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Hu B, Moiseev D, Schena I, Faezov B, Dunbrack R, Chernoff J, Li J. PAK2 is necessary for myelination in the peripheral nervous system. Brain 2024; 147:1809-1821. [PMID: 38079473 PMCID: PMC11068108 DOI: 10.1093/brain/awad413] [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: 07/19/2023] [Revised: 10/03/2023] [Accepted: 11/12/2023] [Indexed: 02/12/2024] Open
Abstract
Myelination enables electrical impulses to propagate on axons at the highest speed, encoding essential life functions. The Rho family GTPases, RAC1 and CDC42, have been shown to critically regulate Schwann cell myelination. P21-activated kinase 2 (PAK2) is an effector of RAC1/CDC42, but its specific role in myelination remains undetermined. We produced a Schwann cell-specific knockout mouse of Pak2 (scPak2-/-) to evaluate PAK2's role in myelination. Deletion of Pak2, specifically in mouse Schwann cells, resulted in severe hypomyelination, slowed nerve conduction velocity and behaviour dysfunctions in the scPak2-/- peripheral nerve. Many Schwann cells in scPak2-/- sciatic nerves were arrested at the stage of axonal sorting. These abnormalities were rescued by reintroducing Pak2, but not the kinase-dead mutation of Pak2, via lentivirus delivery to scPak2-/- Schwann cells in vivo. Moreover, ablation of Pak2 in Schwann cells blocked the promyelinating effect driven by neuregulin-1, prion protein and inactivated RAC1/CDC42. Conversely, the ablation of Pak2 in neurons exhibited no phenotype. Such PAK2 activity can also be either enhanced or inhibited by different myelin lipids. We have identified a novel promyelinating factor, PAK2, that acts as a critical convergence point for multiple promyelinating signalling pathways. The promyelination by PAK2 is Schwann cell-autonomous. Myelin lipids, identified as inhibitors or activators of PAK2, may be utilized to develop therapies for repairing abnormal myelin in peripheral neuropathies.
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Affiliation(s)
- Bo Hu
- Department of Neurology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Daniel Moiseev
- Department of Neurology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Isabella Schena
- Department of Neurology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Bulat Faezov
- Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Roland Dunbrack
- Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jonathan Chernoff
- Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jun Li
- Department of Neurology, Houston Methodist Research Institute, Houston, TX 77030, USA
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2
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Bhuria V, Franz T, Baldauf C, Böttcher M, Chatain N, Koschmieder S, Brümmendorf TH, Mougiakakos D, Schraven B, Kahlfuß S, Fischer T. Activating mutations in JAK2 and CALR differentially affect intracellular calcium flux in store operated calcium entry. Cell Commun Signal 2024; 22:186. [PMID: 38509561 PMCID: PMC10956330 DOI: 10.1186/s12964-024-01530-z] [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: 12/05/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Calcium (Ca2+) signaling regulates various vital cellular functions, including integrin activation and cell migration. Store-operated calcium entry (SOCE) via calcium release-activated calcium (CRAC) channels represents a major pathway for Ca2+ influx from the extracellular space in multiple cell types. The impact of JAK2-V617F and CALR mutations which are disease initiating in myeloproliferative neoplasms (MPN) on SOCE, calcium flux from the endoplasmic reticulum (ER) to the cytosol, and related key signaling pathways in the presence or absence of erythropoietin (EPO) or thrombopoietin (TPO) is poorly understood. Thus, this study aimed to elucidate the effects of these mutations on the aforementioned calcium dynamics, in cellular models of MPN. METHODS Intracellular Ca2+ levels were measured over a time frame of 0-1080 s in Fura-2 AM labeled myeloid progenitor 32D cells expressing various mutations (JAK2-WT/EpoR, JAK2-V617F/EpoR; CALR-WT/MPL, CALR-ins5/MPL, and del52/MPL). Basal Ca2+ concentrations were assessed from 0-108 s. Subsequently, cells were stimulated with EPO/TPO in Ca2+-free Ringer solution, measuring Ca2+ levels from 109-594 s (store depletion). Then, 2 mM of Ca2+ buffer resembling physiological concentrations was added to induce SOCE, and Ca2+ levels were measured from 595-1080 s. Fura-2 AM emission ratios (F340/380) were used to quantify the integrated Ca2+ signal. Statistical significance was assessed by unpaired Student's t-test or Mann-Whitney-U-test, one-way or two-way ANOVA followed by Tukey's multiple comparison test. RESULTS Following EPO stimulation, the area under the curve (AUC) representing SOCE significantly increased in 32D-JAK2-V617F cells compared to JAK2-WT cells. In TPO-stimulated CALR cells, we observed elevated Ca2+ levels during store depletion and SOCE in CALR-WT cells compared to CALR-ins5 and del52 cells. Notably, upon stimulation, key components of the Ca2+ signaling pathways, including PLCγ-1 and IP3R, were differentially affected in these cell lines. Hyper-activated PLCγ-1 and IP3R were observed in JAK2-V617F but not in CALR mutated cells. Inhibition of calcium regulatory mechanisms suppressed cellular growth and induced apoptosis in JAK2-V617F cells. CONCLUSIONS This report highlights the impact of JAK2 and CALR mutations on Ca2+ flux (store depletion and SOCE) in response to stimulation with EPO and TPO. The study shows that the JAK2-V617F mutation strongly alters the regulatory mechanism of EpoR/JAK2-dependent intracellular calcium balance, affecting baseline calcium levels, EPO-induced calcium entry, and PLCγ-1 signaling pathways. Our results reveal an important role of calcium flux in the homeostasis of JAK2-V617F positive cells.
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Affiliation(s)
- Vikas Bhuria
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany.
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany.
- Center for Health and Medical Prevention - CHaMP, Otto-von-Guericke University, Magdeburg, Germany.
| | - Tobias Franz
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Conny Baldauf
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Martin Böttcher
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany
- Department of Hematology and Oncology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Nicolas Chatain
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center of Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center of Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center of Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Dimitrios Mougiakakos
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany
- Department of Hematology and Oncology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Burkhart Schraven
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany
- Center for Health and Medical Prevention - CHaMP, Otto-von-Guericke University, Magdeburg, Germany
| | - Sascha Kahlfuß
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany
- Center for Health and Medical Prevention - CHaMP, Otto-von-Guericke University, Magdeburg, Germany
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Thomas Fischer
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany.
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany.
- Center for Health and Medical Prevention - CHaMP, Otto-von-Guericke University, Magdeburg, Germany.
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Ghomlaghi M, Theocharous M, Hoang N, Shin SY, von Kriegsheim A, O’ Neill E, Zhang T, Nguyen LK. Integrative modeling and analysis of signaling crosstalk reveal molecular switches coordinating Yes-associated protein transcriptional activities. iScience 2024; 27:109031. [PMID: 38380257 PMCID: PMC10877689 DOI: 10.1016/j.isci.2024.109031] [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: 01/28/2022] [Revised: 12/07/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
The transcriptional co-activator YAP forms complexes with distinct transcription factors, controlling cell fate decisions, such as proliferation and apoptosis. However, the mechanisms underlying its context-dependent function are poorly defined. This study explores the interplay between the TGF-β and Hippo pathways and their influence on YAP's association with specific transcription factors. By integrating iterative mathematical modeling with experimental validation, we uncover molecular switches, predominantly controlled by RASSF1A and ITCH, which dictate the formation of YAP-SMAD (proliferative) and YAP-p73 (apoptotic) complexes. Our results show that RASSF1A enhances the formation of apoptotic complexes, whereas ITCH promotes the formation of proliferative complexes. Notably, higher levels of ITCH transform YAP-SMAD activity from a transient to a sustained state, impacting cellular behaviors. Extending these findings to various breast cancer cell lines highlights the role of cellular context in YAP regulation. Our study provides new insights into the mechanisms of YAP transcriptional activities and their therapeutic implications.
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Affiliation(s)
- Milad Ghomlaghi
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Mandy Theocharous
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Nhan Hoang
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sung-Young Shin
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Alex von Kriegsheim
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Eric O’ Neill
- CRUK/MRC Institute for Radiation Oncology and Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Tao Zhang
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Lan K. Nguyen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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Ramesh V, Krishnan J. A unified approach to dissecting biphasic responses in cell signaling. eLife 2023; 13:e86520. [PMID: 38054655 DOI: 10.7554/elife.86520] [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: 01/30/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023] Open
Abstract
Biphasic responses are encountered at all levels in biological systems. At the cellular level, biphasic dose-responses are widely encountered in cell signaling and post-translational modification systems and represent safeguards against overactivation or overexpression of species. In this paper, we provide a unified theoretical synthesis of biphasic responses in cell signaling systems, by assessing signaling systems ranging from basic biochemical building blocks to canonical network structures to well-characterized exemplars on one hand, and examining different types of doses on the other. By using analytical and computational approaches applied to a range of systems across levels (described by broadly employed models), we reveal (i) design principles enabling the presence of biphasic responses, including in almost all instances, an explicit characterization of the parameter space (ii) structural factors which preclude the possibility of biphasic responses (iii) different combinations of the presence or absence of enzyme-biphasic and substrate-biphasic responses, representing safeguards against overactivation and overexpression, respectively (iv) the possibility of broadly robust biphasic responses (v) the complete alteration of signaling behavior in a network due to biphasic interactions between species (biphasic regulation) (vi) the propensity of different co-existing biphasic responses in the Erk signaling network. These results both individually and in totality have a number of important consequences for systems and synthetic biology.
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Affiliation(s)
- Vaidhiswaran Ramesh
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London, London, United Kingdom
| | - J Krishnan
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London, London, United Kingdom
- Institute for Systems and Synthetic Biology, Imperial College London, South Kensington Campus, London, United Kingdom
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5
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Jin J, Xu F, Liu Z, Qi H, Yao C, Shuai J, Li X. Biphasic amplitude oscillator characterized by distinct dynamics of trough and crest. Phys Rev E 2023; 108:064412. [PMID: 38243441 DOI: 10.1103/physreve.108.064412] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024]
Abstract
Biphasic amplitude dynamics (BAD) of oscillation have been observed in many biological systems. However, the specific topology structure and regulatory mechanisms underlying these biphasic amplitude dynamics remain elusive. Here, we searched all possible two-node circuit topologies and identified the core oscillator that enables robust oscillation. This core oscillator consists of a negative feedback loop between two nodes and a self-positive feedback loop of the input node, which result in the fast and slow dynamics of the two nodes, thereby achieving relaxation oscillation. Landscape theory was employed to study the stochastic dynamics and global stability of the system, allowing us to quantitatively describe the diverse positions and sizes of the Mexican hat. With increasing input strength, the size of the Mexican hat exhibits a gradual increase followed by a subsequent decrease. The self-activation of input node and the negative feedback on input node, which dominate the fast dynamics of the input node, were observed to regulate BAD in a bell-shaped manner. Both deterministic and statistical analysis results reveal that BAD is characterized by the linear and nonlinear dependence of the oscillation trough and crest on the input strength. In addition, combining with computational and theoretical analysis, we addressed that the linear response of trough to input is predominantly governed by the negative feedback, while the nonlinear response of crest is jointly regulated by the negative feedback loop and the self-positive feedback loop within the oscillator. Overall, this study provides a natural and physical basis for comprehending the occurrence of BAD in oscillatory systems, yielding guidance for the design of BAD in synthetic biology applications.
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Affiliation(s)
- Jun Jin
- Department of Physics, Xiamen University, Xiamen, Fujian 361005, China
| | - Fei Xu
- Department of Physics, Anhui Normal University, Wuhu, Anhui 241002, China
| | - Zhilong Liu
- Department of Physics, Xiamen University, Xiamen, Fujian 361005, China
| | - Hong Qi
- Complex Systems Research Center, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Chenggui Yao
- College of Data Science, Jiaxing University, Jiaxing, Zhejiang 314000, China
| | - Jianwei Shuai
- Department of Physics, Xiamen University, Xiamen, Fujian 361005, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health) and Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Xiang Li
- Department of Physics, Xiamen University, Xiamen, Fujian 361005, China
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6
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Marrone JI, Sepulchre JA, Ventura AC. A nested bistable module within a negative feedback loop ensures different types of oscillations in signaling systems. Sci Rep 2023; 13:529. [PMID: 36631477 PMCID: PMC9834387 DOI: 10.1038/s41598-022-27047-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023] Open
Abstract
In this article, we consider a double phosphorylation cycle, a ubiquitous signaling component, having the ability to display bistability, a behavior strongly related to the existence of positive feedback loops. If this component is connected to other signaling elements, it very likely undergoes some sort of protein-protein interaction. In several cases, these interactions result in a non-explicit negative feedback effect, leading to interlinked positive and negative feedbacks. This combination was studied in the literature as a way to generate relaxation-type oscillations. Here, we show that the two feedbacks together ensure two types of oscillations, the relaxation-type ones and a smoother type of oscillations functioning in a very narrow range of frequencies, in such a way that outside that range, the amplitude of the oscillations is severely compromised. Even more, we show that the two feedbacks are essential for both oscillatory types to emerge, and it is their hierarchy what determines the type of oscillation at work. We used bifurcation analyses and amplitude vs. frequency curves to characterize and classify the oscillations. We also applied the same ideas to another simple model, with the goal of generalizing what we learned from signaling models. The results obtained display the wealth of oscillatory dynamics that exists in a system with a bistable module nested within a negative feedback loop, showing how to transition between different types of oscillations and other dynamical behaviors such as excitability. Our work provides a framework for the study of other oscillatory systems based on bistable modules, from simple two-component models to more complex examples like the MAPK cascade and experimental cases like cell cycle oscillators.
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Affiliation(s)
- Juan Ignacio Marrone
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE UBA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | | | - Alejandra C Ventura
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina.
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE UBA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina.
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7
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Almowallad S, Alqahtani LS, Mobashir M. NF-kB in Signaling Patterns and Its Temporal Dynamics Encode/Decode Human Diseases. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122012. [PMID: 36556376 PMCID: PMC9788026 DOI: 10.3390/life12122012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Defects in signaling pathways are the root cause of many disorders. These malformations come in a wide variety of types, and their causes are also very diverse. Some of these flaws can be brought on by pathogenic organisms and viruses, many of which can obstruct signaling processes. Other illnesses are linked to malfunctions in the way that cell signaling pathways work. When thinking about how errors in signaling pathways might cause disease, the idea of signalosome remodeling is helpful. The signalosome may be conveniently divided into two types of defects: phenotypic remodeling and genotypic remodeling. The majority of significant illnesses that affect people, including high blood pressure, heart disease, diabetes, and many types of mental illness, appear to be caused by minute phenotypic changes in signaling pathways. Such phenotypic remodeling modifies cell behavior and subverts normal cellular processes, resulting in illness. There has not been much progress in creating efficient therapies since it has been challenging to definitively confirm this connection between signalosome remodeling and illness. The considerable redundancy included into cell signaling systems presents several potential for developing novel treatments for various disease conditions. One of the most important pathways, NF-κB, controls several aspects of innate and adaptive immune responses, is a key modulator of inflammatory reactions, and has been widely studied both from experimental and theoretical perspectives. NF-κB contributes to the control of inflammasomes and stimulates the expression of a number of pro-inflammatory genes, including those that produce cytokines and chemokines. Additionally, NF-κB is essential for controlling innate immune cells and inflammatory T cells' survival, activation, and differentiation. As a result, aberrant NF-κB activation plays a role in the pathogenesis of several inflammatory illnesses. The activation and function of NF-κB in relation to inflammatory illnesses was covered here, and the advancement of treatment approaches based on NF-κB inhibition will be highlighted. This review presents the temporal behavior of NF-κB and its potential relevance in different human diseases which will be helpful not only for theoretical but also for experimental perspectives.
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Affiliation(s)
- Sanaa Almowallad
- Department of Biochemistry, Faculty of Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Leena S. Alqahtani
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah 23445, Saudi Arabia
- Correspondence: (L.S.A.); (M.M.)
| | - Mohammad Mobashir
- SciLifeLab, Department of Oncology and Pathology, Karolinska Institutet, P.O. Box 1031, S-17121 Stockholm, Sweden
- Department of Biosciences, Faculty of Natural Science, Jamia Millia Islamia, New Delhi 110025, India
- Special Infectious Agents Unit—BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Correspondence: (L.S.A.); (M.M.)
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8
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Gu W, Shen H, Xie L, Zhang X, Yang J. The Role of Feedback Loops in Targeted Therapy for Pancreatic Cancer. Front Oncol 2022; 12:800140. [PMID: 35651786 PMCID: PMC9148955 DOI: 10.3389/fonc.2022.800140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Pancreatic cancer is the leading cause of cancer-related deaths worldwide, with limited treatment options and low long-term survival rates. The complex and variable signal regulation networks are one of the important reasons why it is difficult for pancreatic cancer to develop precise targeted therapy drugs. Numerous studies have associated feedback loop regulation with the development and therapeutic response of cancers including pancreatic cancer. Therefore, we review researches on the role of feedback loops in the progression of pancreatic cancer, and summarize the connection between feedback loops and several signaling pathways in pancreatic cancer, as well as recent advances in the intervention of feedback loops in pancreatic cancer treatment, highlighting the potential of capitalizing on feedback loops modulation in targeted therapy for pancreatic cancer.
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Affiliation(s)
- Weigang Gu
- Department of Gastroenterology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - HongZhang Shen
- Department of Gastroenterology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lu Xie
- Department of Gastroenterology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaofeng Zhang
- Department of Gastroenterology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, China
- *Correspondence: Xiaofeng Zhang, ; Jianfeng Yang,
| | - Jianfeng Yang
- Department of Gastroenterology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Xiaofeng Zhang, ; Jianfeng Yang,
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Fan X, Walther A. 1D Colloidal chains: recent progress from formation to emergent properties and applications. Chem Soc Rev 2022; 51:4023-4074. [PMID: 35502721 DOI: 10.1039/d2cs00112h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Integrating nanoscale building blocks of low dimensionality (0D; i.e., spheres) into higher dimensional structures endows them and their corresponding materials with emergent properties non-existent or only weakly existent in the individual building blocks. Constructing 1D chains, 2D arrays and 3D superlattices using nanoparticles and colloids therefore continues to be one of the grand goals in colloid and nanomaterial science. Amongst these higher order structures, 1D colloidal chains are of particular interest, as they possess unique anisotropic properties. In recent years, the most relevant advances in 1D colloidal chain research have been made in novel synthetic methodologies and applications. In this review, we first address a comprehensive description of the research progress concerning various synthetic strategies developed to construct 1D colloidal chains. Following this, we highlight the amplified and emergent properties of the resulting materials, originating from the assembly of the individual building blocks and their collective behavior, and discuss relevant applications in advanced materials. In the discussion of synthetic strategies, properties, and applications, particular attention will be paid to overarching concepts, fresh trends, and potential areas of future research. We believe that this comprehensive review will be a driver to guide the interdisciplinary field of 1D colloidal chains, where nanomaterial synthesis, self-assembly, physical property studies, and material applications meet, to a higher level, and open up new research opportunities at the interface of classical disciplines.
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Affiliation(s)
- Xinlong Fan
- Institute for Macromolecular Chemistry, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 31, 79104, Freiburg, Germany.
| | - Andreas Walther
- A3BMS Lab, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
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10
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Abegaz F, Martines ACMF, Vieira-Lara MA, Rios-Morales M, Reijngoud DJ, Wit EC, Bakker BM. Bistability in fatty-acid oxidation resulting from substrate inhibition. PLoS Comput Biol 2021; 17:e1009259. [PMID: 34383741 PMCID: PMC8396765 DOI: 10.1371/journal.pcbi.1009259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 08/27/2021] [Accepted: 07/07/2021] [Indexed: 11/18/2022] Open
Abstract
In this study we demonstrated through analytic considerations and numerical studies that the mitochondrial fatty-acid β-oxidation can exhibit bistable-hysteresis behavior. In an experimentally validated computational model we identified a specific region in the parameter space in which two distinct stable and one unstable steady state could be attained with different fluxes. The two stable states were referred to as low-flux (disease) and high-flux (healthy) state. By a modular kinetic approach we traced the origin and causes of the bistability back to the distributive kinetics and the conservation of CoA, in particular in the last rounds of the β-oxidation. We then extended the model to investigate various interventions that may confer health benefits by activating the pathway, including (i) activation of the last enzyme MCKAT via its endogenous regulator p46-SHC protein, (ii) addition of a thioesterase (an acyl-CoA hydrolysing enzyme) as a safety valve, and (iii) concomitant activation of a number of upstream and downstream enzymes by short-chain fatty-acids (SCFA), metabolites that are produced from nutritional fibers in the gut. A high concentration of SCFAs, thioesterase activity, and inhibition of the p46Shc protein led to a disappearance of the bistability, leaving only the high-flux state. A better understanding of the switch behavior of the mitochondrial fatty-acid oxidation process between a low- and a high-flux state may lead to dietary and pharmacological intervention in the treatment or prevention of obesity and or non-alcoholic fatty-liver disease.
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Affiliation(s)
- Fentaw Abegaz
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Statistics and Probability Unit, University of Groningen, Groningen, The Netherlands
| | - Anne-Claire M. F. Martines
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcel A. Vieira-Lara
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Melany Rios-Morales
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dirk-Jan Reijngoud
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ernst C. Wit
- Statistics and Probability Unit, University of Groningen, Groningen, The Netherlands
- Institute of Computational Science, Università della Svizzera italiana, Lugano, Switzerland
| | - Barbara M. Bakker
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- * E-mail:
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11
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Koch D, Alexandrovich A, Funk F, Kho AL, Schmitt JP, Gautel M. Molecular noise filtering in the β-adrenergic signaling network by phospholamban pentamers. Cell Rep 2021; 36:109448. [PMID: 34320358 PMCID: PMC8333238 DOI: 10.1016/j.celrep.2021.109448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/16/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
Phospholamban (PLN) is an important regulator of cardiac calcium handling due to its ability to inhibit the calcium ATPase SERCA. β-Adrenergic stimulation reverses SERCA inhibition via PLN phosphorylation and facilitates fast calcium reuptake. PLN also forms pentamers whose physiological significance has remained elusive. Using mathematical modeling combined with biochemical and cell biological experiments, we show that pentamers regulate both the dynamics and steady-state levels of monomer phosphorylation. Substrate competition by pentamers and a feed-forward loop involving inhibitor-1 can delay monomer phosphorylation by protein kinase A (PKA), whereas cooperative pentamer dephosphorylation enables bistable PLN steady-state phosphorylation. Simulations show that phosphorylation delay and bistability act as complementary filters that reduce the effect of random fluctuations in PKA activity, thereby ensuring consistent monomer phosphorylation and SERCA activity despite noisy upstream signals. Preliminary analyses suggest that the PLN mutation R14del could impair noise filtering, offering a new perspective on how this mutation causes cardiac arrhythmias.
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Affiliation(s)
- Daniel Koch
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK.
| | | | - Florian Funk
- Institute of Pharmacology and Clinical Pharmacology, and Cardiovascular Research Institute Düsseldorf (CARID), University Hospital Düsseldorf, 40225 Düsseldorf, Germany
| | - Ay Lin Kho
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK
| | - Joachim P Schmitt
- Institute of Pharmacology and Clinical Pharmacology, and Cardiovascular Research Institute Düsseldorf (CARID), University Hospital Düsseldorf, 40225 Düsseldorf, Germany
| | - Mathias Gautel
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK
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12
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Ghomlaghi M, Hart A, Hoang N, Shin S, Nguyen LK. Feedback, Crosstalk and Competition: Ingredients for Emergent Non-Linear Behaviour in the PI3K/mTOR Signalling Network. Int J Mol Sci 2021; 22:6944. [PMID: 34203293 PMCID: PMC8267830 DOI: 10.3390/ijms22136944] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 12/15/2022] Open
Abstract
The PI3K/mTOR signalling pathway plays a central role in the governing of cell growth, survival and metabolism. As such, it must integrate and decode information from both external and internal sources to guide efficient decision-making by the cell. To facilitate this, the pathway has evolved an intricate web of complex regulatory mechanisms and elaborate crosstalk with neighbouring signalling pathways, making it a highly non-linear system. Here, we describe the mechanistic biological details that underpin these regulatory mechanisms, covering a multitude of negative and positive feedback loops, feed-forward loops, competing protein interactions, and crosstalk with major signalling pathways. Further, we highlight the non-linear and dynamic network behaviours that arise from these regulations, uncovered through computational and experimental studies. Given the pivotal role of the PI3K/mTOR network in cellular homeostasis and its frequent dysregulation in pathologies including cancer and diabetes, a coherent and systems-level understanding of the complex regulation and consequential dynamic signalling behaviours within this network is imperative for advancing biology and development of new therapeutic approaches.
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Affiliation(s)
- Milad Ghomlaghi
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia; (M.G.); (A.H.); (N.H.); (S.S.)
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Anthony Hart
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia; (M.G.); (A.H.); (N.H.); (S.S.)
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Nhan Hoang
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia; (M.G.); (A.H.); (N.H.); (S.S.)
| | - Sungyoung Shin
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia; (M.G.); (A.H.); (N.H.); (S.S.)
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Lan K. Nguyen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia; (M.G.); (A.H.); (N.H.); (S.S.)
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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13
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Fan X, Walther A. pH Feedback Lifecycles Programmed by Enzymatic Logic Gates Using Common Foods as Fuels. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xinlong Fan
- Institute for Macromolecular Chemistry University of Freiburg Stefan-Meier-Str. 31 79104 Freiburg Germany
| | - Andreas Walther
- Institute for Macromolecular Chemistry University of Freiburg Stefan-Meier-Str. 31 79104 Freiburg Germany
- A3BMS Lab Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
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14
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Fan X, Walther A. pH Feedback Lifecycles Programmed by Enzymatic Logic Gates Using Common Foods as Fuels. Angew Chem Int Ed Engl 2021; 60:11398-11405. [PMID: 33682231 PMCID: PMC8252529 DOI: 10.1002/anie.202017003] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/22/2021] [Indexed: 12/12/2022]
Abstract
Artificial temporal signaling systems, which mimic living out-of-equilibrium conditions, have made large progress. However, systems programmed by enzymatic reaction networks in multicomponent and unknown environments, and using biocompatible components remain a challenge. Herein, we demonstrate an approach to program temporal pH signals by enzymatic logic gates. They are realized by an enzymatic disaccharide-to-monosaccharide-to-sugar acid reaction cascade catalyzed by two metabolic chains: invertase-glucose oxidase and β-galactosidase-glucose oxidase, respectively. Lifetimes of the transient pH signal can be programmed from less than 15 min to more than 1 day. We study enzymatic kinetics of the reaction cascades and reveal the underlying regulatory mechanisms. Operating with all-food grade chemicals and coupling to self-regulating hydrogel, our system is quite robust to work in a complicated medium with unknown components and in a biocompatible fashion.
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Affiliation(s)
- Xinlong Fan
- Institute for Macromolecular ChemistryUniversity of FreiburgStefan-Meier-Str. 3179104FreiburgGermany
| | - Andreas Walther
- Institute for Macromolecular ChemistryUniversity of FreiburgStefan-Meier-Str. 3179104FreiburgGermany
- ABMS LabDepartment of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
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15
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Ding J, Hostallero DE, El Khili MR, Fonseca GJ, Milette S, Noorah N, Guay-Belzile M, Spicer J, Daneshtalab N, Sirois M, Tremblay K, Emad A, Rousseau S. A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil extracellular traps as mediators of thrombosis in COVID-19. PLoS Comput Biol 2021; 17:e1008810. [PMID: 33684134 PMCID: PMC7971900 DOI: 10.1371/journal.pcbi.1008810] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 03/18/2021] [Accepted: 02/17/2021] [Indexed: 01/10/2023] Open
Abstract
Abnormal coagulation and an increased risk of thrombosis are features of severe COVID-19, with parallels proposed with hemophagocytic lymphohistiocytosis (HLH), a life-threating condition associated with hyperinflammation. The presence of HLH was described in severely ill patients during the H1N1 influenza epidemic, presenting with pulmonary vascular thrombosis. We tested the hypothesis that genes causing primary HLH regulate pathways linking pulmonary thromboembolism to the presence of SARS-CoV-2 using novel network-informed computational algorithms. This approach led to the identification of Neutrophils Extracellular Traps (NETs) as plausible mediators of vascular thrombosis in severe COVID-19 in children and adults. Taken together, the network-informed analysis led us to propose the following model: the release of NETs in response to inflammatory signals acting in concert with SARS-CoV-2 damage the endothelium and direct platelet-activation promoting abnormal coagulation leading to serious complications of COVID-19. The underlying hypothesis is that genetic and/or environmental conditions that favor the release of NETs may predispose individuals to thrombotic complications of COVID-19 due to an increase risk of abnormal coagulation. This would be a common pathogenic mechanism in conditions including autoimmune/infectious diseases, hematologic and metabolic disorders.
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Affiliation(s)
- Jun Ding
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- The Meakins-Christie Laboratories at the Research Institute of the McGill University Heath Centre Research Institute, Montréal, Canada
| | - David Earl Hostallero
- Department of Electrical and Computer Engineering, McGill University, Montréal, Canada
| | - Mohamed Reda El Khili
- Department of Electrical and Computer Engineering, McGill University, Montréal, Canada
| | - Gregory Joseph Fonseca
- The Meakins-Christie Laboratories at the Research Institute of the McGill University Heath Centre Research Institute, Montréal, Canada
| | - Simon Milette
- Goodman Cancer Research Centre, McGill University, Montréal, Canada
| | - Nuzha Noorah
- The Meakins-Christie Laboratories at the Research Institute of the McGill University Heath Centre Research Institute, Montréal, Canada
| | - Myriam Guay-Belzile
- The Meakins-Christie Laboratories at the Research Institute of the McGill University Heath Centre Research Institute, Montréal, Canada
| | - Jonathan Spicer
- Division of Thoracic and Upper Gastrointestinal Surgery, McGill University Health Centre Research Institute, Montréal, Canada
| | - Noriko Daneshtalab
- School of Pharmacy, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Martin Sirois
- Montreal Heart Institute and Department of pharmacology and physiology, Faculty of medicine, Université de Montréal, Montréal, Canada
| | - Karine Tremblay
- Pharmacology-physiology Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Centre intégré universitaire de santé et de services sociaux du Saguenay-Lac-Saint-Jean (Chicoutimi University Hospital) Research Center, Saguenay, Canada
| | - Amin Emad
- Department of Electrical and Computer Engineering, McGill University, Montréal, Canada
| | - Simon Rousseau
- The Meakins-Christie Laboratories at the Research Institute of the McGill University Heath Centre Research Institute, Montréal, Canada
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16
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Disentangling a complex response in cell reprogramming and probing the Waddington landscape by automatic construction of Petri nets. Biosystems 2020; 189:104092. [PMID: 31917281 DOI: 10.1016/j.biosystems.2019.104092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/02/2019] [Accepted: 12/20/2019] [Indexed: 01/19/2023]
Abstract
We analyzed the developmental switch to sporulation of a multinucleate Physarum polycephalum plasmodial cell, a complex response to phytochrome photoreceptor activation. Automatic construction of Petri nets representing finite state machines assembled from trajectories of differential gene expression in single cells revealed alternative, genotype-dependent interconnected developmental routes and identified reversible steps, metastable states, commitment points, and subsequent irreversible steps together with molecular signatures associated with cell fate decision and differentiation. Formation of cyclic transits identified by transition invariants in mutants that are locked in a proliferative state is remarkable considering the view that oncogenic alterations may cause the formation of cancer attractors. We conclude that the Petri net approach is useful to probe the Waddington landscape of cellular reprogramming, to disentangle developmental routes for the reconstruction of the gene regulatory network, and to understand how genetic alterations or physiological conditions reshape the landscape eventually creating new basins of attraction. Unraveling the complexity of pathogenesis, disease progression, drug response or the analysis of attractor landscapes in other complex systems of uncertain structure might be additional fields of application.
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17
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Goh GH, Maloney SK, Mark PJ, Blache D. Episodic Ultradian Events-Ultradian Rhythms. BIOLOGY 2019; 8:E15. [PMID: 30875767 PMCID: PMC6466064 DOI: 10.3390/biology8010015] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/24/2019] [Accepted: 03/09/2019] [Indexed: 11/16/2022]
Abstract
In the fast lane of chronobiology, ultradian events are short-term rhythms that have been observed since the beginning of modern biology and were quantified about a century ago. They are ubiquitous in all biological systems and found in all organisms, from unicellular organisms to mammals, and from single cells to complex biological functions in multicellular animals. Since these events are aperiodic and last for a few minutes to a few hours, they are better classified as episodic ultradian events (EUEs). Their origin is unclear. However, they could have a molecular basis and could be controlled by hormonal inputs-in vertebrates, they originate from the activity of the central nervous system. EUEs are receiving increasing attention but their aperiodic nature requires specific sampling and analytic tools. While longer scale rhythms are adaptations to predictable changes in the environment, in theory, EUEs could contribute to adaptation by preparing organisms and biological functions for unpredictability.
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Affiliation(s)
- Grace H Goh
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
| | - Shane K Maloney
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
| | - Peter J Mark
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
| | - Dominique Blache
- School of Agriculture and Environment and UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
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18
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Goldbeter A. Dissipative structures in biological systems: bistability, oscillations, spatial patterns and waves. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2018; 376:rsta.2017.0376. [PMID: 29891498 PMCID: PMC6000149 DOI: 10.1098/rsta.2017.0376] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/26/2018] [Indexed: 05/05/2023]
Abstract
The goal of this review article is to assess how relevant is the concept of dissipative structure for understanding the dynamical bases of non-equilibrium self-organization in biological systems, and to see where it has been applied in the five decades since it was initially proposed by Ilya Prigogine. Dissipative structures can be classified into four types, which will be considered, in turn, and illustrated by biological examples: (i) multistability, in the form of bistability and tristability, which involve the coexistence of two or three stable steady states, or in the form of birhythmicity, which involves the coexistence between two stable rhythms; (ii) temporal dissipative structures in the form of sustained oscillations, illustrated by biological rhythms; (iii) spatial dissipative structures, known as Turing patterns; and (iv) spatio-temporal structures in the form of propagating waves. Rhythms occur with widely different periods at all levels of biological organization, from neural, cardiac and metabolic oscillations to circadian clocks and the cell cycle; they play key roles in physiology and in many disorders. New rhythms are being uncovered while artificial ones are produced by synthetic biology. Rhythms provide the richest source of examples of dissipative structures in biological systems. Bistability has been observed experimentally, but has primarily been investigated in theoretical models in an increasingly wide range of biological contexts, from the genetic to the cell and animal population levels, both in physiological conditions and in disease. Bistable transitions have been implicated in the progression between the different phases of the cell cycle and, more generally, in the process of cell fate specification in the developing embryo. Turing patterns are exemplified by the formation of some periodic structures in the course of development and by skin stripe patterns in animals. Spatio-temporal patterns in the form of propagating waves are observed within cells as well as in intercellular communication. This review illustrates how dissipative structures of all sorts abound in biological systems.This article is part of the theme issue 'Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)'.
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Affiliation(s)
- Albert Goldbeter
- Unité de Chronobiologie théorique, Service de Chimie physique et Biologie théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus Plaine, CP 231, 1050 Brussels, Belgium
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19
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Ignatius Pang CN, Goel A, Wilkins MR. Investigating the Network Basis of Negative Genetic Interactions in Saccharomyces cerevisiae with Integrated Biological Networks and Triplet Motif Analysis. J Proteome Res 2018; 17:1014-1030. [DOI: 10.1021/acs.jproteome.7b00649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Chi Nam Ignatius Pang
- Systems
Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Apurv Goel
- Systems
Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Marc R. Wilkins
- Systems
Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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20
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Varusai TM, Nguyen LK. Dynamic modelling of the mTOR signalling network reveals complex emergent behaviours conferred by DEPTOR. Sci Rep 2018; 8:643. [PMID: 29330362 PMCID: PMC5766521 DOI: 10.1038/s41598-017-18400-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/01/2017] [Indexed: 01/10/2023] Open
Abstract
The mechanistic Target of Rapamycin (mTOR) signalling network is an evolutionarily conserved network that controls key cellular processes, including cell growth and metabolism. Consisting of the major kinase complexes mTOR Complex 1 and 2 (mTORC1/2), the mTOR network harbours complex interactions and feedback loops. The DEP domain-containing mTOR-interacting protein (DEPTOR) was recently identified as an endogenous inhibitor of both mTORC1 and 2 through direct interactions, and is in turn degraded by mTORC1/2, adding an extra layer of complexity to the mTOR network. Yet, the dynamic properties of the DEPTOR-mTOR network and the roles of DEPTOR in coordinating mTORC1/2 activation dynamics have not been characterised. Using computational modelling, systems analysis and dynamic simulations we show that DEPTOR confers remarkably rich and complex dynamic behaviours to mTOR signalling, including abrupt, bistable switches, oscillations and co-existing bistable/oscillatory responses. Transitions between these distinct modes of behaviour are enabled by modulating DEPTOR expression alone. We characterise the governing conditions for the observed dynamics by elucidating the network in its vast multi-dimensional parameter space, and develop strategies to identify core network design motifs underlying these dynamics. Our findings provide new systems-level insights into the complexity of mTOR signalling contributed by DEPTOR.
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Affiliation(s)
- Thawfeek M Varusai
- European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.,Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Lan K Nguyen
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia. .,Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, 3800, Australia. .,Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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21
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Korcsmaros T, Schneider MV, Superti-Furga G. Next generation of network medicine: interdisciplinary signaling approaches. Integr Biol (Camb) 2017; 9:97-108. [PMID: 28106223 DOI: 10.1039/c6ib00215c] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the last decade, network approaches have transformed our understanding of biological systems. Network analyses and visualizations have allowed us to identify essential molecules and modules in biological systems, and improved our understanding of how changes in cellular processes can lead to complex diseases, such as cancer, infectious and neurodegenerative diseases. "Network medicine" involves unbiased large-scale network-based analyses of diverse data describing interactions between genes, diseases, phenotypes, drug targets, drug transport, drug side-effects, disease trajectories and more. In terms of drug discovery, network medicine exploits our understanding of the network connectivity and signaling system dynamics to help identify optimal, often novel, drug targets. Contrary to initial expectations, however, network approaches have not yet delivered a revolution in molecular medicine. In this review, we propose that a key reason for the limited impact, so far, of network medicine is a lack of quantitative multi-disciplinary studies involving scientists from different backgrounds. To support this argument, we present existing approaches from structural biology, 'omics' technologies (e.g., genomics, proteomics, lipidomics) and computational modeling that point towards how multi-disciplinary efforts allow for important new insights. We also highlight some breakthrough studies as examples of the potential of these approaches, and suggest ways to make greater use of the power of interdisciplinarity. This review reflects discussions held at an interdisciplinary signaling workshop which facilitated knowledge exchange from experts from several different fields, including in silico modelers, computational biologists, biochemists, geneticists, molecular and cell biologists as well as cancer biologists and pharmacologists.
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Affiliation(s)
- Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich, UK. and Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, UK
| | | | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria and Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
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22
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Unveiling Hidden Dynamics of Hippo Signalling: A Systems Analysis. Genes (Basel) 2016; 7:genes7080044. [PMID: 27527217 PMCID: PMC4999832 DOI: 10.3390/genes7080044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 12/29/2022] Open
Abstract
The Hippo signalling pathway has recently emerged as an important regulator of cell apoptosis and proliferation with significant implications in human diseases. In mammals, the pathway contains the core kinases MST1/2, which phosphorylate and activate LATS1/2 kinases. The pro-apoptotic function of the MST/LATS signalling axis was previously linked to the Akt and ERK MAPK pathways, demonstrating that the Hippo pathway does not act alone but crosstalks with other signalling pathways to coordinate network dynamics and cellular outcomes. These crosstalks were characterised by a multitude of complex regulatory mechanisms involving competitive protein-protein interactions and phosphorylation mediated feedback loops. However, how these different mechanisms interplay in different cellular contexts to drive the context-specific network dynamics of Hippo-ERK signalling remains elusive. Using mathematical modelling and computational analysis, we uncovered that the Hippo-ERK network can generate highly diverse dynamical profiles that can be clustered into distinct dose-response patterns. For each pattern, we offered mechanistic explanation that defines when and how the observed phenomenon can arise. We demonstrated that Akt displays opposing, dose-dependent functions towards ERK, which are mediated by the balance between the Raf-1/MST2 protein interaction module and the LATS1 mediated feedback regulation. Moreover, Ras displays a multi-functional role and drives biphasic responses of both MST2 and ERK activities; which are critically governed by the competitive protein interaction between MST2 and Raf-1. Our study represents the first in-depth and systematic analysis of the Hippo-ERK network dynamics and provides a concrete foundation for future studies.
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23
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Nguyen LK, Kholodenko BN. Feedback regulation in cell signalling: Lessons for cancer therapeutics. Semin Cell Dev Biol 2016; 50:85-94. [DOI: 10.1016/j.semcdb.2015.09.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 09/28/2015] [Indexed: 02/06/2023]
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