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Doloman A, Besteman MS, Sanders MG, Sousa DZ. Methanogenic partner influences cell aggregation and signalling of Syntrophobacterium fumaroxidans. Appl Microbiol Biotechnol 2024; 108:127. [PMID: 38229305 DOI: 10.1007/s00253-023-12955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/18/2024]
Abstract
For several decades, the formation of microbial self-aggregates, known as granules, has been extensively documented in the context of anaerobic digestion. However, current understanding of the underlying microbial-associated mechanisms responsible for this phenomenon remains limited. This study examined morphological and biochemical changes associated with cell aggregation in model co-cultures of the syntrophic propionate oxidizing bacterium Syntrophobacterium fumaroxidans and hydrogenotrophic methanogens, Methanospirillum hungatei or Methanobacterium formicicum. Formerly, we observed that when syntrophs grow for long periods with methanogens, cultures tend to form aggregates visible to the eye. In this study, we maintained syntrophic co-cultures of S. fumaroxidans with either M. hungatei or M. formicicum for a year in a fed-batch growth mode to stimulate aggregation. Millimeter-scale aggregates were observed in both co-cultures within the first 5 months of cultivation. In addition, we detected quorum sensing molecules, specifically N-acyl homoserine lactones, in co-culture supernatants preceding the formation of macro-aggregates (with diameter of more than 20 μm). Comparative transcriptomics revealed higher expression of genes related to signal transduction, polysaccharide secretion and metal transporters in the late-aggregation state co-cultures, compared to the initial ones. This is the first study to report in detail both biochemical and physiological changes associated with the aggregate formation in syntrophic methanogenic co-cultures. KEYPOINTS: • Syntrophic co-cultures formed mm-scale aggregates within 5 months of fed-batch cultivation. • N-acyl homoserine lactones were detected during the formation of aggregates. • Aggregated co-cultures exhibited upregulated expression of adhesins- and polysaccharide-associated genes.
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Affiliation(s)
- Anna Doloman
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands.
| | - Maaike S Besteman
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Mark G Sanders
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Princetonlaan 6, 3584, CB, Utrecht, The Netherlands
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2
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Vincent AE, Chen C, Gomes TB, Di Leo V, Laalo T, Pabis K, Capaldi R, Marusich MF, McDonald D, Filby A, Fuller A, Lehmann Urban D, Zierz S, Deschauer M, Turnbull D, Reeve AK, Lawless C. A stagewise response to mitochondrial dysfunction in mitochondrial DNA maintenance disorders. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167131. [PMID: 38521420 DOI: 10.1016/j.bbadis.2024.167131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
Mitochondrial DNA (mtDNA) deletions which clonally expand in skeletal muscle of patients with mtDNA maintenance disorders, impair mitochondrial oxidative phosphorylation dysfunction. Previously we have shown that these mtDNA deletions arise and accumulate in perinuclear mitochondria causing localised mitochondrial dysfunction before spreading through the muscle fibre. We believe that mito-nuclear signalling is a key contributor in the accumulation and spread of mtDNA deletions, and that knowledge of how muscle fibres respond to mitochondrial dysfunction is key to our understanding of disease mechanisms. To understand the contribution of mito-nuclear signalling to the spread of mitochondrial dysfunction, we use imaging mass cytometry. We characterise the levels of mitochondrial Oxidative Phosphorylation proteins alongside a mitochondrial mass marker, in a cohort of patients with mtDNA maintenance disorders. Our expanded panel included protein markers of key signalling pathways, allowing us to investigate cellular responses to different combinations of oxidative phosphorylation dysfunction and ragged red fibres. We find combined Complex I and IV deficiency to be most common. Interestingly, in fibres deficient for one or more complexes, the remaining complexes are often upregulated beyond the increase of mitochondrial mass typically observed in ragged red fibres. We further find that oxidative phosphorylation deficient fibres exhibit an increase in the abundance of proteins involved in proteostasis, e.g. HSP60 and LONP1, and regulation of mitochondrial metabolism (including oxidative phosphorylation and proteolysis, e.g. PHB1). Our analysis suggests that the cellular response to mitochondrial dysfunction changes depending on the combination of deficient oxidative phosphorylation complexes in each fibre.
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Affiliation(s)
- Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK; NIHR Biomedical Research Centre, Faculty of Medical Sciences, Newcastle University, Newcastle, UK; John Walton Muscular Dystrophy Research Centre, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
| | - Chun Chen
- Wellcome Centre for Mitochondrial Research, Bioscience Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Tiago Bernardino Gomes
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK; NIHR Biomedical Research Centre, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Valeria Di Leo
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Tuomas Laalo
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kamil Pabis
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | | | | | - David McDonald
- Innovation, Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; Flow Cytometry Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Andrew Filby
- Innovation, Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; Flow Cytometry Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Andrew Fuller
- Innovation, Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; Flow Cytometry Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | | | - Stephan Zierz
- Department of Neurology, Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
| | - Marcus Deschauer
- Department of Neurology, Technical University Munich, Munich, Germany
| | - Doug Turnbull
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Amy K Reeve
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Conor Lawless
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK; NIHR Biomedical Research Centre, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
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3
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Cui Sun M, Otálora-Alcaraz A, Prenderville JA, Downer EJ. Toll-like receptor signalling as a cannabinoid target. Biochem Pharmacol 2024; 222:116082. [PMID: 38438052 DOI: 10.1016/j.bcp.2024.116082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/01/2024] [Accepted: 02/22/2024] [Indexed: 03/06/2024]
Abstract
Toll-like receptors (TLRs) have become a focus in biomedicine and biomedical research given the roles of this unique family of innate immune proteins in immune activation, infection, and autoimmunity. It is evident that TLR dysregulation, and subsequent alterations in TLR-mediated inflammatory signalling, can contribute to disease pathogenesis, and TLR targeted therapies are in development. This review highlights evidence that cannabinoids are key regulators of TLR signalling. Cannabinoids include component of the plant Cannabis sativa L. (C. sativa), synthetic and endogenous ligands, and overall represent a class of compounds whose therapeutic potential and mechanism of action continues to be elucidated. Cannabinoid-based medicines are in the clinic, and are furthermore under intense investigation for broad clinical development to manage symptoms of a range of disorders. In this review, we present an overview of research evidence that signalling linked to a range of TLRs is targeted by cannabinoids, and such cannabinoid mediated effects represent therapeutic avenues for further investigation. First, we provide an overview of TLRs, adaptors and key signalling events, alongside a summary of evidence that TLRs are linked to disease pathologies. Next, we discuss the cannabinoids system and the development of cannabinoid-based therapeutics. Finally, for the bulk of this review, we systematically outline the evidence that cannabinoids (plant-derived cannabinoids, synthetic cannabinoids, and endogenous cannabinoid ligands) can cross-talk with innate immune signalling governed by TLRs, focusing specifically on each member of the TLR family. Cannabinoids should be considered as key regulators of signalling controlled by TLRs, and such regulation should be a major focus in terms of the anti-inflammatory propensity of the cannabinoid system.
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Affiliation(s)
- Melody Cui Sun
- Discipline of Physiology, School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Almudena Otálora-Alcaraz
- Discipline of Physiology, School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Jack A Prenderville
- Discipline of Physiology, School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland; Transpharmation Ireland Limited, Institute of Neuroscience, Trinity College, Dublin 2, Ireland
| | - Eric J Downer
- Discipline of Physiology, School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.
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4
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Maroto IB, Moreno E, Costas-Insua C, Merino-Gracia J, Diez-Alarcia R, Álvaro-Blázquez A, Canales Á, Canela EI, Casadó V, Urigüen L, Rodríguez-Crespo I, Guzmán M. Selective inhibition of cannabinoid CB 1 receptor-evoked signalling by the interacting protein GAP43. Neuropharmacology 2023; 240:109712. [PMID: 37689260 DOI: 10.1016/j.neuropharm.2023.109712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
Cannabinoids exert pleiotropic effects on the brain by engaging the cannabinoid CB1 receptor (CB1R), a presynaptic metabotropic receptor that regulates key neuronal functions in a highly context-dependent manner. We have previously shown that CB1R interacts with growth-associated protein of 43 kDa (GAP43) and that this interaction inhibits CB1R function on hippocampal excitatory synaptic transmission, thereby impairing the therapeutic effect of cannabinoids on epileptic seizures in vivo. However, the underlying molecular features of this interaction remain unexplored. Here, we conducted mechanistic experiments on HEK293T cells co-expressing CB1R and GAP43 and show that GAP43 modulates CB1R signalling in a strikingly selective manner. Specifically, GAP43 did not affect the archetypical agonist-evoked (i) CB1R/Gi/o protein-coupled signalling pathways, such as cAMP/PKA and ERK, or (ii) CB1R internalization and intracellular trafficking. In contrast, GAP43 blocked an alternative agonist-evoked CB1R-mediated activation of the cytoskeleton-associated ROCK signalling pathway, which relied on the GAP43-mediated impairment of CB1R/Gq/11 protein coupling. GAP43 also abrogated CB1R-mediated ROCK activation in mouse hippocampal neurons, and this process led in turn to a blockade of cannabinoid-evoked neurite collapse. An NMR-based characterization of the CB1R-GAP43 interaction supported that GAP43 binds directly and specifically through multiple amino acid stretches to the C-terminal domain of the receptor. Taken together, our findings unveil a CB1R-Gq/11-ROCK signalling axis that is selectively impaired by GAP43 and may ultimately control neurite outgrowth.
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Affiliation(s)
- Irene B Maroto
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Estefanía Moreno
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine of the University of Barcelona, University of Barcelona, 08028, Barcelona, Spain
| | - Carlos Costas-Insua
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Javier Merino-Gracia
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
| | - Rebeca Diez-Alarcia
- Department of Pharmacology, University of the Basque Country/Euskal Herriko Unibertsitatea, 48940, Leioa, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029, Madrid, Spain; Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | - Alicia Álvaro-Blázquez
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Ángeles Canales
- Department of Organic Chemistry, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
| | - Enric I Canela
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine of the University of Barcelona, University of Barcelona, 08028, Barcelona, Spain
| | - Vicent Casadó
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine of the University of Barcelona, University of Barcelona, 08028, Barcelona, Spain
| | - Leyre Urigüen
- Department of Pharmacology, University of the Basque Country/Euskal Herriko Unibertsitatea, 48940, Leioa, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029, Madrid, Spain; Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | - Ignacio Rodríguez-Crespo
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Manuel Guzmán
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain.
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5
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Fyfe J, Dye D, Razak NBA, Metharom P, Falasca M. Immune evasion on the nanoscale: Small extracellular vesicles in pancreatic ductal adenocarcinoma immunity. Semin Cancer Biol 2023; 96:36-47. [PMID: 37748738 DOI: 10.1016/j.semcancer.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a type of cancer alarmingly expanding in our modern societies that is still proving to be very challenging to counteract. This disease constitutes a quintessential example of the multiple interactions existing between the tumour and its surrounding microenvironment. In particular, PDAC is characterized by a very immunosuppressive environment that favours cancer growth and makes this cancer type very resistant to immunotherapy. The primary tumour releases many factors that influence both the microenvironment and the immune landscape. Extracellular vesicles (EVs), recently identified as indispensable entities ensuring cell-to-cell communication in both physiological and pathological processes, seem to play a pivotal function in ensuring the delivery of these factors to the tumour-surrounding tissues. In this review, we summarize the present understanding on the crosstalk among tumour cells and the cellular immune microenvironment emphasizing the pro-malignant role played by extracellular vesicles. We also discuss how a greater knowledge of the roles of EVs in tumour immune escape could be translated into clinical applications.
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Affiliation(s)
- Jordan Fyfe
- Metabolic Signalling Group, Curtin Medical School, Curtin Health and Innovation Research Institute [1], Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Danielle Dye
- Curtin Medical School, Curtin Health and Innovation Research Institute [1], Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Norbaini Binti Abdol Razak
- Platelet Research Laboratory, Curtin Medical School, Curtin Health and Innovation Research Institute [1], Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Pat Metharom
- Platelet Research Laboratory, Curtin Medical School, Curtin Health and Innovation Research Institute [1], Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Marco Falasca
- Metabolic Signalling Group, Curtin Medical School, Curtin Health and Innovation Research Institute [1], Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia; University of Parma, Department of Medicine and Surgery, Via Volturno 39, 43125 Parma, Italy.
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6
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Glover HJ, Holliday H, Shparberg RA, Winkler D, Day M, Morris MB. Signalling pathway crosstalk stimulated by L-proline drives mouse embryonic stem cells to primitive-ectoderm-like cells. Development 2023; 150:dev201704. [PMID: 37823343 PMCID: PMC10652046 DOI: 10.1242/dev.201704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023]
Abstract
The amino acid L-proline exhibits growth factor-like properties during development - from improving blastocyst development to driving neurogenesis in vitro. Addition of 400 μM L-proline to self-renewal medium drives naïve mouse embryonic stem cells (ESCs) to early primitive ectoderm-like (EPL) cells - a transcriptionally distinct primed or partially primed pluripotent state. EPL cells retain expression of pluripotency genes, upregulate primitive ectoderm markers, undergo a morphological change and have increased cell number. These changes are facilitated by a complex signalling network hinging on the Mapk, Fgfr, Pi3k and mTor pathways. Here, we use a factorial experimental design coupled with statistical modelling to understand which signalling pathways are involved in the transition between ESCs and EPL cells, and how they underpin changes in morphology, cell number, apoptosis, proliferation and gene expression. This approach reveals pathways which work antagonistically or synergistically. Most properties were affected by more than one inhibitor, and each inhibitor blocked specific aspects of the naïve-to-primed transition. These mechanisms underpin progression of stem cells across the in vitro pluripotency continuum and serve as a model for pre-, peri- and post-implantation embryogenesis.
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Affiliation(s)
- Hannah J. Glover
- School of Medical Sciences, University of Sydney, Sydney 2006, Australia
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Holly Holliday
- School of Medical Sciences, University of Sydney, Sydney 2006, Australia
| | | | - David Winkler
- Department of Biochemistry and Chemistry, Latrobe Institute for Molecular Science, Latrobe University, Bundoora 3083, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
- Advanced Materials and Healthcare Technologies, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Margot Day
- School of Medical Sciences, University of Sydney, Sydney 2006, Australia
| | - Michael B. Morris
- School of Medical Sciences, University of Sydney, Sydney 2006, Australia
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Borah P, Sharma A, Sharma AK, Khurana P, Khurana JP. SCFOsFBK1 E3 ligase mediates jasmonic acid-induced turnover of OsATL53 and OsCCR14 to regulate lignification of rice anthers and roots. J Exp Bot 2023; 74:6188-6204. [PMID: 36317370 DOI: 10.1093/jxb/erac434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
The rice F-box protein OsFBK1, which mediates the turnover of a cinnamoyl CoA-reductase, OsCCR14, has previously been shown to regulate anther and root lignification. Here, we identify OsATL53, a member of the ATL family of RING-H2 proteins that interacts with OsCCR14 in the cytoplasm. OsATL53 was identified in the same yeast two-hybrid library screening as reported previously for OsCCR14, and we show it to have cytoplasmic localization and E3 ligase ubiquitination properties. SCFOsFBK1 mediates turnover of OsATL53 in the cytoplasm and the nucleus, and that of OsCCR14 only in the nucleus, as shown by cell-free degradation assays. Confocal fluorescence lifetime imaging microscopy analyses demonstrate that in presence of jasmonic acid (JA), which plays a role in anther dehiscence, OsATL53-OsCCR14 undergoes conformational changes that trigger the complex to accumulate around the nuclear periphery and signals OsFBK1 to initiate degradation of the proteins in the respective cellular compartments. OsATL53 decreases the enzymatic activity of OsCCR14 and sequesters it in the cytoplasm, thereby regulating the lignification process. Transgenic rice with knockdown of OsATL53 display increased lignin deposition in the anthers and roots compared to the wild type, whilst knockdown of OsCCR14 results in decreased lignin content. Our results show that OsATL53 affects the activity of OsCCR14, and that their JA-induced degradation by SCFOsFBK1 regulates lignification of rice anthers and roots.
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Affiliation(s)
- Pratikshya Borah
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi - 110021, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi - 110021, India
| | - Aishwarye Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi - 110021, India
| | - Arun Kumar Sharma
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi - 110021, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi - 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi - 110021, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi - 110021, India
| | - Jitendra Paul Khurana
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi - 110021, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi - 110021, India
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8
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Farnsworth KD. How biological codes break causal chains to enable autonomy for organisms. Biosystems 2023; 232:105013. [PMID: 37657747 DOI: 10.1016/j.biosystems.2023.105013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/03/2023]
Abstract
Autonomy, meaning freedom from exogenous control, requires independence of both constitution and cybernetic regulation. Here, the necessity of biological codes to achieve both is explained, assuming that Aristotelian efficient cause is 'formal cause empowered by physical force'. Constitutive independence requires closure to efficient causation (in the Rosen sense); cybernetic independence requires transformation of cause-effect into signal-response relations at the organism boundary; the combination of both kinds of independence enables adaptation and evolution. Codes and cyphers translate information from one form of physical embodiment (domain) to another. Because information can only contribute as formal cause to efficient cause within the domain of its embodiment, translation can extend or restrict the range over which information is effective. Closure to efficient causation requires internalised information to be isolated from the cycle of efficient causes that it informs: e.g. Von Neumann self-replicator requires a (template) source of information that is causally isolated from the physical replication system. Life operationalises this isolation with the genetic code translating from the (isolated) domain of codons to that of protein interactions. Separately, cybernetic freedom is achieved at the cell boundary because transducers, which embody molecular coding, translate exogenous information into a domain where it no longer has the power of efficient cause. Information, not efficient cause, passes through the boundary to serve as stimulus for an internally generated response. Coding further extends freedom by enabling historically accumulated information to be selectively transformed into efficient cause under internal control, leaving it otherwise stored inactive. Code-based translation thus enables selective causal isolation, controlling the flow from cause to effect. Genetic code, cell-signalling codes and, in eukaryotes, the histone code, signal sequence based protein sorting and other code-dependent processes all regulate and separate causal chains. The existence of life can be seen as an expression of the power of molecular codes to selectively isolate and thereby organise causal relations among molecular interactions to form an organism.
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Affiliation(s)
- Keith D Farnsworth
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT95DL, UK.
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9
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Abukwaik R, Vera-Siguenza E, Tennant DA, Spill F. Interplay of p53 and XIAP protein dynamics orchestrates cell fate in response to chemotherapy. J Theor Biol 2023; 572:111562. [PMID: 37348784 DOI: 10.1016/j.jtbi.2023.111562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/06/2023] [Accepted: 06/16/2023] [Indexed: 06/24/2023]
Abstract
Chemotherapeutic drugs are used to treat almost all types of cancer, but the intended response, i.e., elimination, is often incomplete, with a subset of cancer cells resisting treatment. Two critical factors play a role in chemoresistance: the p53 tumour suppressor gene and the X-linked inhibitor of apoptosis (XIAP). These proteins have been shown to act synergistically to elicit cellular responses upon DNA damage induced by chemotherapy, yet, the mechanism is poorly understood. This study introduces a mathematical model characterising the apoptosis pathway activation by p53 before and after mitochondrial outer membrane permeabilisation upon treatment with the chemotherapy Doxorubicin (Dox). "In-silico" simulations show that the p53 dynamics change dose-dependently. Under medium to high doses of Dox, p53 concentration ultimately stabilises to a high level regardless of XIAP concentrations. However, caspase-3 activation may be triggered or not depending on the XIAP induction rate, ultimately determining whether the cell will perish or resist. Consequently, the model predicts that failure to activate apoptosis in some cancer cells expressing wild-type p53 might be due to heterogeneity between cells in upregulating the XIAP protein, rather than due to the p53 protein concentration. Our model suggests that the interplay of the p53 dynamics and the XIAP induction rate is critical to determine the cancer cells' therapeutic response.
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Affiliation(s)
- Roba Abukwaik
- Mathematics Department, Faculty of Science and Arts, King Abdulaziz University, Rabigh, Saudi Arabia; School of Mathematics, University of Birmingham, B15 2TS, United Kingdom.
| | - Elias Vera-Siguenza
- School of Mathematics, University of Birmingham, B15 2TS, United Kingdom; Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, B15 2TT, United Kingdom.
| | - Daniel A Tennant
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, B15 2TT, United Kingdom
| | - Fabian Spill
- School of Mathematics, University of Birmingham, B15 2TS, United Kingdom.
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Abstract
Although recognized earlier as subcellular entities by microscopists, mitochondria have been the subject of functional studies since 1922, when their biochemical similarities with bacteria were first noted. In this overview I trace the history of research on mitochondria from that time up to the present day, focussing on the major milestones of the overlapping eras of mitochondrial biochemistry, genetics, pathology and cell biology, and its explosion into new areas in the past 25 years. Nowadays, mitochondria are considered to be fully integrated into cell physiology, rather than serving specific functions in isolation.
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Affiliation(s)
- Howard T Jacobs
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Department of Environment and Genetics, La Trobe University, Melbourne, VIC, Australia.
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11
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Cerqueira JVA, de Andrade MT, Rafael DD, Zhu F, Martins SVC, Nunes-Nesi A, Benedito V, Fernie AR, Zsögön A. Anthocyanins and reactive oxygen species: a team of rivals regulating plant development? Plant Mol Biol 2023; 112:213-223. [PMID: 37351824 PMCID: PMC10352431 DOI: 10.1007/s11103-023-01362-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
Abstract
Anthocyanins are a family of water-soluble vacuolar pigments present in almost all flowering plants. The chemistry, biosynthesis and functions of these flavonoids have been intensively studied, in part due to their benefit for human health. Given that they are efficient antioxidants, intense research has been devoted to studying their possible roles against damage caused by reactive oxygen species (ROS). However, the redox homeostasis established between antioxidants and ROS is important for plant growth and development. On the one hand, high levels of ROS can damage DNA, proteins, and lipids, on the other, they are also required for cell signaling, plant development and stress responses. Thus, a balance is needed in which antioxidants can remove excessive ROS, while not precluding ROS from triggering important cellular signaling cascades. In this article, we discuss how anthocyanins and ROS interact and how a deeper understanding of the balance between them could help improve plant productivity, nutritional value, and resistance to stress, while simultaneously maintaining proper cellular function and plant growth.
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Affiliation(s)
- João Victor A Cerqueira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Moab T de Andrade
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Diego D Rafael
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Feng Zhu
- Max-Planck-Institute for Molecular Plant Physiology, 14476, Potsdam, Germany
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, National R&D Center for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Samuel V C Martins
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Vagner Benedito
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Alisdair R Fernie
- Max-Planck-Institute for Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- Max-Planck-Institute for Molecular Plant Physiology, 14476, Potsdam, Germany
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12
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Yuan L, Bu S, Du M, Wang Y, Ju C, Huang D, Xu W, Tan X, Liang M, Deng S, Yang L, Huang K. RNF207 exacerbates pathological cardiac hypertrophy via post-translational modification of TAB1. Cardiovasc Res 2023; 119:183-194. [PMID: 35352799 DOI: 10.1093/cvr/cvac039] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/14/2022] [Accepted: 03/14/2022] [Indexed: 11/14/2022] Open
Abstract
AIMS The heart undergoes pathological remodelling, featured by the hypertrophic growth of cardiomyocytes and increased cardiac fibrosis, under biomechanical stress such as haemodynamic overload. Ring Finger Protein 207 (RNF207) is an E3 ubiquitin ligase that is predominantly expressed in the heart, but its function remains elusive. In this study, we aimed to explore the role of RNF207 in the development of pathological cardiac hypertrophy and dysfunction. METHODS AND RESULTS Transverse aortic constriction (TAC) surgery was performed on mice to induce cardiac hypertrophy. Cardiac function and remodelling were evaluated by echocardiography, histological assessment, and molecular analyses. Our data indicated that RNF207 overexpression (OE) exacerbated cardiac hypertrophy, fibrosis, and systolic dysfunction. In contrast, TAC-induced cardiac remodelling was profoundly blunted in RNF207 knockdown (KD) hearts. In line with the in vivo findings, RNF207 OE augmented, whereas RNF207 KD alleviated, phenylephrine-induced cardiomyocyte hypertrophy in vitro. Mechanistically, we demonstrated that RNF207 elicited detrimental effects by promoting K63-linked ubiquitination of TAK1-binding protein 1 (TAB1), which triggered the autophosphorylation of transforming growth factor-β activated kinase 1 (TAK1) and the activation of downstream p38 and c-Jun N-terminal kinase (JNK)1/2 signalling pathways. In the TAB1-KD cardiomyocytes, RNF207-OE-induced cell hypertrophy was significantly attenuated, indicating that RNF207-induced hypertrophy is, at least in part, TAB1-dependent. CONCLUSIONS This study demonstrates that RNF207 exacerbates pressure overload-induced cardiac hypertrophy and dysfunction via post-translational modification of TAB1.
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Affiliation(s)
- Lin Yuan
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
- Department of Cardiology, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, China
| | - Shichen Bu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Meng Du
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Yilong Wang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Chenhui Ju
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Dandan Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Wenjing Xu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Xin Tan
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Minglu Liang
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Shan Deng
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Liu Yang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Kai Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Ave, Wuhan 430022, Hubei, China
- Clinic Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, Hubei, China
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13
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Yang J, Niu H, Pang S, Liu M, Chen F, Li Z, He L, Mo J, Yi H, Xiao J, Huang Y. MARK3 kinase: Regulation and physiologic roles. Cell Signal 2023; 103:110578. [PMID: 36581219 DOI: 10.1016/j.cellsig.2022.110578] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/14/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022]
Abstract
Microtubule affinity-regulating kinase 3 (MARK3), a member of the MARK family, regulates several essential pathways, including the cell cycle, ciliated cell differentiation, and osteoclast differentiation. It is important to understand the control of their activities as MARK3 contains an N-terminal serine/threonine kinase domain, ubiquitin-associated domain, and C-terminal kinase-associated domain, which perform multiple regulatory functions. These functions include post-translational modification (e.g., phosphorylation) and interaction with scaffolding and other proteins. Differences in the amino acid sequence and domain position result in different three-dimensional protein structures and affect the function of MARK3, which distinguish it from the other MARK family members. Recent data indicate a potential role of MARK3 in several pathological conditions, including congenital blepharophimosis syndrome, osteoporosis, and tumorigenesis. The present review focuses on the physiological and pathological role of MARK3, its regulation, and recent developments in the small molecule inhibitors of the MARK3 signalling cascade.
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Affiliation(s)
- Jingyu Yang
- Surgery of Mammary Gland and Thyroid Gland, the First People's Hospital of Yunnan Province, Panlong Campus, 157 Jinbi Road, Kunming 650032, Yunnan, People's Republic of China
| | - Heng Niu
- Surgery of Mammary Gland and Thyroid Gland, the First People's Hospital of Yunnan Province, Panlong Campus, 157 Jinbi Road, Kunming 650032, Yunnan, People's Republic of China
| | - ShiGui Pang
- Cancer Research Institute, The Affiliated Hospital of Guilin Medical University, Xiufeng Campus, 15 Lequn Road, Guilin 541001, Guangxi, People's Republic of China
| | - Mignlong Liu
- Cancer Research Institute, The Affiliated Hospital of Guilin Medical University, Xiufeng Campus, 15 Lequn Road, Guilin 541001, Guangxi, People's Republic of China
| | - Feng Chen
- Cancer Research Institute, The Affiliated Hospital of Guilin Medical University, Xiufeng Campus, 15 Lequn Road, Guilin 541001, Guangxi, People's Republic of China
| | - Zhaoxin Li
- Cancer Research Institute, The Affiliated Hospital of Guilin Medical University, Xiufeng Campus, 15 Lequn Road, Guilin 541001, Guangxi, People's Republic of China
| | - Lifei He
- Cancer Research Institute, The Affiliated Hospital of Guilin Medical University, Xiufeng Campus, 15 Lequn Road, Guilin 541001, Guangxi, People's Republic of China
| | - Jianmei Mo
- Cancer Research Institute, The Affiliated Hospital of Guilin Medical University, Xiufeng Campus, 15 Lequn Road, Guilin 541001, Guangxi, People's Republic of China
| | - Huijun Yi
- Cancer Research Institute, The Affiliated Hospital of Guilin Medical University, Xiufeng Campus, 15 Lequn Road, Guilin 541001, Guangxi, People's Republic of China
| | - Juanjuan Xiao
- Cancer Research Institute, The Affiliated Hospital of Guilin Medical University, Xiufeng Campus, 15 Lequn Road, Guilin 541001, Guangxi, People's Republic of China
| | - Yingze Huang
- Cancer Research Institute, The Affiliated Hospital of Guilin Medical University, Xiufeng Campus, 15 Lequn Road, Guilin 541001, Guangxi, People's Republic of China.
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14
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Roy A, Patra SK. Lipid Raft Facilitated Receptor Organization and Signaling: A Functional Rheostat in Embryonic Development, Stem Cell Biology and Cancer. Stem Cell Rev Rep 2023; 19:2-25. [PMID: 35997871 DOI: 10.1007/s12015-022-10448-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2022] [Indexed: 01/29/2023]
Abstract
Molecular views of plasma membrane organization and dynamics are gradually changing over the past fifty years. Dynamics of plasma membrane instigate several signaling nexuses in eukaryotic cells. The striking feature of plasma membrane dynamics is that, it is internally transfigured into various subdomains of clustered macromolecules. Lipid rafts are nanoscale subdomains, enriched with cholesterol and sphingolipids, reside as floating entity mostly on the exoplasmic leaflet of the lipid bilayer. In terms of functionality, lipid rafts are unique among other membrane subdomains. Herein, advances on the roles of lipid rafts in cellular physiology and homeostasis are discussed, precisely, on how rafts dynamically harbor signaling proteins, including GPCRs, catalytic receptors, and ionotropic receptors within it and orchestrate multiple signaling pathways. In the developmental proceedings signaling are designed for patterning of overall organism and they differ from the somatic cell physiology and signaling of fully developed organisms. Some of the developmental signals are characteristic in maintenance of stemness and activated during several types of tumor development and cancer progression. The harmony between extracellular signaling and lineage specific transcriptional programs are extremely important for embryonic development. The roles of plasma membrane lipid rafts mediated signaling in lineage specificity, early embryonic development, stem cell maintenance are emerging. In view of this, we have highlighted and analyzed the roles of lipid rafts in receptor organization, cell signaling, and gene expression during embryonic development; from pre-implantation through the post-implantation phase, in stem cell and cancer biology.
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Affiliation(s)
- Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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15
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Fullstone G. Rapid Particle-Based Simulations of Cellular Signalling with the FLAME-Accelerated Signalling Tool (FaST) and GPUs. Methods Mol Biol 2023; 2634:191-212. [PMID: 37074580 DOI: 10.1007/978-1-0716-3008-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Cellular signalling is a vital process in living organisms for coordinating highly diverse responses to various stimuli. Particle-based modelling excels in its ability to model complex features of cellular signalling pathways including stochasticity, spatial effects, and heterogeneity, thus improving our understanding of critical decision processes in biology. Yet, particle-based modelling is computationally prohibitive to implement. We recently developed FaST (FLAME-accelerated signalling tool), a software tool that harnesses the power of high-performance computation to reduce the computational burden of particle-based modelling. In particular, employing the unique massively parallel architecture of graphic processing units (GPUs) provided extreme speed ups of simulations by >650-fold. In this chapter, we provide a step-by-step walkthrough of how to use FaST to create GPU-accelerated simulations of a simple cellular signalling network. We further explore how the flexibility of FaST can be used to implement entirely customized simulations while still including the intrinsic speed up advantages of GPU-based parallelization.
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Affiliation(s)
- Gavin Fullstone
- Institute for Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.
- Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany.
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16
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Halder S, Ghosh S, Chattopadhyay J, Chatterjee S. Understanding noise in cell signalling in the prospect of drug-targets. J Theor Biol 2022; 555:111298. [PMID: 36202233 DOI: 10.1016/j.jtbi.2022.111298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/04/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
Abstract
The introduction of noise to signals can alter central regulatory switches of cellular processes leading to diseases. Noise is inherently present in the cellular signalling system and plays a decisive role in the input-output (I/O) relation. The current study aims to understand the noise tolerance of motif structures in the cell signalling processes. The vulnerability of a node to noise could be a significant factor in causing signalling error and need to be controlled. We developed stochastic differential equation (SDE) based mathematical models for different network motifs with two nodes and studied the association between motif structure and signal-noise relation. A two-dimensional parameter space analysis on motif sensitivity with noise and input signal variation was performed to classify and rank the motifs. Identifying sensitive motifs and their high druggability infers their significance in screening potential drug-target candidates. Finally, we proposed a theoretical framework to identify nodes from a network as potential drug targets. We applied this mathematical formalism to three cancer networks to identify drug-targets and validated them with existing databases.
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Affiliation(s)
- Suvankar Halder
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India
| | - Sumana Ghosh
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India
| | - Joydev Chattopadhyay
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata 700108, India
| | - Samrat Chatterjee
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India.
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17
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Wu Y, Clark KC, Nguyen EV, Niranjan B, Horvath LG, Taylor RA, Daly RJ. Proteomic characterisation of prostate cancer intercellular communication reveals cell type-selective signalling and TMSB4X-dependent fibroblast reprogramming. Cell Oncol (Dordr) 2022; 45:1311-1328. [PMID: 36169805 DOI: 10.1007/s13402-022-00719-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In prostate cancer, the tumour microenvironment (TME) represents an important regulator of disease progression and response to treatment. In the TME, cancer-associated fibroblasts (CAFs) play a key role in tumour progression, however the mechanisms underpinning fibroblast-cancer cell interactions are incompletely resolved. Here, we address this by applying cell type-specific labelling with amino acid precursors (CTAP) and mass spectrometry (MS)-based (phospho)proteomics to prostate cancer for the first time. METHODS Reciprocal interactions between PC3 prostate cancer cells co-cultured with WPMY-1 prostatic fibroblasts were characterised using CTAP-MS. Signalling network changes were determined using Metascape and Enrichr and visualised using Cytoscape. Thymosin β4 (TMSB4X) overexpression was achieved via retroviral transduction and assayed by ELISA. Cell motility was determined using Transwell and random cell migration assays and expression of CAF markers by indirect immunofluorescence. RESULTS WPMY-1 cells co-cultured with PC3s demonstrated a CAF-like phenotype, characterised by enhanced PDGFRB expression and alterations in signalling pathways regulating epithelial-mesenchymal transition, cytoskeletal organisation and cell polarisation. In contrast, co-cultured PC3 cells exhibited more modest network changes, with alterations in mTORC1 signalling and regulation of the actin cytoskeleton. The expression of the actin binding protein TMSB4X was significantly decreased in co-cultured WPMY-1 fibroblasts, and overexpression of TMSB4X in fibroblasts decreased migration of co-cultured PC3 cells, reduced fibroblast motility, and protected the fibroblasts from being educated to a CAF-like phenotype by prostate cancer cells. CONCLUSIONS This study highlights the potential of CTAP-MS to characterise intercellular communication within the prostate TME and identify regulators of cellular crosstalk such as TMSB4X.
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Affiliation(s)
- Yunjian Wu
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Kimberley C Clark
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Elizabeth V Nguyen
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Birunthi Niranjan
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Lisa G Horvath
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- University of Sydney, Camperdown, NSW, 2006, Australia
- Chris O'Brien Lifehouse, Camperdown, NSW, 2050, Australia
| | - Renea A Taylor
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Department of Physiology, Monash University, Clayton, VIC, 3800, Australia
- Cancer Research Division, Peter MacCallum Cancer Centre, The University of Melbourne, Melbourne, VIC, 3800, Australia
| | - Roger J Daly
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.
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18
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Riley JS, Bock FJ. Voices from beyond the grave: The impact of apoptosis on the microenvironment. Biochim Biophys Acta Mol Cell Res 2022; 1869:119341. [PMID: 35987283 DOI: 10.1016/j.bbamcr.2022.119341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/22/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Programmed cell death, in particular apoptosis, has vital functions in every healthy organism. In a highly regulated manner cells which are no longer needed or are harmful to the organism undergo suicide. More than just the mere elimination of a cell, apoptosis is increasingly being recognized performing important roles in cellular communication with the microenvironment. These interactions with surrounding cells can have various, and sometimes competing outcomes. Apoptotic cells can promote survival, proliferation and inflammation, but depending on the context also prevent survival and inflammation. In this review, we will summarize the emerging literature on how dying cells can transfer information to their neighbours, and which outcomes this communication has for the whole tissue.
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Affiliation(s)
- Joel S Riley
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
| | - Florian J Bock
- Department of Radiotherapy (MAASTRO), GROW-School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands.
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19
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Wuerz M, Lawson CA, Ueland M, Oakley CA, Grossman AR, Weis VM, Suggett DJ, Davy SK. Symbiosis induces unique volatile profiles in the model cnidarian Aiptasia. J Exp Biol 2022; 225:277243. [PMID: 36156083 DOI: 10.1242/jeb.244600] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022]
Abstract
The establishment and maintenance of the symbiosis between a cnidarian host and its dinoflagellate symbionts is central to the success of coral reefs. To explore the metabolite production underlying this symbiosis, we focused on a group of low weight secondary metabolites, biogenic volatile organic compounds (BVOCs). BVOCs are released from an organism or environment, and can be collected in the gas phase, allowing non-invasive analysis of an organism's metabolism (i.e. 'volatilomics'). We characterised volatile profiles of the sea anemone Exaiptasia diaphana ('Aiptasia'), a model system for cnidarian-dinoflagellate symbiosis, using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry. We compared volatile profiles between: 1) symbiotic anemones containing their native symbiont, Breviolum minutum; 2) aposymbiotic anemones; and 3) cultured isolates of B. minutum. Overall, 152 BVOCs were detected, and classified into 14 groups based on their chemical structure, the most numerous groups being alkanes and aromatic compounds. A total of 53 BVOCs were differentially abundant between aposymbiotic anemones and B. minutum cultures; 13 between aposymbiotic and symbiotic anemones; and 60 between symbiotic anemones and cultures of B. minutum. More BVOCs were differentially abundant between cultured and symbiotic dinoflagellates than between aposymbiotic and symbiotic anemones, suggesting that symbiosis may modify symbiont physiology more than host physiology. This is the first volatilome analysis of the Aiptasia model system and provides a foundation from which to explore how BVOC production is perturbed under environmental stress, and ultimately the role they play in this important symbiosis.
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Affiliation(s)
- Maggie Wuerz
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Caitlin A Lawson
- Climate Change Cluster, University of Technology Sydney, Sydney Broadway, NSW, Australia.,School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Maiken Ueland
- Centre for Forensic Science, School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney Broadway, NSW, Australia
| | - Clinton A Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Arthur R Grossman
- Carnegie Institution of Washington, Department of Plant Biology, Stanford, California, USA
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, Sydney Broadway, NSW, Australia
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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20
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Zhdanov AV, Golubeva AV, Yordanova MM, Andreev DE, Ventura-Silva AP, Schellekens H, Baranov PV, Cryan JF, Papkovsky DB. Ghrelin rapidly elevates protein synthesis in vitro by employing the rpS6K-eEF2K-eEF2 signalling axis. Cell Mol Life Sci 2022; 79:426. [PMID: 35841486 PMCID: PMC9288388 DOI: 10.1007/s00018-022-04446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 11/27/2022]
Abstract
Activated ghrelin receptor GHS-R1α triggers cell signalling pathways that modulate energy homeostasis and biosynthetic processes. However, the effects of ghrelin on mRNA translation are unknown. Using various reporter assays, here we demonstrate a rapid elevation of protein synthesis in cells within 15–30 min upon stimulation of GHS-R1α by ghrelin. We further show that ghrelin-induced activation of translation is mediated, at least in part, through the de-phosphorylation (de-suppression) of elongation factor 2 (eEF2). The levels of eEF2 phosphorylation at Thr56 decrease due to the reduced activity of eEF2 kinase, which is inhibited via Ser366 phosphorylation by rpS6 kinases. Being stress-susceptible, the ghrelin-mediated decrease in eEF2 phosphorylation can be abolished by glucose deprivation and mitochondrial uncoupling. We believe that the observed burst of translation benefits rapid restocking of neuropeptides, which are released upon GHS-R1α activation, and represents the most time- and energy-efficient way of prompt recharging the orexigenic neuronal circuitry.
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Affiliation(s)
- Alexander V Zhdanov
- School of Biochemistry & Cell Biology, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, Ireland.
| | - Anna V Golubeva
- Department of Anatomy & Neuroscience, University College Cork, Cork, Ireland
| | - Martina M Yordanova
- School of Biochemistry & Cell Biology, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, Ireland
| | - Dmitry E Andreev
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Ana Paula Ventura-Silva
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Harriet Schellekens
- Department of Anatomy & Neuroscience, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry & Cell Biology, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, Ireland
| | - John F Cryan
- Department of Anatomy & Neuroscience, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Dmitri B Papkovsky
- School of Biochemistry & Cell Biology, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, Ireland
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21
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Gómez-Jaramillo L, Cano-Cano F, Campos-Caro A, Álcala M, Álvarez-Gallego F, Arroba AI, Aguilar-Diosdado M. Adult kidney explants is a physiologic model for studying diabetic nephropathy. Life Sci 2022; 300:120575. [PMID: 35472452 DOI: 10.1016/j.lfs.2022.120575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022]
Abstract
Inflammatory processes play a central role in the pathogenesis of diabetic nephropathy (DN) in the early stages of the disease. In vitro approach using cell lines help to understand the mechanisms involves and allow the molecular and biochemical processes. Adult kidney (AK) explants remain an essential instrument for advancing our understanding of the molecular and cellular regulation of signalling pathways from an organotipic view with physiological system interaction integrated. AK explants from T1DM animal model (BB rat) are obtained by slicing central kidney area preserving the organ's cytoarchitecture and reproduce the classical events detected during the DN in an in vivo model such as inflammation, epithelial-mesenchymal transition (EMT) processes by the modulation of a-SMA and e-Cadherin among others which have been determined by qRT-PCR, western-blot and immunohistochemistry. In this regard, AK explants reproduce the signalling pathways involve in DN progression (proinflammatory NFkB and inflammasome complex). This work demonstrates AK explants is a physiological experimental approach for studying the development and progression of DN. Furthermore, the inflammatory processes in AK explants under a diabetic environment and/or BB rats could be modulated by potential treatments for DN.
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Affiliation(s)
- Laura Gómez-Jaramillo
- Unidad de Investigación, Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain; Departamento de Endocrinología y Nutrición, Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, Spain.
| | - Fátima Cano-Cano
- Unidad de Investigación, Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain; Departamento de Endocrinología y Nutrición, Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, Spain.
| | - Antonio Campos-Caro
- Unidad de Investigación, Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain; Área de Genética, Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Cádiz, Spain.
| | - Martín Álcala
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad CEU-San Pablo, CEU Universities, 28668, Madrid, Spain.
| | - Fabiola Álvarez-Gallego
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad CEU-San Pablo, CEU Universities, 28668, Madrid, Spain.
| | - Ana I Arroba
- Unidad de Investigación, Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain; Departamento de Endocrinología y Nutrición, Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, Spain.
| | - Manuel Aguilar-Diosdado
- Unidad de Investigación, Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain; Departamento de Endocrinología y Nutrición, Hospital Universitario Puerta del Mar, Universidad de Cádiz, Cádiz, Spain.
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22
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Oyagbemi AA, Adejumobi OA, Jarikre TA, Ajani OS, Asenuga ER, Gbadamosi IT, Adedapo ADA, Aro AO, Ogunpolu BS, Hassan FO, Falayi OO, Ogunmiluyi IO, Omobowale TO, Arojojoye OA, Ola-Davies OE, Saba AB, Adedapo AA, Emikpe BO, Oyeyemi MO, Nkadimeng SM, McGaw LJ, Kayoka-Kabongo PN, Oguntibeju OO, Yakubu MA. Clofibrate, a Peroxisome Proliferator-Activated Receptor-Alpha (PPARα) Agonist, and Its Molecular Mechanisms of Action against Sodium Fluoride-Induced Toxicity. Biol Trace Elem Res 2022; 200:1220-1236. [PMID: 33893992 DOI: 10.1007/s12011-021-02722-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/12/2021] [Indexed: 01/16/2023]
Abstract
Sodium fluoride (NaF) is one of the neglected environmental pollutants. It is ubiquitously found in the soil, water, and environment. Interestingly, fluoride has been extensively utilized for prevention of dental caries and tartar formation, and may be added to mouthwash, mouth rinse, and toothpastes. This study is aimed at mitigating fluoride-induced hypertension and nephrotoxicity with clofibrate, a peroxisome proliferator-activated receptor-alpha (PPARα) agonist. For this study, forty male Wistar rats were used and randomly grouped into ten rats per group, control, sodium fluoride (NaF; 300 ppm) only, NaF plus clofibrate (250 mg/kg) and NaF plus lisinopril (10 mg/kg), respectively, for 7 days. The administration of NaF was by drinking water ad libitum, while clofibrate and lisinopril were administered by oral gavage. Administration of NaF induced hypertension, and was accompanied with exaggerated oxidative stress; depletion of antioxidant defence system; reduced nitric oxide production; increased systolic, diastolic and mean arterial pressure; activation of angiotensin-converting enzyme activity and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB); and testicular apoptosis. Treatment of rats with clofibrate reduced oxidative stress, improved antioxidant status, lowered high blood pressure through the inhibition of angiotensin-converting enzyme activity, mineralocorticoid receptor over-activation, and abrogated testicular apoptosis. Taken together, clofibrate could offer exceptional therapeutic benefit in mitigating toxicity associated with sodium fluoride.
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Affiliation(s)
- Ademola Adetokunbo Oyagbemi
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria.
| | - Olumuyiwa Abiola Adejumobi
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Theophilus Aghogho Jarikre
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olumide Samuel Ajani
- Department of Theriogenology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Ebunoluwa Racheal Asenuga
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Benin, Benin, Nigeria
| | | | | | - Abimbola Obemisola Aro
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, University of South Africa, Florida, South Africa
| | - Blessing Seun Ogunpolu
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Fasilat Oluwakemi Hassan
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olufunke Olubunmi Falayi
- Department of Veterinary Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Iyanuoluwa Omolola Ogunmiluyi
- Department of Veterinary Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Temidayo Olutayo Omobowale
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Olufunke Eunice Ola-Davies
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adebowale Benard Saba
- Department of Veterinary Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeolu Alex Adedapo
- Department of Veterinary Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Benjamin Obukowho Emikpe
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Sanah Malomile Nkadimeng
- Phytomedicine Programme, Department of Paraclinical Science, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, Pretoria, 0110, South Africa
| | - Lyndy Joy McGaw
- Phytomedicine Programme, Department of Paraclinical Science, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, Pretoria, 0110, South Africa
| | - Prudence Ngalula Kayoka-Kabongo
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, University of South Africa, Florida, South Africa
| | - Oluwafemi Omoniyi Oguntibeju
- Phytomedicine and Phytochemistry Group, Oxidative Stress Research Centre, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, Cape Town, 7535, South Africa
| | - Momoh Audu Yakubu
- Department of Environmental & Interdisciplinary Sciences, College of Science, Engineering & Technology, Vascular Biology Unit, Center for Cardiovascular Diseases, Texas Southern University, Houston, TX, USA
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23
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Arora A, Taskinen JH, Olkkonen VM. Coordination of inter-organelle communication and lipid fluxes by OSBP-related proteins. Prog Lipid Res 2022; 86:101146. [PMID: 34999137 DOI: 10.1016/j.plipres.2022.101146] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/10/2021] [Accepted: 01/03/2022] [Indexed: 12/31/2022]
Abstract
Oxysterol-binding protein (OSBP) and OSBP-related proteins (ORPs) constitute one of the largest families of lipid-binding/transfer proteins (LTPs) in eukaryotes. The current view is that many of them mediate inter-organelle lipid transfer over membrane contact sites (MCS). The transfer occurs in several cases in a 'counter-current' fashion: A lipid such as cholesterol or phosphatidylserine (PS) is transferred against its concentration gradient driven by transport of a phosphoinositide in the opposite direction. In this way ORPs are envisioned to maintain the distinct organelle lipid compositions, with impacts on multiple organelle functions. However, the functions of ORPs extend beyond lipid homeostasis to regulation of processes such as cell survival, proliferation and migration. Important expanding areas of mammalian ORP research include their roles in viral and bacterial infections, cancers, and neuronal function. The yeast OSBP homologue (Osh) proteins execute multifaceted functions in sterol and glycerophospholipid homeostasis, post-Golgi vesicle transport, phosphatidylinositol-4-phosphate, sphingolipid and target of rapamycin (TOR) signalling, and cell cycle control. These observations identify ORPs as lipid transporters and coordinators of signals with an unforeseen variety of cellular processes. Understanding their activities not only enlightens the biology of the living cell but also allows their employment as targets of new therapeutic approaches for disease.
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Affiliation(s)
- Amita Arora
- Minerva Foundation Institute for Medical Research, and Department of Anatomy, Faculty of Medicine, University of Helsinki, Finland
| | - Juuso H Taskinen
- Minerva Foundation Institute for Medical Research, and Department of Anatomy, Faculty of Medicine, University of Helsinki, Finland
| | - Vesa M Olkkonen
- Minerva Foundation Institute for Medical Research, and Department of Anatomy, Faculty of Medicine, University of Helsinki, Finland.
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24
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Bellizzi Y, Anselmi Relats JM, Cornier PG, Delpiccolo CML, Mata EG, Cayrol F, Cremaschi GA, Blank VC, Roguin LP. Contribution of endoplasmic reticulum stress, MAPK and PI3K/Akt pathways to the apoptotic death induced by a penicillin derivative in melanoma cells. Apoptosis 2021. [PMID: 34773171 DOI: 10.1007/s10495-021-01697-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2021] [Indexed: 12/21/2022]
Abstract
We have previously examined the in vitro and in vivo antitumor action of TAP7f, a synthetic triazolylpeptidyl penicillin, on murine melanoma cells. In this work, we explored the signal transduction pathways modulated by TAP7f in murine B16-F0 and human A375 melanoma cells, and the contribution of some intracellular signals to the apoptotic cell death. TAP7f decreased ERK1/2 phosphorylation and increased phospho-p38, phospho-JNK and phospho-Akt levels. ERK1/2 blockage suppressed cell growth, while inhibition of p38, JNK and PI3K-I pathways reduced the antitumor effect of TAP7f. Pharmacological inhibition of p38 and JNK, or blockage of PI3K-I/Akt cascade with a dominant negative PI3K-I mutant diminished Bax expression levels and PARP-1 cleavage, indicating the involvement of these pathways in apoptosis. PI3K-I/Akt inhibition also favored an autophagic response, as evidenced by the higher expression levels of Beclin-1 and LC3-II detected in transfected cells exposed to TAP7f. However, although PI3K-I/Akt blockage promoted an autophagic survival response, this mechanism appears not to be critical for TAP7f antitumor action. It was also shown that TAP7f induced ER stress by enhancing the expression of ER stress-related genes and proteins. Downregulation of CHOP protein with specific siRNA increased cell growth and decreased cleavage of PARP-1, supporting its role in apoptosis. Furthermore, it was found that activation of p38, JNK and Akt occurred downstream ER perturbation. In summary, our results showed that TAP7f triggers an apoptotic cell death in melanoma cells through induction of ER stress and activation of p38, JNK and PI3K-I/Akt pathways.
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25
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Girisa S, Henamayee S, Parama D, Rana V, Dutta U, Kunnumakkara AB. Targeting Farnesoid X receptor (FXR) for developing novel therapeutics against cancer. Mol Biomed 2021; 2:21. [PMID: 35006466 PMCID: PMC8607382 DOI: 10.1186/s43556-021-00035-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/17/2021] [Indexed: 12/14/2022] Open
Abstract
Cancer is one of the lethal diseases that arise due to the molecular alterations in the cell. One of those alterations associated with cancer corresponds to differential expression of Farnesoid X receptor (FXR), a nuclear receptor regulating bile, cholesterol homeostasis, lipid, and glucose metabolism. FXR is known to regulate several diseases, including cancer and cardiovascular diseases, the two highly reported causes of mortality globally. Recent studies have shown the association of FXR overexpression with cancer development and progression in different types of cancers of breast, lung, pancreas, and oesophagus. It has also been associated with tissue-specific and cell-specific roles in various cancers. It has been shown to modulate several cell-signalling pathways such as EGFR/ERK, NF-κB, p38/MAPK, PI3K/AKT, Wnt/β-catenin, and JAK/STAT along with their targets such as caspases, MMPs, cyclins; tumour suppressor proteins like p53, C/EBPβ, and p-Rb; various cytokines; EMT markers; and many more. Therefore, FXR has high potential as novel biomarkers for the diagnosis, prognosis, and therapy of cancer. Thus, the present review focuses on the diverse role of FXR in different cancers and its agonists and antagonists.
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Affiliation(s)
- Sosmitha Girisa
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory and DBT-AIST International Center for Translational and Environmental Research (DAICENTER), Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Sahu Henamayee
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory and DBT-AIST International Center for Translational and Environmental Research (DAICENTER), Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Dey Parama
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory and DBT-AIST International Center for Translational and Environmental Research (DAICENTER), Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Varsha Rana
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory and DBT-AIST International Center for Translational and Environmental Research (DAICENTER), Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Uma Dutta
- Cell and Molecular Biology Lab, Department of Zoology, Cotton University, Guwahati, Assam, 781001, India.
| | - Ajaikumar B Kunnumakkara
- Department of Biosciences and Bioengineering, Cancer Biology Laboratory and DBT-AIST International Center for Translational and Environmental Research (DAICENTER), Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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26
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Lim WK, Kaur P, Huang H, Jo RS, Ramamoorthy A, Ng LF, Suresh J, Maisha FI, Mathuru AS, Tolwinski NS. Optogenetic approaches for understanding homeostatic and degenerative processes in Drosophila. Cell Mol Life Sci 2021; 78:5865-5880. [PMID: 34232330 PMCID: PMC8260576 DOI: 10.1007/s00018-021-03836-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/22/2021] [Accepted: 04/08/2021] [Indexed: 12/18/2022]
Abstract
Many organs and tissues have an intrinsic ability to regenerate from a dedicated, tissue-specific stem cell pool. As organisms age, the process of self-regulation or homeostasis begins to slow down with fewer stem cells available for tissue repair. Tissues become more fragile and organs less efficient. This slowdown of homeostatic processes leads to the development of cellular and neurodegenerative diseases. In this review, we highlight the recent use and future potential of optogenetic approaches to study homeostasis. Optogenetics uses photosensitive molecules and genetic engineering to modulate cellular activity in vivo, allowing precise experiments with spatiotemporal control. We look at applications of this technology for understanding the mechanisms governing homeostasis and degeneration as applied to widely used model organisms, such as Drosophila melanogaster, where other common tools are less effective or unavailable.
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Affiliation(s)
- Wen Kin Lim
- Science Division, Yale-NUS College, Singapore, Singapore
| | - Prameet Kaur
- Science Division, Yale-NUS College, Singapore, Singapore
| | - Huanyan Huang
- Science Division, Yale-NUS College, Singapore, Singapore
| | | | | | - Li Fang Ng
- Science Division, Yale-NUS College, Singapore, Singapore
| | - Jahnavi Suresh
- Science Division, Yale-NUS College, Singapore, Singapore
| | | | - Ajay S Mathuru
- Science Division, Yale-NUS College, Singapore, Singapore
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27
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Maiques O, Sanz-Moreno V. Location, location, location: Melanoma cells "living at the edge". Exp Dermatol 2021; 31:82-88. [PMID: 34185923 DOI: 10.1111/exd.14423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/13/2021] [Accepted: 06/11/2021] [Indexed: 01/26/2023]
Abstract
Abnormal cell migration and invasion underlie metastatic dissemination, one of the major challenges for cancer treatment. Melanoma is one of the deadliest and most aggressive forms of skin cancer due in part to its migratory and metastatic potential. Cancer cells use a variety of migratory strategies regulated by cytoskeletal remodelling. In particular, we discuss the importance of amoeboid invasive melanoma strategies, since they have been identified at the edge of human melanomas. We hypothesize that the presence of amoeboid melanoma cells will favour tumor progression since they are invasive and metastatic; they support immunosuppression; they harbour cancer stem cell properties and they are involved in therapy resistance. The Rho-ROCK-Myosin II pathway is key to maintain amoeboid melanoma invasion but this pathway is further regulated by pro-tumorigenic/pro-metastatic/pro-survival signalling pathways such as JAK-STAT3, TGFβ-SMAD, NF-κB, Wnt11/5-FDZ7 and BRAFV600E -MEK-ERK. These pathways support amoeboid behaviour and are actionable in the clinic. After melanoma wide surgical margin removal, we propose that possible remaining melanoma cells should be eradicated using anti-amoeboid therapies.
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Affiliation(s)
- Oscar Maiques
- Barts Cancer Institute, John Vane Science Building, Queen Mary University of London, London, UK
| | - Victoria Sanz-Moreno
- Barts Cancer Institute, John Vane Science Building, Queen Mary University of London, London, UK
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28
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Storniolo CE, Pequera M, Company F, Moreno JJ. 12(S)-hydroxyheptadeca-5Z,8E,10E-trienoic acid (12-HHT) induces cell growth and improves barrier function through BLT2 interaction in intestinal epithelial Caco-2 cell cultures. Biochem Pharmacol 2021; 190:114663. [PMID: 34161796 DOI: 10.1016/j.bcp.2021.114663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 11/23/2022]
Abstract
12(S)-hydroxyheptadeca-5Z,8E,10E-trienoic acid (12-HHT) is an unusual product of the cyclooxygenase pathway that is an endogenous ligand of the low-affinity receptor for leukotriene 4 (LTB4), BLT2. Recent findings suggested that BLT2 possibly plays an important role in the healing of intestinal lesions and the regulation of barrier function. Here, we studied the role of 12-HHT on intestinal epithelial cell growth and the paracellular permeability of intestinal epithelium using Caco-2 cell cultures as experimental model. Our results demonstrated that 12-HHT stimulates intestinal epithelial Caco-2 cell growth through 12-HHT-BLT2-p38-PKC axis and improves paracellular permeability in differentiated Caco-2 cell cultures through the regulation of tight junction elements such as myosin light chain phosphorylation through 12-HHT-BLT2-p38-PKC-MYPT1 axis. Thus, 12-HHT-BLT2 interaction can be involved in intestinal epithelial cell growth and consequently in the epithelium regeneration/repair processes, together with an interesting improvement on the paracellular permeability. These effects appoint that 12-HHT/BLT2 axis may be a suitable strategy for treating wound healing epithelium and barrier-disrupted intestinal processes.
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29
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Swaroop B SS, Kanumuri R, Ezhil I, Naidu Sampangi JK, Kremerskothen J, Rayala SK, Venkatraman G. KIBRA connects Hippo signaling and cancer. Exp Cell Res 2021; 403:112613. [PMID: 33901448 DOI: 10.1016/j.yexcr.2021.112613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 12/14/2022]
Abstract
The Hippo signaling pathway is a tumor suppressor pathway that plays an important role in tissue homeostasis and organ size control. KIBRA is one of the many upstream regulators of the Hippo pathway. It functions as a tumor suppressor by positively regulating the core Hippo kinase cascade. However, there are accumulating shreds of evidence showing that KIBRA has an oncogenic function, which we speculate may arise from its functions away from the Hippo pathway. In this review, we have attempted to provide an overview of the Hippo signaling with a special emphasis on evidence showing the paradoxical role of KIBRA in cancer.
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Affiliation(s)
- Srikanth Swamy Swaroop B
- Department of Human Genetics, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, 600116, Tamil Nadu, India; Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, 600036, Tamil Nadu, India
| | - Rahul Kanumuri
- Department of Human Genetics, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, 600116, Tamil Nadu, India; Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, 600036, Tamil Nadu, India
| | - Inemai Ezhil
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, 600036, Tamil Nadu, India
| | - Jagadeesh Kumar Naidu Sampangi
- Department of Human Genetics, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, 600116, Tamil Nadu, India
| | - Joachim Kremerskothen
- Department of Nephrology, Hypertension and Rheumatology, University Hospital Münster, Münster, Germany
| | - Suresh Kumar Rayala
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, 600036, Tamil Nadu, India.
| | - Ganesh Venkatraman
- Department of Human Genetics, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, 600116, Tamil Nadu, India.
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30
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Lu J, Wood D, Ingley E, Koks S, Wong D. Update on genomic and molecular landscapes of well-differentiated liposarcoma and dedifferentiated liposarcoma. Mol Biol Rep 2021; 48:3637-3647. [PMID: 33893924 DOI: 10.1007/s11033-021-06362-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/16/2021] [Indexed: 01/13/2023]
Abstract
Well-differentiated liposarcoma (WDLPS) is the most frequent subtype of liposarcoma and may transform into dedifferentiated liposarcoma (DDLPS) which is a more aggressive subtype. Retroperitoneal lesions of WDLPS/DDLPS tend to recur repeatedly due to incomplete resections, and adjuvant chemotherapy and radiotherapy have little effect on patient survival. Consequently, identifying therapeutic targets and developing targeted drugs is critical for improving the outcome of WDLPS/DDLPS patients. In this review, we summarised the mutational landscape of WDLPS/DDLPS from recent studies focusing on potential oncogenic drivers and the development of molecular targeted drugs for DDLPS. Due to the limited number of studies on the molecular networks driving WDLPS to DDLPS development, we looked at other dedifferentiation-related tumours to identify potential parallel mechanisms that could be involved in the dedifferentiation process generating DDLPS.
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Affiliation(s)
- Jun Lu
- Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, 6009, Australia. .,Cell Signalling Group, Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
| | - David Wood
- Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Evan Ingley
- Cell Signalling Group, Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.,Discipline of Medical, Molecular and Forensic Sciences, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6009, Australia
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, 6009, Australia
| | - Daniel Wong
- Anatomical Pathology, PathWest, QEII Medical Centre, Perth, WA, 6009, Australia
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Melo CM, Nader HB, Justo GZ, Pinhal MAS. Heparanase modulation by Wingless/INT (Wnt). Mol Biol Rep 2021; 48:3117-3125. [PMID: 33891270 DOI: 10.1007/s11033-021-06348-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
Heparanase is an endo-beta-glucuronidase, the only enzyme in mammals capable of cleaving heparan sulfate/heparin chains from proteoglycans. The oligosaccharides generated by heparanase present extensive biological functions since such oligosaccharides interact with adhesion molecules, growth factors, angiogenic factors and cytokines, modulating cell proliferation, migration, inflammation, and carcinogenesis. However, the regulation of heparanase activity is not fully understood. It is known that heparanase is synthesized as an inactive 65 kDa isoform and that post-translation processing forms an active 50 kDa enzyme. In the present study, we are interested in investigating whether heparanase is regulated by its own substrate as observed with many other enzymes. Wild-type Chinese hamster (Cricetulus griséus) ovary cells (CHO-K1) were treated with different doses of heparin. Heparanase expression was analyzed by Real-time PCR and flow cytometry. Also, heparanase activity was measured. The heparanase activity assay was performed using a coated plate with biotinylated heparan sulfate. In the present assay, a competitive heparin inhibition scenario was set aside. Exogenous heparin trigged a cell signaling pathway that increased heparanase mRNA and protein levels. The Wnt/beta-catenin pathway, judged by TCF-driven luciferase activity, seems to be involved to enhance heparanase profile during treatment with exogenous heparin. Lithium chloride treatment, an activator of the Wnt/beta-catenin pathway, confirmed such mechanism of transduction in vivo using zebrafish embryos and in vitro using CHO-K1 cells. Taken together the results suggest that heparin modulates heparanase expression by Wnt/beta-catenin.
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Affiliation(s)
- Carina Mucciolo Melo
- Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio, 100, 4a. andar, Biologia Molecular, São Paulo, SP, 04044-020, Brazil.,Department of Biochemistry, Faculdade de Medicina do ABC, Avenida Príncipe de Gales, 821, Bioquímica, Santo André, SP, 09060-650, Brazil
| | - Helena Bonciani Nader
- Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio, 100, 4a. andar, Biologia Molecular, São Paulo, SP, 04044-020, Brazil
| | - Giselle Zenker Justo
- Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio, 100, 4a. andar, Biologia Molecular, São Paulo, SP, 04044-020, Brazil.,Department of Biochemistry, Universidade Federal de São Paulo, Rua Prof. Artur Riedel, no. 275 - Jd. Eldorado, Diadema, SP, CEP: 09972-270, Brazil
| | - Maria Aparecida Silva Pinhal
- Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio, 100, 4a. andar, Biologia Molecular, São Paulo, SP, 04044-020, Brazil. .,Department of Biochemistry, Faculdade de Medicina do ABC, Avenida Príncipe de Gales, 821, Bioquímica, Santo André, SP, 09060-650, Brazil.
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Redza-Dutordoir M, Averill-Bates DA. Interactions between reactive oxygen species and autophagy: Special issue: Death mechanisms in cellular homeostasis. Biochim Biophys Acta Mol Cell Res 2021; 1868:119041. [PMID: 33872672 DOI: 10.1016/j.bbamcr.2021.119041] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023]
Abstract
Oxidative stress is defined as "a serious imbalance between the generation of reactive oxygen species (ROS) and antioxidant defences in favour of ROS, causing excessive oxidative damage to biomolecules". Different stressors that induce autophagy, such as starvation and hypoxia, can increase production of ROS such as superoxide and hydrogen peroxide. This review provides brief summaries about oxidative stress and macroautophagy, and then considers current knowledge about the complex interactions between ROS and autophagy. ROS-induced autophagy could be a cellular protective mechanism that alleviates oxidative stress, or a destructive process. Increased ROS levels can regulate autophagy through several different pathways, such as activation of the AMPK signalling cascade and ULK1 complex, Atg4 oxidation, disruption of the Bcl-2/Beclin-1 interaction, and alteration of mitochondrial homeostasis leading to mitophagy. Autophagic degradation of Keap1 activates the antioxidant transcription factor Nrf2 and protects cells against ROS. Autophagy activation can, in turn, regulate oxidative stress by recycling damaged ROS-producing mitochondria. Macroautophagy plays an important role in degradation of large aggregates of oxidatively damaged/unfolded proteins, which are removed by the autophagy-lysosomal system. ROS can regulate autophagy, and in turn, autophagy can regulate oxidative stress. Future studies are necessary to improve understanding of the complex interactions between autophagy and oxidative stress.
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Araújo RDS, Bernardes RC, Martins GF. A mixture containing the herbicides Mesotrione and Atrazine imposes toxicological risks on workers of Partamona helleri. Sci Total Environ 2021; 763:142980. [PMID: 33121769 DOI: 10.1016/j.scitotenv.2020.142980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/30/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
A mixture of Mesotrione and Atrazine (Calaris®) has been reported as an improvement of the atrazine herbicides, which are agrochemicals used for weed control. However, its possible harmful effects on non-target organisms, including pollinators, needs to be better understood. In this work, the effects of the mix of herbicides on food consumption, behaviour (walking distance, and meandering), and the morphology of the midgut of the stingless bee Partamona helleri were studied. Foragers were orally exposed to different concentrations of the mix. The concentrations leading to 10% and 50% mortality (LC10 and LC50, respectively) were estimated and used in the analysis of behaviour and morphology. The ingestion of contaminated diets (50% aqueous sucrose solution + mix) led to a reduction in food consumption by the bees when compared to the control, bees fed a non-contaminated diet (sucrose solution). Ingestion of the LC50 diet reduced locomotor activity, increased meandering, induced the degradation of the epithelium and peritrophic matrix, and also changed the number of cells positive for signalling-pathway proteins in the midgut. These results show the potential toxicological effects and environmental impacts of the mix of herbicides in beneficial insects, including a native bee.
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du Plessis M, Davis T, Loos B, Pretorius E, de Villiers WJS, Engelbrecht AM. Molecular regulation of autophagy in a pro-inflammatory tumour microenvironment: New insight into the role of serum amyloid A. Cytokine Growth Factor Rev 2021; 59:71-83. [PMID: 33727011 DOI: 10.1016/j.cytogfr.2021.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023]
Abstract
Chronic inflammation, systemic or local, plays a vital role in tumour progression and metastasis. Dysregulation of key physiological processes such as autophagy elicit unfavourable immune responses to induce chronic inflammation. Cytokines, growth factors and acute phase proteins present in the tumour microenvironment regulate inflammatory responses and alter crosstalk between various signalling pathways involved in the progression of cancer. Serum amyloid A (SAA) is a key acute phase protein secreted by the liver during the acute phase response (APR) following infection or injury. However, cancer and cancer-associated cells produce SAA, which when present in high levels in the tumour microenvironment contributes to cancer initiation, progression and metastasis. SAA can activate several signalling pathways such as the PI3K and MAPK pathways, which are also known modulators of the intracellular degradation process, autophagy. Autophagy can be regarded as having a double edged sword effect in cancer. Its dysregulation can induce malignant transformation through metabolic stress which manifests as oxidative stress, endoplasmic reticulum (ER) stress and DNA damage. On the other hand, autophagy can promote cancer survival during metabolic stress, hypoxia and senescence. Autophagy has been utilised to promote the efficiency of chemotherapeutic agents and can either be inhibited or induced to improve treatment outcomes. This review aims to address the known mechanisms that regulate autophagy as well as illustrating the role of SAA in modulating these pathways and its clinical implications for cancer therapy.
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Affiliation(s)
- M du Plessis
- Department of Physiological Sciences, University of Stellenbosch, Stellenbosch, South Africa.
| | - T Davis
- Department of Physiological Sciences, University of Stellenbosch, Stellenbosch, South Africa
| | - B Loos
- Department of Physiological Sciences, University of Stellenbosch, Stellenbosch, South Africa
| | - E Pretorius
- Department of Physiological Sciences, University of Stellenbosch, Stellenbosch, South Africa
| | - W J S de Villiers
- African Cancer Institute (ACI), Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa; Department of Internal Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Campus, South Africa
| | - A M Engelbrecht
- Department of Physiological Sciences, University of Stellenbosch, Stellenbosch, South Africa; Department of Internal Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Campus, South Africa
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Abstract
Cysteine relays, where a protein or small molecule is transferred multiple times via transthiolation, are central to the production of biological polymers. Enzymes that utilise relay mechanisms display broad substrate specificity and are readily engineered to produce new polymers. In this review, I discuss recent advances in the discovery, engineering and biophysical characterisation of cysteine relays. I will focus on eukaryotic ubiquitin (Ub) cascades and prokaryotic polyhydroxyalkanoate (PHA) synthesis. These evolutionarily distinct processes employ similar chemistry and are readily modified for biotechnological applications. Both processes have been studied intensively for decades, yet recent studies suggest we do not fully understand their mechanistic diversity or plasticity. I will discuss the important role that activity-based probes (ABPs) and other chemical tools have had in identifying and delineating Ub cysteine-relays and the potential for ABPs to be applied to PHA synthases. Finally, I will offer a personal perspective on the potential of engineering cysteine-relays for non-native polymer production.
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36
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Roy D, Sadanandom A. SUMO mediated regulation of transcription factors as a mechanism for transducing environmental cues into cellular signaling in plants. Cell Mol Life Sci 2021; 78:2641-2664. [PMID: 33452901 PMCID: PMC8004507 DOI: 10.1007/s00018-020-03723-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/25/2020] [Accepted: 11/25/2020] [Indexed: 12/31/2022]
Abstract
Across all species, transcription factors (TFs) are the most frequent targets of SUMOylation. The effect of SUMO conjugation on the functions of transcription factors has been extensively studied in animal systems, with over 200 transcription factors being documented to be modulated by SUMOylation. This has resulted in the establishment of a number of paradigms that seek to explain the mechanisms by which SUMO regulates transcription factor functions. For instance, SUMO has been shown to modulate TF DNA binding activity; regulate both localization as well as the abundance of TFs and also influence the association of TFs with chromatin. With transcription factors being implicated as master regulators of the cellular signalling pathways that maintain phenotypic plasticity in all organisms, in this review, we will discuss how SUMO mediated regulation of transcription factor activity facilitates molecular pathways to mount an appropriate and coherent biological response to environmental cues.
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Affiliation(s)
- Dipan Roy
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK.
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37
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Luu BE, Hawkins LJ, Storey KB. Insights from a vertebrate model organism on the molecular mechanisms of whole-body dehydration tolerance. Mol Cell Biochem 2021; 476:2381-92. [PMID: 33595794 DOI: 10.1007/s11010-021-04072-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/16/2021] [Indexed: 10/25/2022]
Abstract
Studies on the molecular mechanisms of dehydration tolerance have been largely limited to plants and invertebrates. Currently, research in whole body dehydration of complex animals is limited to cognitive and behavioral effects in humans, leaving the molecular mechanisms of vertebrate dehydration relatively unexplored. The present review summarizes studies to date on the African clawed frog (Xenopus laevis) and examines whole-body dehydration on physiological, cellular and molecular levels. This aquatic frog is exposed to seasonal droughts in its native habitat and can endure a loss of over 30% of its total body water. When coping with dehydration, osmoregulatory processes prioritize water retention in skeletal tissues and vital organs over plasma volume. Although systemic blood circulation is maintained in the vital organs and even elevated in the brain during dehydration, it is done so at the expense of reduced circulation to the skeletal muscles. Increased hemoglobin affinity for oxygen helps to counteract impaired blood circulation and metabolic enzymes show altered kinetic and regulatory parameters that support the use of anaerobic glycolysis. Recent studies with X. laevis also show that pro-survival pathways such as antioxidant defenses and heat shock proteins are activated in an organ-specific manner during dehydration. These pathways are tightly coordinated at the post-transcriptional level by non-coding RNAs, and at the post-translational level by reversible protein phosphorylation. Paired with ongoing research on the X. laevis genome, the African clawed frog is poised to be an ideal animal model with which to investigate the molecular adaptations for dehydration tolerance much more deeply.
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38
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Setiawan I, Sanjaya A, Lesmana R, Yen PM, Goenawan H. Hippo pathway effectors YAP and TAZ and their association with skeletal muscle ageing. J Physiol Biochem 2021; 77:63-73. [PMID: 33495890 DOI: 10.1007/s13105-021-00787-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 01/07/2021] [Indexed: 12/17/2022]
Abstract
Skeletal muscle atrophy commonly occurs during ageing, thus pathways that regulate muscle mass may represent a potential therapeutic avenue for interventions. In this review, we explored the Hippo signalling pathway which plays an essential role in human oncogenesis and the pathway's influence on myogenesis and satellite cell functions, on supporting cells such as fibroblasts, and autophagy. YAP/TAZ was found to regulate both myoblast proliferation and differentiation, albeit with unique roles. Additionally, YAP/TAZ has different functions depending on the expressing cell type, making simple inference of their effects difficult. Studies in cancers have shown that the Hippo pathway influenced the autophagy pathway, although with mixed results. Most of the present researches on YAP/TAZ are focused on its oncogenicity and further studies are needed to translate these findings to physiological ageing. Taken together, the modulation of YAP/TAZ or the Hippo pathway in general may offer potential new strategies for the prevention or treatment of ageing.
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Abstract
Cell division, differentiation and function are largely dependent on accurate proteome composition and regulated gene expression. To control this, protein synthesis is an intricate process governed by upstream signalling pathways. Eukaryotic translation is a multistep process and can be separated into four distinct phases: initiation, elongation, termination and recycling of ribosomal subunits. Translation initiation, the focus of this article, is highly regulated to control the activity and/or function of eukaryotic initiation factors (eIFs) and permit recruitment of mRNAs to the ribosomes. In this Cell Science at a Glance and accompanying poster, we outline the mechanisms by which tumour cells alter the process of translation initiation and discuss how this benefits tumour formation, proliferation and metastasis.
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Affiliation(s)
- Rachael C L Smith
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, G61 1QH, UK
| | - Georgios Kanellos
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Nikola Vlahov
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | | | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge CB2 1QW, UK
| | - John R P Knight
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Owen J Sansom
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, G61 1QH, UK
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40
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Makino T, Mizawa M, Yoshihisa Y, Yamamoto S, Tabuchi Y, Miyai M, Hibino T, Sasahara M, Shimizu T. Trichohyalin-like 1 protein plays a crucial role in proliferation and anti-apoptosis of normal human keratinocytes and squamous cell carcinoma cells. Cell Death Discov 2020; 6:109. [PMID: 33133644 PMCID: PMC7591909 DOI: 10.1038/s41420-020-00344-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
Epidermal differentiation is a complex process that requires the regulated and sequential expression of various genes. Most fused-type S100 proteins are expressed in the granular layer and it is hypothesized that these proteins may be associated with cornification and barrier formation. We previously identified a member of the fused-type S100 proteins, Trichohyalin-like 1 (TCHHL1) protein. TCHHL1 is distributed in the basal layer of the normal epidermis. Furthermore, the expression is markedly increased in cancerous/non-cancerous skin samples with the hyperproliferation of keratinocytes. We herein examined the role of TCHHL1 in normal human keratinocytes (NHKs) and squamous cell carcinoma (SCC). The knockdown of TCHHL1 by transfection with TCHHL1 siRNA significantly inhibited proliferation and induced the early apoptosis of NHKs. In TCHHL1-knockdown NHKs, the level of extracellular signal-regulated kinase 1/2 (ERK1/2) phosphorylation was markedly decreased. In addition, the slight inhibition of v-akt murine thymoma viral oncogene homolog (AKT) phosphorylation and upregulation of forkhead box-containing protein O1(FOXO1), B-cell lymphoma2 (BCL2) and Bcl2-like protein 11 (BCL2L11) was observed. Skin-equivalent models built by TCHHL1-knockdown NHKs showed a markedly hypoplastic epidermis. These findings highlight that TCHHL1 plays an important role in homeostasis of the normal epidermis. TCHHL1 was expressed in the growing cells of cutaneous SCC; therefore, we next examined an association with the cell growth in HSC-1 cells (a human SCC line). In HSC-1 cells, the knockdown of TCHHL1 also suppressed cell proliferation and induced apoptosis. These cells showed an inhibition of phosphorylation of ERK1/2, AKT and signal transducers and activator of transcription 3, and the significant upregulation of FOXO1, BCL2, and BCL2L11. Accordingly, TCHHL1 is associated with survival of cutaneous SCC. In addition, we hypothesize that TCHHL1 may be a novel therapeutic target in cutaneous SCC.
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Affiliation(s)
- Teruhiko Makino
- Department of Dermatology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Toyama, Japan
| | - Megumi Mizawa
- Department of Dermatology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Toyama, Japan
| | - Yoko Yoshihisa
- Department of Dermatology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Toyama, Japan
| | - Seiji Yamamoto
- Department of Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Toyama, Japan
| | - Yoshiaki Tabuchi
- Division of Molecular Genetics Research, Life Science Center, University of Toyama, Toyama, Toyama, Japan
| | - Masashi Miyai
- Shiseido Global Innovation Center, Yokohama, Kanagawa Japan
| | | | - Masakiyo Sasahara
- Department of Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Toyama, Japan
| | - Tadamichi Shimizu
- Department of Dermatology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Toyama, Japan
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Foster AD, Downing P, Figredo E, Polain N, Stott A, Layfield R, Rea SL. ALS-associated TBK1 variant p.G175S is defective in phosphorylation of p62 and impacts TBK1-mediated signalling and TDP-43 autophagic degradation. Mol Cell Neurosci 2020; 108:103539. [PMID: 32835772 DOI: 10.1016/j.mcn.2020.103539] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
Mutations affecting SQSTM1 coding for p62 and TANK-Binding Kinase 1 (TBK1) have been implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). TBK1 is a serine-threonine kinase that regulates p62's activity as an autophagy receptor via phosphorylation and also has roles in neuroinflammatory signalling pathways. The mechanisms underlying ALS and FTLD pathogenesis as a result of TBK1 mutations are incompletely understood, however, loss of TBK1 function can lead to dysregulated autophagy and mitophagy. Here, we report that an ALS-associated TBK1 variant affecting the kinase domain, p.G175S, is defective in phosphorylation of p62 at Ser-403, a modification critical for regulating its ubiquitin-binding function, as well as downstream phosphorylation at Ser-349. Consistent with these findings, expression of p.G175S TBK1 was associated with decreased induction of autophagy compared to wild type and reduced degradation of the ALS-linked protein TDP-43. Expression of wild type TBK1 increased NF-κB signalling ~300 fold in comparison to empty vector cells, whereas p.G175S TBK1 was unable to promote NF-κB signalling above levels observed in empty vector transfected cells. We also noted a hitherto unknown role for TBK1 as a suppressor of oxidative stress (Nrf2) signalling and show that p.G175S TBK1 expressing cells lose this inhibitory function. Our data suggest that TBK1 ALS mutations may broadly impair p62-mediated cell signalling, which ultimately may reduce neuronal survival, in addition TDP-43 was not efficiently degraded, together these effects may contribute to TBK1 mutation associated ALS and FTLD pathogenesis.
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Affiliation(s)
- A D Foster
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, Western Australia, Australia; Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia; Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, Western Australia, Australia; Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Health Research Building, Discovery Way, Murdoch, WA, Australia
| | - P Downing
- School of Health Sciences, Notre Dame University, Fremantle, Western Australia, Australia
| | - E Figredo
- School of Health Sciences, Notre Dame University, Fremantle, Western Australia, Australia
| | - N Polain
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Health Research Building, Discovery Way, Murdoch, WA, Australia
| | - A Stott
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, Western Australia, Australia; Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - R Layfield
- School of Health Sciences, Notre Dame University, Fremantle, Western Australia, Australia; School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - S L Rea
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, Western Australia, Australia; Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia; Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, Western Australia, Australia; Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Health Research Building, Discovery Way, Murdoch, WA, Australia.
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42
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Tonello E, Siebert H. Boolean analysis of lateral inhibition. J Math Biol 2020; 81:463-86. [PMID: 32728826 DOI: 10.1007/s00285-020-01515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 12/09/2019] [Indexed: 11/03/2022]
Abstract
We study Boolean networks which are simple spatial models of the highly conserved Delta-Notch system. The models assume the inhibition of Delta in each cell by Notch in the same cell, and the activation of Notch in presence of Delta in surrounding cells. We consider fully asynchronous dynamics over undirected graphs representing the neighbour relation between cells. In this framework, one can show that all attractors are fixed points for the system, independently of the neighbour relation, for instance by using known properties of simplified versions of the models, where only one species per cell is defined. The fixed points correspond to the so-called fine-grained "patterns" that emerge in discrete and continuous modelling of lateral inhibition. We study the reachability of fixed points, giving a characterisation of the trap spaces and the basins of attraction for both the full and the simplified models. In addition, we use a characterisation of the trap spaces to investigate the robustness of patterns to perturbations. The results of this qualitative analysis can complement and guide simulation-based approaches, and serve as a basis for the investigation of more complex mechanisms.
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43
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Ethier SP, Guest ST, Garrett-Mayer E, Armeson K, Wilson RC, Duchinski K, Couch D, Gray JW, Kappler C. Development and implementation of the SUM breast cancer cell line functional genomics knowledge base. NPJ Breast Cancer 2020; 6:30. [PMID: 32715085 PMCID: PMC7374090 DOI: 10.1038/s41523-020-0173-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/23/2020] [Indexed: 12/24/2022] Open
Abstract
Several years ago, the SUM panel of human breast cancer cell lines was developed, and these cell lines have been distributed to hundreds of labs worldwide. Our lab and others have developed extensive omics data sets from these cells. More recently, we performed genome-scale shRNA essentiality screens on the entire SUM line panel, as well as on MCF10A cells, MCF-7 cells, and MCF-7LTED cells. These gene essentiality data sets allowed us to perform orthogonal analyses that functionalize the otherwise descriptive genomic data obtained from traditional genomics platforms. To make these omics data sets available to users of the SUM lines, and to allow users to mine these data sets, we developed the SUM Breast Cancer Cell Line Knowledge Base. This knowledge base provides information on the derivation of each cell line, provides protocols for the proper maintenance of the cells, and provides a series of data mining tools that allow rapid identification of the oncogene signatures for each line, the enrichment of KEGG pathways with screen hit and gene expression data, an analysis of protein and phospho-protein expression for the cell lines, as well as a gene search tool and a functional-druggable signature tool. Recently, we expanded our database to include genomic data for an additional 27 commonly used breast cancer cell lines. Thus, the SLKBase provides users with deep insights into the biology of human breast cancer cell lines that can be used to develop strategies for the reverse engineering of individual breast cancer cell lines.
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Affiliation(s)
- Stephen P Ethier
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
| | - Stephen T Guest
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
- Present Address: Department of Biomedical Informatics, University of Michigan Medical School, Ann Arbor, MI USA
| | - Elizabeth Garrett-Mayer
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
- Present Address: American Society for Clinical Oncology, Charleston, SC USA
| | - Kent Armeson
- Biostatistics Core, Hollings Cancer Center, Charleston, SC USA
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
| | - Kathryn Duchinski
- Department of Computer Science, The College of Charleston, Charleston, SC USA
- Present Address: Program in Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA USA
| | - Daniel Couch
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health and Sciences University, Portland, OR USA
| | - Christiana Kappler
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC USA
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Abstract
Profilin is a ubiquitously expressed protein well known as a key regulator of actin polymerisation. The actin cytoskeleton is involved in almost all cellular processes including motility, endocytosis, metabolism, signal transduction and gene transcription. Hence, profilin's role in the cell goes beyond its direct and essential function in regulating actin dynamics. This review will focus on the interactions of Profilin 1 and its ligands at the plasma membrane, in the cytoplasm and the nucleus of the cells and the regulation of profilin activity within those cell compartments. We will discuss the interactions of profilin in cell signalling pathways and highlight the importance of the cell context in the multiple functions that this small essential protein has in conjunction with its role in cytoskeletal organisation and dynamics. We will review some of the mechanisms that control profilin expression and the implications of changed expression of profilin in the light of cancer biology and other pathologies.
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45
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Zhang Y, Yang F, Ling S, Lv P, Zhou Y, Fang W, Sun W, Zhang L, Shi P, Tian C. Single-particle cryo-EM structural studies of the β 2AR-Gs complex bound with a full agonist formoterol. Cell Discov 2020; 6:45. [PMID: 32655881 PMCID: PMC7338445 DOI: 10.1038/s41421-020-0176-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 05/07/2020] [Indexed: 01/19/2023] Open
Affiliation(s)
- Yanan Zhang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Fan Yang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Shenglong Ling
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Pei Lv
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Yingxin Zhou
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Wei Fang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Wenjing Sun
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Longhua Zhang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Pan Shi
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Changlin Tian
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 230030 Hefei, Anhui China
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Ni Z, Min Y, Han C, Yuan T, Lu W, Ashktorab H, Smoot DT, Wu Q, Wu J, Zeng W, Shi Y. TGR5-HNF4α axis contributes to bile acid-induced gastric intestinal metaplasia markers expression. Cell Death Discov 2020; 6:56. [PMID: 32655894 PMCID: PMC7338499 DOI: 10.1038/s41420-020-0290-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/18/2020] [Accepted: 06/03/2020] [Indexed: 12/24/2022] Open
Abstract
Intestinal metaplasia (IM) increases the risk of gastric cancer. Our previous results indicated that bile acids (BAs) reflux promotes gastric IM development through kruppel-like factor 4 (KLF4) and caudal-type homeobox 2 (CDX2) activation. However, the underlying mechanisms remain largely elusive. Herein, we verified that secondary BAs responsive G-protein-coupled bile acid receptor 1 (GPBAR1, also known as TGR5) was increased significantly in IM specimens. Moreover, TGR5 contributed to deoxycholic acid (DCA)-induced metaplastic phenotype through positively regulating KLF4 and CDX2 at transcriptional level. Then we employed PCR array and identified hepatocyte nuclear factor 4α (HNF4α) as a candidate mediator. Mechanically, DCA treatment could induce HNF4α expression through TGR5 and following ERK1/2 pathway activation. Furthermore, HNF4α mediated the effects of DCA treatment through directly regulating KLF4 and CDX2. Finally, high TGR5 levels were correlated with high HNF4α, KLF4, and CDX2 levels in IM tissues. These findings highlight the TGR5-ERK1/2-HNF4α axis during IM development in patients with BAs reflux, which may help to understand the mechanism underlying IM development and provide prospective strategies for IM treatment.
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Affiliation(s)
- Zhen Ni
- State Key Laboratory of Cancer Biology and Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
- Department of Gastroenterology, General Hospital of Western Theater Command, Chengdu, Sichuan 610083 China
| | - Yali Min
- Department of Gastroenterology, Second Affiliated Hospital of Xi’an Medical College, Xi’an, Shaanxi 710038 China
| | - Chuan Han
- Department of Endocrinology, General Hospital of Western Theater Command, Chengdu, Sichuan 610083 China
| | - Ting Yuan
- Department of Gastroenterology, 989 Hospital of the People’s Liberation Army, Luoyang, Henan 471003 China
| | - Wenquan Lu
- Department of Gastroenterology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052 China
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University, Washington, DC 20060 USA
| | - Duane T. Smoot
- Department of Internal Medicine, Meharry Medical College, Nashville, TN 37208 USA
| | - Qiong Wu
- State Key Laboratory of Cancer Biology and Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| | - Jian Wu
- State Key Laboratory of Cancer Biology and Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
| | - Weizheng Zeng
- Department of Gastroenterology, General Hospital of Western Theater Command, Chengdu, Sichuan 610083 China
| | - Yongquan Shi
- State Key Laboratory of Cancer Biology and Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi 710032 China
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Zheng D, Liwinski T, Elinav E. Inflammasome activation and regulation: toward a better understanding of complex mechanisms. Cell Discov 2020; 6:36. [PMID: 32550001 PMCID: PMC7280307 DOI: 10.1038/s41421-020-0167-x] [Citation(s) in RCA: 433] [Impact Index Per Article: 108.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/05/2020] [Indexed: 02/07/2023] Open
Abstract
Inflammasomes are cytoplasmic multiprotein complexes comprising a sensor protein, inflammatory caspases, and in some but not all cases an adapter protein connecting the two. They can be activated by a repertoire of endogenous and exogenous stimuli, leading to enzymatic activation of canonical caspase-1, noncanonical caspase-11 (or the equivalent caspase-4 and caspase-5 in humans) or caspase-8, resulting in secretion of IL-1β and IL-18, as well as apoptotic and pyroptotic cell death. Appropriate inflammasome activation is vital for the host to cope with foreign pathogens or tissue damage, while aberrant inflammasome activation can cause uncontrolled tissue responses that may contribute to various diseases, including autoinflammatory disorders, cardiometabolic diseases, cancer and neurodegenerative diseases. Therefore, it is imperative to maintain a fine balance between inflammasome activation and inhibition, which requires a fine-tuned regulation of inflammasome assembly and effector function. Recently, a growing body of studies have been focusing on delineating the structural and molecular mechanisms underlying the regulation of inflammasome signaling. In the present review, we summarize the most recent advances and remaining challenges in understanding the ordered inflammasome assembly and activation upon sensing of diverse stimuli, as well as the tight regulations of these processes. Furthermore, we review recent progress and challenges in translating inflammasome research into therapeutic tools, aimed at modifying inflammasome-regulated human diseases.
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Affiliation(s)
- Danping Zheng
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001 Israel
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Timur Liwinski
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001 Israel
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001 Israel
- Cancer-Microbiome Division Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120 Heidelberg, Germany
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Liu Z, Jiang J, Dai W, Wei H, Zhang X, Yang Z, Xiong Y. MicroRNA-674-5p induced by HIF-1α targets XBP-1 in intestinal epithelial cell injury during endotoxemia. Cell Death Discov 2020; 6:44. [PMID: 32550011 PMCID: PMC7272402 DOI: 10.1038/s41420-020-0280-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/30/2020] [Accepted: 05/19/2020] [Indexed: 01/15/2023] Open
Abstract
Intestinal mucosal integrity dysfunction during endotoxemia can contribute to translocation of intestinal bacteria and a persistent systemic inflammatory response, which both fuel the pathophysiological development of sepsis or endotoxemia. The pathogenesis of intestinal damage induced by endotoxemia remains poorly understood. Here, we identified the microRNA (miR)-674-5p/X-box binding protein 1 (XBP-1) axis as a critical regulator and therapeutic target in preventing intestinal crypt cell proliferation during endotoxemia. MiR-674-5p was markedly increased in intestinal epithelial cells (IECs) during endotoxemia and its induction depended on hypoxia-inducible factor-1α (HIF-1α). Intriguingly, gene expression microanalysis revealed that expression of XBP-1 was down-regulated in IECs with over-expression of miR-674-5p. miR-674-5p was found to directly target XBP-1 protein expression. Upon in vitro, anti-miR-674-5p enhanced sXBP-1 expression and facilitated intestinal crypt cell proliferation. Blockade of miR-674-5p promoted XBP-1 activity, attenuated intestinal inflammation, and expedited intestinal regeneration, resulting in protection against endotoxemia-induced intestinal injury in mice. More importantly, the survival in endotoxemia mice was significantly improved by inhibiting intestinal miR-674-5p. Collectively, these data indicate that control of a novel miR-674-5p/XBP-1 signaling axis may mitigate endotoxemia -induced intestinal injury.
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Affiliation(s)
- Zhihao Liu
- Division of Emergency Medicine, Department of General Internal Medicine, Department of Emergency Intensive Care Unit, The First Affiliated Hospital of Sun Yat-sen University, No.58, Zhongshan 2nd Road, 510080 Guangzhou, China
| | - Jie Jiang
- Department of Gastroenterology, The Third Affiliated Hospital of Sun Yat-Sen University, No.600, Tianhe Road, 510360 Guangzhou, China
| | - Weigang Dai
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, No.58, Zhongshan 2nd Road, 510080 Guangzhou, China
| | - Hongyan Wei
- Division of Emergency Medicine, Department of General Internal Medicine, Department of Emergency Intensive Care Unit, The First Affiliated Hospital of Sun Yat-sen University, No.58, Zhongshan 2nd Road, 510080 Guangzhou, China
| | - Xiaofei Zhang
- Department of Critical Care Medicine, The Sixth Affiliated Hospital of Sun Yat-sen University, No.26, YuanCunErHeng Road, 510655 Guangzhou, China
| | - Zhen Yang
- Division of Emergency Medicine, Department of General Internal Medicine, Department of Emergency Intensive Care Unit, The First Affiliated Hospital of Sun Yat-sen University, No.58, Zhongshan 2nd Road, 510080 Guangzhou, China
| | - Yan Xiong
- Division of Emergency Medicine, Department of General Internal Medicine, Department of Emergency Intensive Care Unit, The First Affiliated Hospital of Sun Yat-sen University, No.58, Zhongshan 2nd Road, 510080 Guangzhou, China
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Priya Dharshini LC, Vishnupriya S, Sakthivel KM, Rasmi RR. Oxidative stress responsive transcription factors in cellular signalling transduction mechanisms. Cell Signal 2020; 72:109670. [PMID: 32418887 DOI: 10.1016/j.cellsig.2020.109670] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 11/18/2022]
Abstract
Oxidative stress results from the imbalances in the development of reactive oxygen species (ROS) and antioxidants defence system resulting in tissue injury. A key issue resulting in the modulation of ROS is that it alters hosts molecular, structural and functional properties which is accomplished via various signalling pathways which either activate or inhibit numerous transcription factors (TFs). Some of the regulators include Nuclear erythroid-2 related factors (Nrf-2), CCAAT/enhancer-binding protein delta (CEBPD), Activator Protein-1 (AP-1), Hypoxia-inducible factor 1(HIF-1), Nuclear factor κB (NF-κB), Specificity Protein-1 (SP-1) and Forkhead Box class O (FoxO) transcription factors. The expression of these transcription factors are dependent upon the stress signal and are sometimes interlinked. They are highly specific having their own regulation cellular events. Depending upon the transcription factors and better knowledge on the type of the oxidative stress help researchers develop safe, novel targets which can serve as efficient therapeutic targets for several disease conditions.
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Affiliation(s)
| | - Selvaraj Vishnupriya
- Department of Biotechnology, PSG College of Arts & Science, Civil Aerodrome Post, Coimbatore, Tamil Nadu 641 014, India
| | - Kunnathur Murugesan Sakthivel
- Department of Biochemistry, PSG College of Arts & Science, Civil Aerodrome Post, Coimbatore, Tamil Nadu 641 014, India
| | - Rajan Radha Rasmi
- Department of Biotechnology, PSG College of Arts & Science, Civil Aerodrome Post, Coimbatore, Tamil Nadu 641 014, India.
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Hicks DA, Jones AC, Corbett NJ, Fisher K, Pickering-Brown SM, Ashe MP, Hooper NM. Extracellular Vesicles Isolated from Human Induced Pluripotent Stem Cell-Derived Neurons Contain a Transcriptional Network. Neurochem Res 2020; 45:1711-28. [PMID: 32361798 DOI: 10.1007/s11064-020-03019-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/23/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022]
Abstract
Healthy brain function is mediated by several complementary signalling pathways, many of which are driven by extracellular vesicles (EVs). EVs are heterogeneous in both size and cargo and are constitutively released from cells into the extracellular milieu. They are subsequently trafficked to recipient cells, whereupon their entry can modify the cellular phenotype. Here, in order to further analyse the mRNA and protein cargo of neuronal EVs, we isolated EVs by size exclusion chromatography from human induced pluripotent stem cell (iPSC)-derived neurons. Electron microscopy and dynamic light scattering revealed that the isolated EVs had a diameter of 30–100 nm. Transcriptomic and proteomics analyses of the EVs and neurons identified key molecules enriched in the EVs involved in cell surface interaction (integrins and collagens), internalisation pathways (clathrin- and caveolin-dependent), downstream signalling pathways (phospholipases, integrin-linked kinase and MAPKs), and long-term impacts on cellular development and maintenance. Overall, we show that key signalling networks and mechanisms are enriched in EVs isolated from human iPSC-derived neurons.
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