1
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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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2
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Gama AR, Miller T, Venkatesan S, Lange JJ, Wu J, Song X, Bradford D, Unruh JR, Halfmann R. Protein supersaturation powers innate immune signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.20.533581. [PMID: 36993308 PMCID: PMC10055258 DOI: 10.1101/2023.03.20.533581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Innate immunity protects us in youth but turns against us as we age. The reason for this tradeoff is unclear. Seeking a thermodynamic basis, we focused on death fold domains (DFDs), whose ordered polymerization has been stoichiometrically linked to innate immune signal amplification. We hypothesized that soluble ensembles of DFDs function as phase change batteries that store energy via supersaturation and subsequently release it through nucleated polymerization. Using imaging and FRET-based cytometry to characterize the phase behaviors of all 109 human DFDs, we found that the hubs of innate immune signaling networks encode large nucleation barriers that are intrinsically insulated from cross-pathway activation. We showed via optogenetics that supersaturation drives signal amplification and that the inflammasome is constitutively supersaturated in vivo. Our findings reveal that the soluble "inactive" states of adaptor DFDs function as essential, yet impermanent, kinetic barriers to inflammatory cell death, suggesting a thermodynamic driving force for aging.
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Affiliation(s)
| | - Tayla Miller
- Stowers Institute for Medical Research, Kansas City, MO
| | | | | | - Jianzheng Wu
- Stowers Institute for Medical Research, Kansas City, MO
| | - Xiaoqing Song
- Stowers Institute for Medical Research, Kansas City, MO
| | - Dan Bradford
- Stowers Institute for Medical Research, Kansas City, MO
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, MO
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
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3
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Sherekar S, Todankar CS, Viswanathan GA. Modulating the dynamics of NFκB and PI3K enhances the ensemble-level TNFR1 signaling mediated apoptotic response. NPJ Syst Biol Appl 2023; 9:57. [PMID: 37973854 PMCID: PMC10654705 DOI: 10.1038/s41540-023-00318-0] [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: 04/26/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Cell-to-cell variability during TNFα stimulated Tumor Necrosis Factor Receptor 1 (TNFR1) signaling can lead to single-cell level pro-survival and apoptotic responses. This variability stems from the heterogeneity in signal flow through intracellular signaling entities that regulate the balance between these two phenotypes. Using systematic Boolean dynamic modeling of a TNFR1 signaling network, we demonstrate that the signal flow path variability can be modulated to enable cells favour apoptosis. We developed a computationally efficient approach "Boolean Modeling based Prediction of Steady-state probability of Phenotype Reachability (BM-ProSPR)" to accurately predict the network's ability to settle into different phenotypes. Model analysis juxtaposed with the experimental observations revealed that NFκB and PI3K transient responses guide the XIAP behaviour to coordinate the crucial dynamic cross-talk between the pro-survival and apoptotic arms at the single-cell level. Model predicted the experimental observations that ~31% apoptosis increase can be achieved by arresting Comp1 - IKK* activity which regulates the NFκB and PI3K dynamics. Arresting Comp1 - IKK* activity causes signal flow path re-wiring towards apoptosis without significantly compromising NFκB levels, which govern adequate cell survival. Priming an ensemble of cancerous cells with inhibitors targeting the specific interaction involving Comp1 and IKK* prior to TNFα exposure could enable driving them towards apoptosis.
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Affiliation(s)
- Shubhank Sherekar
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Chaitra S Todankar
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Ganesh A Viswanathan
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India.
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4
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Moldovan C, Onaciu A, Toma V, Munteanu RA, Gulei D, Moldovan AI, Stiufiuc GF, Feder RI, Cenariu D, Iuga CA, Stiufiuc RI. Current trends in luminescence-based assessment of apoptosis. RSC Adv 2023; 13:31641-31658. [PMID: 37908656 PMCID: PMC10613953 DOI: 10.1039/d3ra05809c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
Apoptosis, the most extensively studied type of cell death, is known to play a crucial role in numerous processes such as elimination of unwanted cells or cellular debris, growth, control of the immune system, and prevention of malignancies. Defective regulation of apoptosis can trigger various diseases and disorders including cancer, neurological conditions, autoimmune diseases and developmental disorders. Knowing the nuances of the cell death type induced by a compound can help decipher which therapy is more effective for specific diseases. The detection of apoptotic cells using classic methods has brought significant contribution over the years, but innovative methods are quickly emerging and allow more in-depth understanding of the mechanisms, aside from a simple quantification. Due to increased sensitivity, time efficiency, pathway specificity and negligible cytotoxicity, these innovative approaches have great potential for both in vitro and in vivo studies. This review aims to shed light on the importance of developing and using novel nanoscale methods as an alternative to the classic apoptosis detection techniques.
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Affiliation(s)
- Cristian Moldovan
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
- Department of Pharmaceutical Physics & Biophysics, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy Louis Pasteur Street No. 4-6 400349 Cluj-Napoca Romania
| | - Anca Onaciu
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Valentin Toma
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Raluca A Munteanu
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Diana Gulei
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Alin I Moldovan
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Gabriela F Stiufiuc
- Faculty of Physics, "Babes Bolyai" University Mihail Kogalniceanu Street No. 1 400084 Cluj-Napoca Romania
| | - Richard I Feder
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Diana Cenariu
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Cristina A Iuga
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
- Pharmaceutical Analysis, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy Louis Pasteur Street 6 Cluj-Napoca 400349 Romania
| | - Rares I Stiufiuc
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
- Department of Pharmaceutical Physics & Biophysics, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy Louis Pasteur Street No. 4-6 400349 Cluj-Napoca Romania
- TRANSCEND Research Center, Regional Institute of Oncology 700483 Iasi Romania
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5
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Sarma U, Ripka L, Anyaegbunam UA, Legewie S. Modeling Cellular Signaling Variability Based on Single-Cell Data: The TGFβ-SMAD Signaling Pathway. Methods Mol Biol 2023; 2634:215-251. [PMID: 37074581 DOI: 10.1007/978-1-0716-3008-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Nongenetic heterogeneity is key to cellular decisions, as even genetically identical cells respond in very different ways to the same external stimulus, e.g., during cell differentiation or therapeutic treatment of disease. Strong heterogeneity is typically already observed at the level of signaling pathways that are the first sensors of external inputs and transmit information to the nucleus where decisions are made. Since heterogeneity arises from random fluctuations of cellular components, mathematical models are required to fully describe the phenomenon and to understand the dynamics of heterogeneous cell populations. Here, we review the experimental and theoretical literature on cellular signaling heterogeneity, with special focus on the TGFβ/SMAD signaling pathway.
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Affiliation(s)
- Uddipan Sarma
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Lorenz Ripka
- Institute of Molecular Biology (IMB), Mainz, Germany
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Uchenna Alex Anyaegbunam
- Institute of Molecular Biology (IMB), Mainz, Germany
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), Mainz, Germany.
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, Stuttgart, Germany.
- Stuttgart Research Center for Systems Biology, University of Stuttgart, Stuttgart, Germany.
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6
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Biswas S, Tikader B, Kar S, Viswanathan GA. Modulation of signaling cross-talk between pJNK and pAKT generates optimal apoptotic response. PLoS Comput Biol 2022; 18:e1010626. [PMID: 36240239 PMCID: PMC9604984 DOI: 10.1371/journal.pcbi.1010626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/26/2022] [Accepted: 10/03/2022] [Indexed: 01/25/2023] Open
Abstract
Tumor necrosis factor alpha (TNFα) is a well-known modulator of apoptosis by maintaining a balance between proliferation and cell-death in normal cells. Cancer cells often evade apoptotic response following TNFα stimulation by altering signaling cross-talks. Thus, varying the extent of signaling cross-talk could enable optimal TNFα mediated apoptotic dynamics. Herein, we use an experimental data-driven mathematical modeling to quantitate the extent of synergistic signaling cross-talk between the intracellular entities phosphorylated JNK (pJNK) and phosphorylated AKT (pAKT) that orchestrate the phenotypic apoptosis level by modulating the activated Caspase3 dynamics. Our study reveals that this modulation is orchestrated by the distinct dynamic nature of the synergism at early and late phases. We show that this synergism in signal flow is governed by branches originating from either TNFα receptor and NFκB, which facilitates signaling through survival pathways. We demonstrate that the experimentally quantified apoptosis levels semi-quantitatively correlates with the model simulated Caspase3 transients. Interestingly, perturbing pJNK and pAKT transient dynamics fine-tunes this accumulated Caspase3 guided apoptotic response. Thus, our study offers useful insights for identifying potential targeted therapies for optimal apoptotic response.
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Affiliation(s)
- Sharmila Biswas
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Baishakhi Tikader
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Sandip Kar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
- * E-mail: (SK); (GAV)
| | - Ganesh A. Viswanathan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
- * E-mail: (SK); (GAV)
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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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Seyrek K, Ivanisenko NV, Wohlfromm F, Espe J, Lavrik IN. Impact of human CD95 mutations on cell death and autoimmunity: a model. Trends Immunol 2021; 43:22-40. [PMID: 34872845 DOI: 10.1016/j.it.2021.11.006] [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: 09/02/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 01/06/2023]
Abstract
CD95/Fas/APO-1 can trigger apoptotic as well as nonapoptotic pathways in immune cells. CD95 signaling in humans can be inhibited by several mechanisms, including mutations in the gene encoding CD95. CD95 mutations lead to autoimmune disorders, such as autoimmune lymphoproliferative syndrome (ALPS). Gaining further insight into the reported mutations of CD95 and resulting alterations of its signaling networks may provide further understanding of their presumed role in certain autoimmune diseases. For illustrative purposes and to better understand the potential outcomes of CD95 mutations, here we assign their positions to the recently determined 3D structures of human CD95. Based on this, we make certain predictions and speculate on the putative role of CD95 mutation defects in CD95-mediated signaling for certain autoimmune diseases.
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Affiliation(s)
- Kamil Seyrek
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Nikita V Ivanisenko
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany; The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; Artificial Intelligence Research Institute, Moscow, Russia
| | - Fabian Wohlfromm
- 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
| | - Inna N Lavrik
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany; The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
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9
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Chen X, Zeh HJ, Kang R, Kroemer G, Tang D. Cell death in pancreatic cancer: from pathogenesis to therapy. Nat Rev Gastroenterol Hepatol 2021; 18:804-823. [PMID: 34331036 DOI: 10.1038/s41575-021-00486-6] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
Abstract
Pancreatic cancer is a devastating gastrointestinal cancer characterized by late diagnosis, limited treatment success and dismal prognosis. Exocrine tumours account for 95% of pancreatic cancers and the most common pathological type is pancreatic ductal adenocarcinoma (PDAC). The occurrence and progression of PDAC involve multiple factors, including internal genetic alterations and external inflammatory stimuli. The biology and therapeutic response of PDAC are further shaped by various forms of regulated cell death, such as apoptosis, necroptosis, ferroptosis, pyroptosis and alkaliptosis. Cell death induced by local or systemic treatments suppresses tumour proliferation, invasion and metastasis. However, unrestricted cell death or tissue damage might result in an inflammation-related immunosuppressive microenvironment, which is conducive to tumour progression or recurrence. The precise extent to which cell death affects PDAC is not yet well described. A growing body of preclinical and clinical studies document significant correlations between mutations (for example, in KRAS and TP53), stress responses (such as hypoxia and autophagy), metabolic reprogramming and chemotherapeutic responses. Here, we describe the molecular machinery of cell death, discuss the complexity and multifaceted nature of lethal signalling in PDAC cells, and highlight the challenges and opportunities for activating cell death pathways through precision oncology treatments.
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Affiliation(s)
- Xin Chen
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, The Third Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China.,Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.,Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Herbert J Zeh
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France. .,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France. .,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France. .,Suzhou Institute for Systems Biology, Chinese Academy of Sciences, Suzhou, China. .,Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
| | - Daolin Tang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, The Third Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China. .,Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA.
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10
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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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11
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Maccari ME, Fuchs S, Kury P, Andrieux G, Völkl S, Bengsch B, Lorenz MR, Heeg M, Rohr J, Jägle S, Castro CN, Groß M, Warthorst U, König C, Fuchs I, Speckmann C, Thalhammer J, Kapp FG, Seidel MG, Dückers G, Schönberger S, Schütz C, Führer M, Kobbe R, Holzinger D, Klemann C, Smisek P, Owens S, Horneff G, Kolb R, Naumann-Bartsch N, Miano M, Staniek J, Rizzi M, Kalina T, Schneider P, Erxleben A, Backofen R, Ekici A, Niemeyer CM, Warnatz K, Grimbacher B, Eibel H, Mackensen A, Frei AP, Schwarz K, Boerries M, Ehl S, Rensing-Ehl A. A distinct CD38+CD45RA+ population of CD4+, CD8+, and double-negative T cells is controlled by FAS. J Exp Med 2021; 218:211525. [PMID: 33170215 PMCID: PMC7658692 DOI: 10.1084/jem.20192191] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 08/06/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
The identification and characterization of rare immune cell populations in humans can be facilitated by their growth advantage in the context of specific genetic diseases. Here, we use autoimmune lymphoproliferative syndrome to identify a population of FAS-controlled TCRαβ+ T cells. They include CD4+, CD8+, and double-negative T cells and can be defined by a CD38+CD45RA+T-BET− expression pattern. These unconventional T cells are present in healthy individuals, are generated before birth, are enriched in lymphoid tissue, and do not expand during acute viral infection. They are characterized by a unique molecular signature that is unambiguously different from other known T cell differentiation subsets and independent of CD4 or CD8 expression. Functionally, FAS-controlled T cells represent highly proliferative, noncytotoxic T cells with an IL-10 cytokine bias. Mechanistically, regulation of this physiological population is mediated by FAS and CTLA4 signaling, and its survival is enhanced by mTOR and STAT3 signals. Genetic alterations in these pathways result in expansion of FAS-controlled T cells, which can cause significant lymphoproliferative disease.
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Affiliation(s)
- Maria Elena Maccari
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Fuchs
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Patrick Kury
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium, Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Simon Völkl
- Department of Internal Medicine 5-Hematology/Oncology, University of Erlangen, Erlangen, Germany
| | - Bertram Bengsch
- Department of Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Integrative Biological Signaling Studies, Albert-Ludwigs University, Freiburg, Germany.,Bioss Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Myriam Ricarda Lorenz
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany.,Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg-Hessen, Ulm, Germany
| | - Maximilian Heeg
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jan Rohr
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sabine Jägle
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carla N Castro
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miriam Groß
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ursula Warthorst
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph König
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ilka Fuchs
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carsten Speckmann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julian Thalhammer
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Friedrich G Kapp
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Markus G Seidel
- Division of Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University Graz, Graz, Austria
| | - Gregor Dückers
- Helios Kliniken Krefeld, Children's Hospital, Krefeld, Germany
| | - Stefan Schönberger
- University of Bonn, Department of Paediatric Haematology and Oncology, University Children's Hospital Bonn, Germany
| | - Catharina Schütz
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Marita Führer
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany.,Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg-Hessen, Ulm, Germany
| | - Robin Kobbe
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dirk Holzinger
- Department of Pediatric Hematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Christian Klemann
- Department of Pediatric Pulmonology, Allergy and Neonatology, Hannover Medical School, Hannover, Germany
| | - Petr Smisek
- Department of Pediatric Hematology and Oncology, University Hospital Motol and Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Stephen Owens
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
| | - Gerd Horneff
- Department of General Paediatrics, Clinic Sankt Augustin, Sankt Augustin, Germany.,Department of Pediatric and Adolescent Medicine, University Hospital of Cologne, Cologne, Germany
| | - Reinhard Kolb
- Department of General Paediatrics, Clinic Oldenburg, Oldenburg, Germany
| | - Nora Naumann-Bartsch
- Department of Pediatrics, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Maurizio Miano
- Haematology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Istituto Giannina Gaslini, Genoa, Italy
| | - Julian Staniek
- Faculty of Biology, University of Freiburg, Freiburg, Germany.,Department of Rheumatology and Clinical Immunology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marta Rizzi
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Rheumatology and Clinical Immunology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tomas Kalina
- Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, Second Medical School, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Pascal Schneider
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Anika Erxleben
- Bioinformatics, Institute for Computer Science, Faculty of Engineering, University of Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics, Institute for Computer Science, Faculty of Engineering, University of Freiburg, Germany
| | - Arif Ekici
- Institute of Human Genetics, University of Erlangen, Erlangen, Germany
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus Warnatz
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Integrative Biological Signaling Studies, Albert-Ludwigs University, Freiburg, Germany.,German Center for Infection Research, Satellite Center, Freiburg, Germany.,Resolving Infection Susceptibility Cluster of Excellence 2155, Hanover Medical School, Satellite Center, Freiburg, Germany
| | - Hermann Eibel
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andreas Mackensen
- Department of Internal Medicine 5-Hematology/Oncology, University of Erlangen, Erlangen, Germany
| | - Andreas Philipp Frei
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany.,Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg-Hessen, Ulm, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium, Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Integrative Biological Signaling Studies, Albert-Ludwigs University, Freiburg, Germany
| | - Anne Rensing-Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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12
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Wohlfromm F, Richter M, Otrin L, Seyrek K, Vidaković-Koch T, Kuligina E, Richter V, Koval O, Lavrik IN. Interplay Between Mitophagy and Apoptosis Defines a Cell Fate Upon Co-treatment of Breast Cancer Cells With a Recombinant Fragment of Human κ-Casein and Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand. Front Cell Dev Biol 2021; 8:617762. [PMID: 33537307 PMCID: PMC7849764 DOI: 10.3389/fcell.2020.617762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022] Open
Abstract
A recombinant fragment of human κ-Casein, termed RL2, induces cell death of breast cancer cells; however, molecular mechanisms of RL2-mediated cell death have remained largely unknown. In the current study, we have decoded the molecular mechanism of the RL2-mediated cell death and found that RL2 acts via the induction of mitophagy. This was monitored by the loss of adenosine triphosphate production, LC3B-II generation, and upregulation of BNIP3 and BNIP3L/NIX, as well as phosphatase and tensin homolog-induced kinase 1. Moreover, we have analyzed the cross talk of this pathway with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis upon combinatorial treatment with RL2 and TRAIL. Strikingly, we found two opposite effects of this co-treatment. RL2 had inhibitory effects on TRAIL-induced cell death upon short-term co-stimulation. In particular, RL2 treatment blocked TRAIL-mediated caspase activation, cell viability loss, and apoptosis, which was mediated via the downregulation of the core proapoptotic regulators. Contrary to short-term co-treatment, upon long-term co-stimulation, RL2 sensitized the cells toward TRAIL-induced cell death; the latter observation provides the basis for the development of therapeutic approaches in breast cancer cells. Collectively, our findings have important implications for cancer therapy and reveal the molecular switches of the cross talk between RL2-induced mitophagy and TRAIL-mediated apoptosis.
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Affiliation(s)
- Fabian Wohlfromm
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Max Richter
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Lado Otrin
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Kamil Seyrek
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Tanja Vidaković-Koch
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Elena Kuligina
- Department of Biotechnology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Vladimir Richter
- Department of Biotechnology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Olga Koval
- Department of Biotechnology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Inna N Lavrik
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
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13
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Abrahams L. Single Cell Systems Analysis: Decision Geometry In Outliers. Bioinformatics 2020; 37:1747-1755. [PMID: 33367486 DOI: 10.1093/bioinformatics/btaa1078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 11/28/2020] [Accepted: 12/16/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Anti-cancer therapeutics of the highest calibre currently focus on combinatorial targeting of specific oncoproteins and tumour suppressors. Clinical relapse depends upon intratumoral heterogeneity which serves as substrate variation during evolution of resistance to therapeutic regimens. RESULTS The present review advocates single cell systems biology as the optimal level of analysis for remediation of clinical relapse. Graph theory approaches to understanding decision-making in single cells may be abstracted one level further, to the geometry of decision-making in outlier cells, in order to define evolution-resistant cancer biomarkers. Systems biologists currently working with omics data are invited to consider phase portrait analysis as a mediator between graph theory and deep learning approaches. Perhaps counter-intuitively, the tangible clinical needs of cancer patients may depend upon the adoption of higher level mathematical abstractions of cancer biology. SUPPLEMENTARY INFORMATION supplementary data available at Bioinformatics online.
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Affiliation(s)
- Lianne Abrahams
- Ronin Institute, 127 Haddon Place, Montclair, New Jersey, 07043-2314, United States
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14
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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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15
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Theoretical study of the impact of adaptation on cell-fate heterogeneity and fractional killing. Sci Rep 2020; 10:17429. [PMID: 33060729 PMCID: PMC7562916 DOI: 10.1038/s41598-020-74238-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Fractional killing illustrates the cell propensity to display a heterogeneous fate response over a wide range of stimuli. The interplay between the nonlinear and stochastic dynamics of biochemical networks plays a fundamental role in shaping this probabilistic response and in reconciling requirements for heterogeneity and controllability of cell-fate decisions. The stress-induced fate choice between life and death depends on an early adaptation response which may contribute to fractional killing by amplifying small differences between cells. To test this hypothesis, we consider a stochastic modeling framework suited for comprehensive sensitivity analysis of dose response curve through the computation of a fractionality index. Combining bifurcation analysis and Langevin simulation, we show that adaptation dynamics enhances noise-induced cell-fate heterogeneity by shifting from a saddle-node to a saddle-collision transition scenario. The generality of this result is further assessed by a computational analysis of a detailed regulatory network model of apoptosis initiation and by a theoretical analysis of stochastic bifurcation mechanisms. Overall, the present study identifies a cooperative interplay between stochastic, adaptation and decision intracellular processes that could promote cell-fate heterogeneity in many contexts.
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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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Seyrek K, Ivanisenko NV, Richter M, Hillert LK, König C, Lavrik IN. Controlling Cell Death through Post-translational Modifications of DED Proteins. Trends Cell Biol 2020; 30:354-369. [PMID: 32302548 DOI: 10.1016/j.tcb.2020.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/12/2020] [Accepted: 02/19/2020] [Indexed: 01/15/2023]
Abstract
Apoptosis is a form of programmed cell death, deregulation of which occurs in multiple disorders, including neurodegenerative and autoimmune diseases as well as cancer. The formation of a death-inducing signaling complex (DISC) and death effector domain (DED) filaments are critical for initiation of the extrinsic apoptotic pathway. Post-translational modifications (PTMs) of DED-containing DISC components such as FADD, procaspase-8, and c-FLIP comprise an additional level of apoptosis regulation, which is necessary to overcome the threshold for apoptosis induction. In this review we discuss the influence of PTMs of FADD, procaspase-8, and c-FLIP on DED filament assembly and cell death induction, with a focus on the 3D organization of the DED filament.
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Affiliation(s)
- Kamil Seyrek
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Nikita V Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - Max Richter
- 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
| | - Corinna König
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Inna N Lavrik
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany; The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
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18
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Information Theory: New Look at Oncogenic Signaling Pathways. Trends Cell Biol 2019; 29:862-875. [DOI: 10.1016/j.tcb.2019.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 12/23/2022]
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19
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Matveeva A, Fichtner M, McAllister K, McCann C, Sturrock M, Longley DB, Prehn JHM. Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform. PLoS Comput Biol 2019; 15:e1007374. [PMID: 31553717 PMCID: PMC6779275 DOI: 10.1371/journal.pcbi.1007374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 10/07/2019] [Accepted: 09/03/2019] [Indexed: 01/29/2023] Open
Abstract
Ligand binding to death receptors activates apoptosis in cancer cells. Stimulation of death receptors results in the formation of intracellular multiprotein platforms that either activate the apoptotic initiator Caspase-8 to trigger cell death, or signal through kinases to initiate inflammatory and cell survival signalling. Two of these platforms, the Death-Inducing Signalling Complex (DISC) and the RIPoptosome, also initiate necroptosis by building filamentous scaffolds that lead to the activation of mixed lineage kinase domain-like pseudokinase. To explain cell decision making downstream of death receptor activation, we developed a semi-stochastic model of DISC/RIPoptosome formation. The model is a hybrid of a direct Gillespie stochastic simulation algorithm for slow assembly of the RIPoptosome and a deterministic model of downstream caspase activation. The model explains how alterations in the level of death receptor-ligand complexes, their clustering properties and intrinsic molecular fluctuations in RIPoptosome assembly drive heterogeneous dynamics of Caspase-8 activation. The model highlights how kinetic proofreading leads to heterogeneous cell responses and results in fractional cell killing at low levels of receptor stimulation. It reveals that the noise in Caspase-8 activation-exclusively caused by the stochastic molecular assembly of the DISC/RIPoptosome platform-has a key function in extrinsic apoptotic stimuli recognition.
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Affiliation(s)
- Anna Matveeva
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Michael Fichtner
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Katherine McAllister
- Centre for Cancer Research and Cell Biology, Queen’s University, Belfast, United Kingdom
| | - Christopher McCann
- Centre for Cancer Research and Cell Biology, Queen’s University, Belfast, United Kingdom
| | - Marc Sturrock
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Daniel B. Longley
- Centre for Cancer Research and Cell Biology, Queen’s University, Belfast, United Kingdom
| | - Jochen H. M. Prehn
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- * E-mail:
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