of the IKK kinase (or kinase complex), but none form a stable complex with IKKγ. Our results further reveal that cFLIPLrequires the linear ubiquitin chain assembly complex and the kinase TAK1 for activation of the IKK kinase. Similarly, cFLIPSand p22-FLIP also require TAK1 but do not require LUBAC. In contrast, these isoforms are both components of complexes that incorporate Fas-associated death domain and RIP1, which appear essential for kinase activation. This conservation of IKK activation among the cFLIP family using different mechanisms suggests that the mechanism plays a critical role in their function.
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Affiliation(s)
- Mehdi Baratchian
- From the Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom, Division of Advanced Therapies, National Institute of Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3QG, United Kingdom, and
| | - Christopher A Davis
- From the Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Akira Shimizu
- From the Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - David Escors
- From the Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Claire Bagnéris
- Institute of Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
| | - Tracey Barrett
- Institute of Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
| | - Mary K Collins
- From the Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom, Division of Advanced Therapies, National Institute of Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3QG, United Kingdom, and
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Balance between short and long isoforms of cFLIP regulates Fas-mediated apoptosis in vivo. Proc Natl Acad Sci U S A 2016; 113:1606-11. [PMID: 26798068 DOI: 10.1073/pnas.1517562113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
cFLIP, an inhibitor of apoptosis, is a crucial regulator of cellular death by apoptosis and necroptosis; its importance in development is exemplified by the embryonic lethality in cFLIP-deficient animals. A homolog of caspase 8 (CASP8), cFLIP exists in two main isoforms: cFLIPL (long) and cFLIPR (short). Although both splice variants regulate death receptor (DR)-induced apoptosis by CASP8, the specific role of each isoform is poorly understood. Here, we report a previously unidentified model of resistance to Fas receptor-mediated liver failure in the wild-derived MSM strain, compared with susceptibility in C57BL/6 (B6) mice. Linkage analysis in F2 intercross (B6 x MSM) progeny identified several MSM loci controlling resistance to Fas-mediated death, including the caspase 8- and FADD-like apoptosis regulator (Cflar) locus encoding cFLIP. Furthermore, we identified a 21-bp insertion in the 3' UTR of the fifth exon of Cflar in MSM that influences differential splicing of cFLIP mRNA. Intriguingly, we observed that MSM liver cells predominantly express the FLIPL variant, in contrast to B6 liver cells, which have higher levels of cFLIPR. In keeping with this finding, genome-wide RNA sequencing revealed a relative abundance of FLIPL transcripts in MSM hepatocytes whereas B6 liver cells had significantly more FLIPR mRNA. Importantly, we show that, in the MSM liver, CASP8 is present exclusively as its cleaved p43 product, bound to cFLIPL. Because of partial enzymatic activity of the heterodimer, it might prevent necroptosis. On the other hand, it prevents cleavage of CASP8 to p10/20 necessary for cleavage of caspase 3 and, thus, apoptosis induction. Therefore, MSM hepatocytes are predisposed for protection from DR-mediated cell death.
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Zhang F, Chen H, Zhao LN, Liu H, Przytycka TM, Zheng J. Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways. BMC SYSTEMS BIOLOGY 2016; 10 Suppl 1:7. [PMID: 26818802 PMCID: PMC4895646 DOI: 10.1186/s12918-015-0249-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Cellular responses to extracellular perturbations require signaling pathways to capture and transmit the signals. However, the underlying molecular mechanisms of signal transduction are not yet fully understood, thus detailed and comprehensive models may not be available for all the signaling pathways. In particular, insufficient knowledge of parameters, which is a long-standing hindrance for quantitative kinetic modeling necessitates the use of parameter-free methods for modeling and simulation to capture dynamic properties of signaling pathways. Results We present a computational model that is able to simulate the graded responses to degradations, the sigmoidal biological relationships between signaling molecules and the effects of scheduled perturbations to the cells. The simulation results are validated using experimental data of protein phosphorylation, demonstrating that the proposed model is capable of capturing the main trend of protein activities during the process of signal transduction. Compared with existing simulators, our model has better performance on predicting the state transitions of signaling networks. Conclusion The proposed simulation tool provides a valuable resource for modeling cellular signaling pathways using a knowledge-based method.
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Affiliation(s)
- Fan Zhang
- Biomedical Informatics Graduate Lab, School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Haoting Chen
- Biomedical Informatics Graduate Lab, School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore. .,Department of Industrial Engineering and Operations Research, Columbia University, New York, NY 10027, USA.
| | - Li Na Zhao
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore 138671, Singapore.
| | - Hui Liu
- Biomedical Informatics Graduate Lab, School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore. .,Lab of Information Management, Changzhou University, Changzhou, Jiangsu 213164, China.
| | - Teresa M Przytycka
- National Center for Biotechnology Information, NLM/NIH, Bethesda, MD 20894, USA.
| | - Jie Zheng
- Biomedical Informatics Graduate Lab, School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore. .,Complexity Institute, Nanyang Technological University, Singapore 637723, Singapore. .,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore.
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Tsuchiya Y, Nakabayashi O, Nakano H. FLIP the Switch: Regulation of Apoptosis and Necroptosis by cFLIP. Int J Mol Sci 2015; 16:30321-41. [PMID: 26694384 PMCID: PMC4691174 DOI: 10.3390/ijms161226232] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/09/2015] [Accepted: 12/11/2015] [Indexed: 12/11/2022] Open
Abstract
cFLIP (cellular FLICE-like inhibitory protein) is structurally related to caspase-8 but lacks proteolytic activity due to multiple amino acid substitutions of catalytically important residues. cFLIP protein is evolutionarily conserved and expressed as three functionally different isoforms in humans (cFLIPL, cFLIPS, and cFLIPR). cFLIP controls not only the classical death receptor-mediated extrinsic apoptosis pathway, but also the non-conventional pattern recognition receptor-dependent apoptotic pathway. In addition, cFLIP regulates the formation of the death receptor-independent apoptotic platform named the ripoptosome. Moreover, recent studies have revealed that cFLIP is also involved in a non-apoptotic cell death pathway known as programmed necrosis or necroptosis. These functions of cFLIP are strictly controlled in an isoform-, concentration- and tissue-specific manner, and the ubiquitin-proteasome system plays an important role in regulating the stability of cFLIP. In this review, we summarize the current scientific findings from biochemical analyses, cell biological studies, mathematical modeling, and gene-manipulated mice models to illustrate the critical role of cFLIP as a switch to determine the destiny of cells among survival, apoptosis, and necroptosis.
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Affiliation(s)
- Yuichi Tsuchiya
- Department of Biochemistry, Toho University School of Medicine, Tokyo 143-8540, Japan.
| | - Osamu Nakabayashi
- Department of Biochemistry, Toho University School of Medicine, Tokyo 143-8540, Japan.
| | - Hiroyasu Nakano
- Department of Biochemistry, Toho University School of Medicine, Tokyo 143-8540, Japan.
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Partial equilibrium approximations in apoptosis. II. The death-inducing signaling complex subsystem. Math Biosci 2015; 270:126-34. [DOI: 10.1016/j.mbs.2015.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 10/01/2015] [Accepted: 10/16/2015] [Indexed: 12/28/2022]
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Leng HJ, Peng F, Zingales S, Huang W, Wang B, Zhao Q, Zhou R, He G, Peng C, Han B. Core-Scaffold-Inspired Asymmetric Synthesis of Polysubstituted Chiral Hexahydropyridazines that Potently Inhibit Breast Cancer Cell Proliferation by Inducing Apoptosis. Chemistry 2015; 21:18100-8. [PMID: 26498568 DOI: 10.1002/chem.201503063] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Indexed: 02/05/2023]
Abstract
The highly enantioselective preparation of pharmacologically interesting hexahydropyridazine derivatives based on a multicomponent cascade reaction is described. This one-pot approach utilizes an organocatalytic Michael reaction followed by intermolecular α-amination and intramolecular hemiaminalization to yield a chiral pyridazine backbone with contiguous stereogenic centers and multiple functional groups in good yield and with high stereoselectivity. Compounds synthesized by this method potently inhibited proliferation of MCF-7 breast cancer cells. Mechanistic studies suggest that compound 5 c exerts these anticancer effects by inducing apoptosis through extracellular signal related kinase (ERK)- and poly(adenosine diphosphate ribose) polymerase (PARP)-regulated pathways, as well as mitochondrial pathways.
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Affiliation(s)
- Hai-Jun Leng
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 (P.R. China)
| | - Fu Peng
- School of Chinese Medicine, University of Hong Kong, Hong Kong (P.R. China)
| | - Sarah Zingales
- Department of Chemistry, Armstrong State University, Savannah, GA (USA)
| | - Wei Huang
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 (P.R. China)
| | - Biao Wang
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 (P.R. China)
| | - Qian Zhao
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 (P.R. China)
| | - Rui Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041 (P.R. China)
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041 (P.R. China).
| | - Cheng Peng
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 (P.R. China).
| | - Bo Han
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 (P.R. China).
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Molecular architecture of the DED chains at the DISC: regulation of procaspase-8 activation by short DED proteins c-FLIP and procaspase-8 prodomain. Cell Death Differ 2015; 23:681-94. [PMID: 26494467 DOI: 10.1038/cdd.2015.137] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/30/2015] [Accepted: 08/03/2015] [Indexed: 12/17/2022] Open
Abstract
The CD95/Fas/APO-1 death-inducing signaling complex (DISC), comprising CD95, FADD, procaspase-8, procaspase-10, and c-FLIP, has a key role in apoptosis induction. Recently, it was demonstrated that procaspase-8 activation is driven by death effector domain (DED) chains at the DISC. Here, we analyzed the molecular architecture of the chains and the role of the short DED proteins in regulating procaspase-8 activation in the chain model. We demonstrate that the DED chains are largely composed of procaspase-8 cleavage products and, in particular, of its prodomain. The DED chain also comprises c-FLIP and procaspase-10 that are present in 10 times lower amounts compared with procaspase-8. We show that short c-FLIP isoforms can inhibit CD95-induced cell death upon overexpression, likely by forming inactive heterodimers with procaspase-8. Furthermore, we have addressed mechanisms of the termination of chain elongation using experimental and mathematical modeling approaches. We show that neither c-FLIP nor procaspase-8 prodomain terminates the DED chain, but rather the dissociation/association rates of procaspase-8 define the stability of the chain and thereby its length. In addition, we provide evidence that procaspase-8 prodomain generated at the DISC constitutes a negative feedback loop in procaspase-8 activation. Overall, these findings provide new insights into caspase-8 activation in DED chains and apoptosis initiation.
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Popik OV, Petrovskiy ED, Mishchenko EL, Lavrik IN, Ivanisenko VA. Mosaic gene network modelling identified new regulatory mechanisms in HCV infection. Virus Res 2015; 218:71-8. [PMID: 26481968 DOI: 10.1016/j.virusres.2015.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 09/25/2015] [Accepted: 10/02/2015] [Indexed: 10/22/2022]
Abstract
Modelling of gene networks is widely used in systems biology to study the functioning of complex biological systems. Most of the existing mathematical modelling techniques are useful for analysis of well-studied biological processes, for which information on rates of reactions is available. However, complex biological processes such as those determining the phenotypic traits of organisms or pathological disease processes, including pathogen-host interactions, involve complicated cross-talk between interacting networks. Furthermore, the intrinsic details of the interactions between these networks are often missing. In this study, we developed an approach, which we call mosaic network modelling, that allows the combination of independent mathematical models of gene regulatory networks and, thereby, description of complex biological systems. The advantage of this approach is that it allows us to generate the integrated model despite the fact that information on molecular interactions between parts of the model (so-called mosaic fragments) might be missing. To generate a mosaic mathematical model, we used control theory and mathematical models, written in the form of a system of ordinary differential equations (ODEs). In the present study, we investigated the efficiency of this method in modelling the dynamics of more than 10,000 simulated mosaic regulatory networks consisting of two pieces. Analysis revealed that this approach was highly efficient, as the mean deviation of the dynamics of mosaic network elements from the behaviour of the initial parts of the model was less than 10%. It turned out that for construction of the control functional, data on perturbation of one or two vertices of the mosaic piece are sufficient. Further, we used the developed method to construct a mosaic gene regulatory network including hepatitis C virus (HCV) as the first piece and the tumour necrosis factor (TNF)-induced apoptosis and NF-κB induction pathways as the second piece. Thus, the mosaic model integrates the model of HCV subgenomic replicon replication with the model of TNF-induced apoptosis and NF-κB induction. Analysis of the mosaic model revealed that the regulation of TNF-induced signaling by the HCV network is crucially dependent on the RIP1, TRADD, TRAF2, FADD, IKK, IκBα, c-FLIP, and BAR genes. Overall, the developed mosaic gene network modelling approach demonstrated good predictive power and allowed the prediction of new regulatory nodes in HCV action on apoptosis and the NF-κB pathway. Those theoretical predictions could be a basis for further experimental verification.
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Affiliation(s)
- Olga V Popik
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Evgeny D Petrovskiy
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia; International Tomography Center SB RAS, Institutskaya 3A, Novosibirsk 630090, Russia
| | - Elena L Mishchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Inna N Lavrik
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia; Otto von Guericke University Magdeburg, Medical Faculty, Department Translational Inflammation Research, Pfälzer Platz Building 28, Magdeburg 39106, Germany
| | - Vladimir A Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia; PB-soft, LLC, Novosibirsk, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia.
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