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Extracellular Vesicles Isolated from Human Induced Pluripotent Stem Cell-Derived Neurons Contain a Transcriptional Network. Neurochem Res 2020; 45:1711-1728. [PMID: 32361798 PMCID: PMC7297870 DOI: 10.1007/s11064-020-03019-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [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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Leprivier G, Rotblat B. How does mTOR sense glucose starvation? AMPK is the usual suspect. Cell Death Discov 2020; 6:27. [PMID: 32351714 PMCID: PMC7176732 DOI: 10.1038/s41420-020-0260-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/13/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022] Open
Abstract
Glucose is a major requirement for biological life. Its concentration is constantly sensed at the cellular level, allowing for adequate responses to any changes of glucose availability. Such responses are mediated by key sensors and signaling pathway components that adapt cellular metabolism to glucose levels. One of the major hubs of these responses is mechanistic target of rapamycin (mTOR) kinase, which forms the mTORC1 and mTORC2 protein complexes. Under physiological glucose concentrations, mTORC1 is activated and stimulates a number of proteins and enzymes involved in anabolic processes, while restricting the autophagic process. Conversely, when glucose levels are low, mTORC1 is inhibited, in turn leading to the repression of numerous anabolic processes, sparing ATP and antioxidants. Understanding how mTORC1 activity is regulated by glucose is not only important to better delineate the biological function of mTOR, but also to highlight potential therapeutic strategies for treating diseases characterized by deregulated glucose availability, as is the case of cancer. In this perspective, we depict the different sensors and upstream proteins responsible of controlling mTORC1 activity in response to changes in glucose concentration. This includes the major energy sensor AMP-activated protein kinase (AMPK), as well as other independent players. The impact of such modes of regulation of mTORC1 on cellular processes is also discussed.
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Hwang BB, Engel L, Goueli SA, Zegzouti H. A homogeneous bioluminescent immunoassay to probe cellular signaling pathway regulation. Commun Biol 2020; 3:8. [PMID: 31909200 PMCID: PMC6941952 DOI: 10.1038/s42003-019-0723-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023] Open
Abstract
Monitoring cellular signaling events can help better understand cell behavior in health and disease. Traditional immunoassays to study proteins involved in signaling can be tedious, require multiple steps, and are not easily adaptable to high throughput screening (HTS). Here, we describe a new immunoassay approach based on bioluminescent enzyme complementation. This immunoassay takes less than two hours to complete in a homogeneous "Add and Read" format and was successfully used to monitor multiple signaling pathways' activation through specific nodes of phosphorylation (e.g pIκBα, pAKT, and pSTAT3). We also tested deactivation of these pathways with small and large molecule inhibitors and obtained the expected pharmacology. This approach does not require cell engineering. Therefore, the phosphorylation of an endogenous substrate is detected in any cell type. Our results demonstrate that this technology can be broadly adapted to streamline the analysis of signaling pathways of interest or the identification of pathway specific inhibitors.
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Kamato D, Do BH, Osman N, Ross BP, Mohamed R, Xu S, Little PJ. Smad linker region phosphorylation is a signalling pathway in its own right and not only a modulator of canonical TGF-β signalling. Cell Mol Life Sci 2020; 77:243-251. [PMID: 31407020 PMCID: PMC11104920 DOI: 10.1007/s00018-019-03266-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/16/2019] [Accepted: 08/05/2019] [Indexed: 01/01/2023]
Abstract
Transforming growth factor (TGF)-β signalling pathways are intensively investigated because of their diverse association with physiological and pathophysiological states. Smad transcription factors are the key mediators of TGF-β signalling. Smads can be directly phosphorylated in the carboxy terminal by the TGF-β receptor or in the linker region via multiple intermediate serine/threonine kinases. Growth factors in addition to hormones and TGF-β can activate many of the same kinases which can phosphorylate the Smad linker region. Historically, Smad linker region phosphorylation was shown to prevent nuclear translocation of Smads and inhibit TGF-β signalling pathways; however, it was subsequently shown that Smad linker region phosphorylation can be a driver of gene expression. This review will cover the signalling pathways of Smad linker region phosphorylation that drive the expression of genes involved in pathology and pathophysiology. The role of Smad signalling in cell biology is expanding rapidly beyond its role in TGF-β signalling and many signalling paradigms need to be re-evaluated in terms of Smad involvement.
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Ganguli S, Shah A, Hamid A, Singh A, Palakurti R, Bhandari R. A high energy phosphate jump - From pyrophospho-inositol to pyrophospho-serine. Adv Biol Regul 2020; 75:100662. [PMID: 31668836 DOI: 10.1016/j.jbior.2019.100662] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/26/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Inositol pyrophosphates (PP-IPs) are a class of energy rich metabolites present in all eukaryotic cells. The hydroxyl groups on these water soluble derivatives of inositol are substituted with diphosphate and monophosphate moieties. Since the discovery of PP-IPs in the early 1990s, enormous progress has been made in uncovering pleiotropic roles for these small molecules in cellular physiology. PP-IPs exert their effect on proteins in two ways - allosteric regulation by direct binding, or post-translational regulation by serine pyrophosphorylation, a modification unique to PP-IPs. Serine pyrophosphorylation is achieved by Mg2+-dependent, but enzyme independent transfer of a β-phosphate from a PP-IP to a pre-phosphorylated serine residue located in an acidic motif, within an intrinsically disordered protein sequence. This distinctive post-translational modification has been shown to regulate diverse cellular processes, including rRNA synthesis, glycolysis, and vesicle transport. However, our understanding of the molecular details of this phosphotransfer from pyrophospho-inositol to generate pyrophospho-serine, is still nascent. This review discusses our current knowledge of protein pyrophosphorylation, and recent advances in understanding the mechanism of this important yet overlooked post-translational modification.
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Del Turco S, Quattrini L, Colucci R, Gaggini M, La Motta C, Basta G. A 2,3-diphenylpyrido[1,2- a] pyrimidin-4-one derivative inhibits specific angiogenic factors induced by TNF-α. Saudi Pharm J 2019; 27:1174-1181. [PMID: 31885477 PMCID: PMC6921196 DOI: 10.1016/j.jsps.2019.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 09/28/2019] [Indexed: 11/30/2022] Open
Abstract
Low-grade chronic inflammation is a key process of angiogenesis in tumour progression. We investigated whether a synthetic analogue of apigenin, the 2-(3,4-dimethoxyphenyl)-3-phenyl-4H-pyrido[1,2-a] pyrimidin-4-one (called DB103), interfered with the mechanisms involved in the angiogenic process induced by the inflammatory cytokine tumour necrosis factor (TNFα). In endothelial cells, DB103 but not apigenin reduced the TNFα-induced oxidative stress. DB103 inhibited the activation of ERK1/2 but not JNK, p38 and Akt kinases, while apigenin was not so selective because it inhibited essentially all examined kinases. Similarly, apigenin inhibited the TNFα-induced transcription factors CREB, STAT3, STAT5 and NF-κB, while DB103 acted only on NF-κB. DB103 inhibited the induced-release of angiogenic factors such as monocyte chemotactic protein-1, interleukin-6 (IL-6) and angiopoietin-2 but not IL-8, while apigenin reduced the IL-6 and IL-8 release. DB103 revealed a better ability than apigenin to modulate proangiogenic responses induced by an inflammatory microenvironment.
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Yamaguchi T, Takizawa F, Furihata M, Soto-Lampe V, Dijkstra JM, Fischer U. Teleost cytotoxic T cells. FISH & SHELLFISH IMMUNOLOGY 2019; 95:422-439. [PMID: 31669897 DOI: 10.1016/j.fsi.2019.10.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Cell-mediated cytotoxicity is one of the major mechanisms by which vertebrates control intracellular pathogens. Two cell types are the main players in this immune response, natural killer (NK) cells and cytotoxic T lymphocytes (CTL). While NK cells recognize altered target cells in a relatively unspecific manner CTLs use their T cell receptor to identify pathogen-specific peptides that are presented by major histocompatibility (MHC) class I molecules on the surface of infected cells. However, several other signals are needed to regulate cell-mediated cytotoxicity involving a complex network of cytokine- and ligand-receptor interactions. Since the first description of MHC class I molecules in teleosts during the early 90s of the last century a remarkable amount of information on teleost immune responses has been published. The corresponding studies describe teleost cells and molecules that are involved in CTL responses of higher vertebrates. These studies are backed by functional investigations on the killing activity of CTLs in a few teleost species. The present knowledge on teleost CTLs still leaves considerable room for further investigations on the mechanisms by which CTLs act. Nevertheless the information on teleost CTLs and their regulation might already be useful for the control of fish diseases by designing efficient vaccines against such diseases where CTL responses are known to be decisive for the elimination of the corresponding pathogen. This review summarizes the present knowledge on CTL regulation and functions in teleosts. In a special chapter, the role of CTLs in vaccination is discussed.
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The Asprosin-OLFR734 hormonal signaling axis modulates male fertility. Cell Discov 2019; 5:55. [PMID: 31798959 PMCID: PMC6868220 DOI: 10.1038/s41421-019-0122-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/22/2019] [Indexed: 01/09/2023] Open
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Lake D, Corrêa SAL, Müller J. NMDA receptor-dependent signalling pathways regulate arginine vasopressin expression in the paraventricular nucleus of the rat. Brain Res 2019; 1722:146357. [PMID: 31369731 DOI: 10.1016/j.brainres.2019.146357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 07/14/2019] [Accepted: 07/29/2019] [Indexed: 02/07/2023]
Abstract
The antidiuretic hormone arginine vasopressin (AVP) regulates water homeostasis, blood pressure and a range of stress responses. It is synthesized in the hypothalamus and released from the posterior pituitary into the general circulation upon a range of stimuli. While the mechanisms leading to AVP secretion have been widely investigated, the molecular mechanisms regulating AVP gene expression are mostly unclear. Here we investigated the neurotransmitters and signal transduction pathways that activate AVP gene expression in the paraventricular nucleus (PVN) of the rat using acute brain slices and quantitative real-time PCR. We show that stimulation with l-glutamate robustly induced AVP gene expression in acute hypothalamic brain slices containing the PVN. More specifically, we show that AVP transcription was stimulated by NMDA. Using pharmacological treatments, our data further reveal that the activation of ERK1/2 (PD184352), CaMKII (KN-62) and PI3K (LY294002; 740 Y-P) is involved in the NMDA-induced AVP gene expression in the PVN. Together, this study identifies NMDA-mediated cell signalling pathways that regulate AVP gene expression in the rat PVN.
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Polyphenols in human nutrition: from the in vitro antioxidant capacity to the beneficial effects on cardiometabolic health and related inter-individual variability - an overview and perspective. Br J Nutr 2019; 123:241-254. [PMID: 31658907 DOI: 10.1017/s0007114519002733] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Oxidative damage of cells and tissues is broadly implicated in human pathophysiology, including cardiometabolic diseases. Polyphenols, as important constituents of the human diet and potent in vitro free radical scavengers, have been extensively studied for their beneficial effects on cardiometabolic health. However, it has been demonstrated that the in vivo antioxidant activity of polyphenols is distinct from their in vitro free radical-scavenging capacity. Indeed, bioavailability of nutritional polyphenols is low and conditioned by complex mechanisms of absorption, distribution, metabolism and excretion. Nowadays, it is commonly accepted that the cellular antioxidant activity of polyphenols is mainly carried out via modification of transcription of genes involved in antioxidant defence. Importantly, polyphenols also contribute to cardiometabolic health by modulation of a plethora of cellular processes that are not directly associated with antioxidant enzymes, through nutri(epi)genomic mechanisms. Numerous human intervention studies have demonstrated beneficial effects of polyphenols on the key cardiometabolic risk factors. However, inconsistency of the results of some studies led to identification of the inter-individual variability in response to consumption of polyphenols. In perspective, a detailed investigation of the determinants of this inter-individual variability will potentially lead us towards personalised dietary recommendations. The phenomenon of inter-individual variability is also of relevance for supplementation with antioxidant (pro)vitamins.
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CUL5-SOCS6 complex regulates mTORC2 function by targeting Sin1 for degradation. Cell Discov 2019; 5:52. [PMID: 31798957 PMCID: PMC6868212 DOI: 10.1038/s41421-019-0118-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/02/2019] [Indexed: 12/15/2022] Open
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Calamera G, Li D, Ulsund AH, Kim JJ, Neely OC, Moltzau LR, Bjørnerem M, Paterson D, Kim C, Levy FO, Andressen KW. FRET-based cyclic GMP biosensors measure low cGMP concentrations in cardiomyocytes and neurons. Commun Biol 2019; 2:394. [PMID: 31701023 PMCID: PMC6820734 DOI: 10.1038/s42003-019-0641-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 10/02/2019] [Indexed: 01/13/2023] Open
Abstract
Several FRET (fluorescence resonance energy transfer)-based biosensors for intracellular detection of cyclic nucleotides have been designed in the past decade. However, few such biosensors are available for cGMP, and even fewer that detect low nanomolar cGMP concentrations. Our aim was to develop a FRET-based cGMP biosensor with high affinity for cGMP as a tool for intracellular signaling studies. We used the carboxyl-terminal cyclic nucleotide binding domain of Plasmodium falciparum cGMP-dependent protein kinase (PKG) flanked by different FRET pairs to generate two cGMP biosensors (Yellow PfPKG and Red PfPKG). Here, we report that these cGMP biosensors display high affinity for cGMP (EC50 of 23 ± 3 nM) and detect cGMP produced through soluble guanylyl cyclase and guanylyl cyclase A in stellate ganglion neurons and guanylyl cyclase B in cardiomyocytes. These biosensors are therefore optimal tools for real-time measurements of low concentrations of cGMP in living cells.
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Talebian A, Henkemeyer M. EphB2 receptor cell-autonomous forward signaling mediates auditory memory recall and learning-driven spinogenesis. Commun Biol 2019; 2:372. [PMID: 31633063 PMCID: PMC6789002 DOI: 10.1038/s42003-019-0625-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/16/2019] [Indexed: 01/09/2023] Open
Abstract
While ephrin-B ligands and EphB receptors are expressed to high levels in the learning centers of the brain, it remains largely unknown how their trans-synaptic interactions contribute to memory. We find that EphB2 forward signaling is needed for contextual and sound-evoked memory recall and that constitutive over-activation of the receptor's intracellular tyrosine kinase domain results in enhanced memory. Loss of EphB2 expression does not affect the number of neurons activated following encoding, although a reduction of neurons activated after the sound-cued retrieval test was detected in the auditory cortex and hippocampal CA1. Further, spine density and maturation was reduced in the auditory cortex of mutants especially in the neurons that were dual-activated during both encoding and retrieval. Our data demonstrates that trans-synaptic ephrin-B-EphB2 interactions and forward signaling facilitate neural activation and structural plasticity in learning-associated neurons involved in the generation of memories.
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Gao Y, Zhou J, Xie Z, Wang J, Ho CK, Zhang Y, Li Q. Mechanical strain promotes skin fibrosis through LRG-1 induction mediated by ELK1 and ERK signalling. Commun Biol 2019; 2:359. [PMID: 31602408 PMCID: PMC6778114 DOI: 10.1038/s42003-019-0600-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
Biomechanical force and pathological angiogenesis are dominant features in fibro-proliferative disorders. Understanding the role and regulation of the mechanical microenvironment in which pathological angiogenesis occurs is an important challenge when investigating numerous angiogenesis-related diseases. In skin fibrosis, dermal fibroblasts and vascular endothelial cells are integral to hypertrophic scar formation. However, few studies have been conducted to closely investigate their relationship. Here we show, that leucine-rich-alpha-2-glycoprotein 1 (LRG-1) a regulator of pathological angiogenesis, links biomechanical force to angiogenesis in skin fibrosis. We discover that LRG-1 is overexpressed in hypertrophic scar tissues, and that depletion of Lrg-1 in mouse skin causes mild neovascularization and skin fibrosis formation in a hypertrophic scarring model. Inhibition of FAK or ERK attenuates LRG-1 expression through the ELK1 transcription factor, which binds to the LRG-1 promoter region after transcription initiation by mechanical force. Using LRG-1 to uncouple mechanical force from angiogenesis may prove clinically successful in treating fibro-proliferative disorders.
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De Luca A, Barile A, Arciello M, Rossi L. Copper homeostasis as target of both consolidated and innovative strategies of anti-tumor therapy. J Trace Elem Med Biol 2019; 55:204-213. [PMID: 31345360 DOI: 10.1016/j.jtemb.2019.06.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/28/2019] [Accepted: 06/14/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Copper was reported to be involved in the onset and progression of cancer. Proteins in charge of copper uptake and distribution, as well as cuproenzymes, are altered in cancer. More recently, proteins involved in signaling cascades, regulating cell proliferation, and anti-apoptotic protein factors were found to interact with copper. Therefore, therapeutic strategies using copper complexing molecules have been proposed for cancer therapy and used in clinical trials. OBJECTIVES This review will focus on novel findings about the involvement of copper and cupro-proteins in cancer dissemination process, epithelium to mesenchymal transition and vascularization. Particularly, implication of well-established (e.g. lysil oxidase) or newly identified copper-binding proteins (e.g. MEMO1), as well as their interplay, will be discussed. Moreover, we will describe recently synthesized copper complexes, including plant-derived ones, and their efficacy in contrasting cancer development. CONCLUSIONS The research on the involvement of copper in cancer is still an open field. Further investigation is required to unveil the mechanisms involved in copper delivery to the novel copper-binding proteins, which may identify other possible gene and protein targets for cancer therapy.
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Caines R, Cochrane A, Kelaini S, Vila-Gonzalez M, Yang C, Eleftheriadou M, Moez A, Stitt AW, Zeng L, Grieve DJ, Margariti A. The RNA-binding protein QKI controls alternative splicing in vascular cells, producing an effective model for therapy. J Cell Sci 2019; 132:jcs.230276. [PMID: 31331967 DOI: 10.1242/jcs.230276] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/10/2019] [Indexed: 12/31/2022] Open
Abstract
Dysfunction of endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) leads to ischaemia, the central pathology of cardiovascular disease. Stem cell technology will revolutionise regenerative medicine, but a need remains to understand key mechanisms of vascular differentiation. RNA-binding proteins have emerged as novel post-transcriptional regulators of alternative splicing and we have previously shown that the RNA-binding protein Quaking (QKI) plays roles in EC differentiation. In this study, we decipher the role of the alternative splicing isoform Quaking 6 (QKI-6) to induce VSMC differentiation from induced pluripotent stem cells (iPSCs). PDGF-BB stimulation induced QKI-6, which bound to HDAC7 intron 1 via the QKI-binding motif, promoting HDAC7 splicing and iPS-VSMC differentiation. Overexpression of QKI-6 transcriptionally activated SM22 (also known as TAGLN), while QKI-6 knockdown diminished differentiation capability. VSMCs overexpressing QKI-6 demonstrated greater contractile ability, and upon combination with iPS-ECs-overexpressing the alternative splicing isoform Quaking 5 (QKI-5), exhibited higher angiogenic potential in vivo than control cells alone. This study demonstrates that QKI-6 is critical for modulation of HDAC7 splicing, regulating phenotypically and functionally robust iPS-VSMCs. These findings also highlight that the QKI isoforms hold key roles in alternative splicing, giving rise to cells which can be used in vascular therapy or for disease modelling.This article has an associated First Person interview with the first author of the paper.
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Bowling JL, Skolfield MC, Riley WA, Nolin AP, Wolf LC, Nelson DE. Temporal integration of mitochondrial stress signals by the PINK1:Parkin pathway. BMC Mol Cell Biol 2019; 20:33. [PMID: 31412778 PMCID: PMC6694515 DOI: 10.1186/s12860-019-0220-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/08/2019] [Indexed: 11/10/2022] Open
Abstract
Background The PINK1:Parkin pathway regulates the autophagic removal of damaged and dysfunctional mitochondria. While the response of this pathway to complete loss of ΔΨm, as caused by high concentrations of mitochondrial ionophores, has been well characterized, it remains unclear how the pathway makes coherent decisions about whether to keep or purge mitochondria in situations where ΔΨm is only partially lost or exhibits fluctuations, as has been observed in response to certain types of cellular stress. Results To investigate the responses of the PINK1:Parkin pathway to mitochondrial insults of different magnitude and duration, controlled titration of the mitochondrial protonophore, CCCP, was used to manipulate ΔΨm in live cells, and the dynamics of PINK1 and Parkin recruitment was measured by fluorescence microscopy. In contrast to the stable accumulation of PINK1 and Parkin seen at completely depolarized mitochondria, partial depolarization produced a transient pulse of PINK1 stabilization and rapid loss, which was driven by small fluctuations in ΔΨm. As the rate of Parkin dissociation from the mitochondria and phospho-polyubiquitin chain removal was comparatively slow, repetitive pulses of PINK1 were able to drive a slow step-wise accumulation of Parkin and phospho-polyubiquitin leading to deferred mitophagy. Conclusion These data suggest that the PINK1:Parkin mitophagy pathway is able to exhibit distinct dynamic responses to complete and partial mitochondrial depolarization. In this way, the pathway is able to differentiate between irretrievably damaged mitochondria and those showing signs of dysfunction, promoting either rapid or delayed autophagy, respectively. Electronic supplementary material The online version of this article (10.1186/s12860-019-0220-5) contains supplementary material, which is available to authorized users.
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Bertinelli M, Paesen GC, Grimes JM, Renner M. High-resolution crystal structure of arthropod Eiger TNF suggests a mode of receptor engagement and altered surface charge within endosomes. Commun Biol 2019; 2:293. [PMID: 31396573 PMCID: PMC6684607 DOI: 10.1038/s42003-019-0541-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022] Open
Abstract
The tumour necrosis factor alpha (TNFα) superfamily of proteins are critical in numerous biological processes, such as in development and immunity. Eiger is the sole TNFα member described in arthropods such as in the important model organism Drosophila. To date there are no structural data on any Eiger protein. Here we present the structure of the TNF domain of Eiger from the fall armyworm Spodoptera frugiperda (SfEiger) to 1.7 Å from a serendipitously obtained crystal without prior knowledge of the protein sequence. Our structure confirms that canonical trimerization is conserved from ancestral TNFs and points towards a mode of receptor engagement. Furthermore, we observe numerous surface histidines on SfEiger, potentially acting as pH switches following internalization into endosomes. Our data contributes to the genome annotation of S. frugiperda, a voracious agricultural pest, and can serve as a basis for future structure-function investigations of the TNF system in related arthropods such as Drosophila.
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Xiao Y, Chen J, Wan Y, Gao Q, Jing N, Zheng Y, Zhu X. Regulation of zebrafish dorsoventral patterning by phase separation of RNA-binding protein Rbm14. Cell Discov 2019; 5:37. [PMID: 31636951 PMCID: PMC6796953 DOI: 10.1038/s41421-019-0106-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 02/08/2023] Open
Abstract
RNA-binding proteins with intrinsically disordered regions (IDRs) such as Rbm14 can phase separate in vitro. To what extent the phase separation contributes to their physiological functions is however unclear. Here we show that zebrafish Rbm14 regulates embryonic dorsoventral patterning through phase separation. Zebrafish rbm14 morphants displayed dorsalized phenotypes associated with attenuated BMP signaling. Consistently, depletion of mammalian Rbm14 downregulated BMP regulators and effectors Nanog, Smad4/5, and Id1/2, whereas overexpression of the BMP-related proteins in the morphants significantly restored the developmental defects. Importantly, the IDR of zebrafish Rbm14 demixed into liquid droplets in vitro despite poor sequence conservation with its mammalian counterpart. While its phase separation mutants or IDR failed to rescue the morphants, its chimeric proteins containing an IDR from divergent phase separation proteins were effective. Rbm14 complexed with proteins involved in RNA metabolism and phase separated into cellular ribonucleoprotein compartments. Consistently, RNA deep sequencing analysis on the morphant embryos revealed increased alternative splicing events as well as large-scale transcriptomic downregulations. Our results suggest that Rbm14 functions in ribonucleoprotein compartments through phase separation to modulate multiple aspects of RNA metabolism. Furthermore, IDRs conserve in phase separation ability but not primary sequence and can be functionally interchangeable.
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Qiu Y, Shan W, Yang Y, Jin M, Dai Y, Yang H, Jiao R, Xia Y, Liu Q, Ju L, Huang G, Zhang J, Yang L, Li L, Li Y. Reversal of sorafenib resistance in hepatocellular carcinoma: epigenetically regulated disruption of 14-3-3η/hypoxia-inducible factor-1α. Cell Death Discov 2019; 5:120. [PMID: 31341646 PMCID: PMC6642098 DOI: 10.1038/s41420-019-0200-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/15/2019] [Accepted: 06/23/2019] [Indexed: 02/07/2023] Open
Abstract
Sorafenib resistance is one of the main obstacles to the treatment of advanced/recurrent hepatocellular carcinoma (HCC). Here, sorafenib-resistant HCC cells and xenografts in nude mice were used as experimental models. A cohort of patients with advanced recurrent HCC who were receiving sorafenib therapy was used to assess the clinical significance of this therapy. Our data showed that 14-3-3η maintained sorafenib resistance in HCC. An analysis of the underlying molecular mechanisms revealed that 14-3-3η stabilizes hypoxia-inducible factor 1α (HIF-1α) through the inhibition of ubiquitin-dependent proteasome protein degradation, which leads to the maintenance of cancer stem cell (CSC) properties. We further found that microRNA-16 (miR-16) is a competent miRNA that reverses sorafenib resistance by targeting the 3'-UTR of 14-3-3η and thereby inhibits 14-3-3η/HIF-1α/CSC properties. In HCC patients, significant negative correlations were found between the expression of miR-16 and 14-3-3η, HIF-1α, or CSC properties. Further analysis showed that low miR-16 expression but high 14-3-3η expression can prognosticate sorafenib resistance and poor survival. Collectively, our present study indicated that miR-16/14-3-3η is involved in sorafenib resistance in HCC and that these two factors could be potential therapeutic targets and biomarkers for predicting the response to sorafenib treatment.
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Prole DL, Taylor CW. A genetically encoded toolkit of functionalized nanobodies against fluorescent proteins for visualizing and manipulating intracellular signalling. BMC Biol 2019; 17:41. [PMID: 31122229 PMCID: PMC6533734 DOI: 10.1186/s12915-019-0662-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Intrabodies enable targeting of proteins in live cells, but generating specific intrabodies against the thousands of proteins in a proteome poses a challenge. We leverage the widespread availability of fluorescently labelled proteins to visualize and manipulate intracellular signalling pathways in live cells by using nanobodies targeting fluorescent protein tags. RESULTS We generated a toolkit of plasmids encoding nanobodies against red and green fluorescent proteins (RFP and GFP variants), fused to functional modules. These include fluorescent sensors for visualization of Ca2+, H+ and ATP/ADP dynamics; oligomerising or heterodimerising modules that allow recruitment or sequestration of proteins and identification of membrane contact sites between organelles; SNAP tags that allow labelling with fluorescent dyes and targeted chromophore-assisted light inactivation; and nanobodies targeted to lumenal sub-compartments of the secretory pathway. We also developed two methods for crosslinking tagged proteins: a dimeric nanobody, and RFP-targeting and GFP-targeting nanobodies fused to complementary hetero-dimerizing domains. We show various applications of the toolkit and demonstrate, for example, that IP3 receptors deliver Ca2+ to the outer membrane of only a subset of mitochondria and that only one or two sites on a mitochondrion form membrane contacts with the plasma membrane. CONCLUSIONS This toolkit greatly expands the utility of intrabodies and will enable a range of approaches for studying and manipulating cell signalling in live cells.
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Weber LM, Nowicka M, Soneson C, Robinson MD. diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering. Commun Biol 2019; 2:183. [PMID: 31098416 PMCID: PMC6517415 DOI: 10.1038/s42003-019-0415-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/05/2019] [Indexed: 12/17/2022] Open
Abstract
High-dimensional flow and mass cytometry allow cell types and states to be characterized in great detail by measuring expression levels of more than 40 targeted protein markers per cell at the single-cell level. However, data analysis can be difficult, due to the large size and dimensionality of datasets as well as limitations of existing computational methods. Here, we present diffcyt, a new computational framework for differential discovery analyses in high-dimensional cytometry data, based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics. Our approach provides improved statistical performance, including for rare cell populations, along with flexible experimental designs and fast runtimes in an open-source framework.
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Kremen1-induced cell death is regulated by homo- and heterodimerization. Cell Death Discov 2019; 5:91. [PMID: 31069116 PMCID: PMC6494814 DOI: 10.1038/s41420-019-0175-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/03/2019] [Accepted: 04/12/2019] [Indexed: 01/16/2023] Open
Abstract
In multicellular organisms, cell death pathways allow the removal of abnormal or unwanted cells. Their dysregulation can lead either to excessive elimination or to inappropriate cell survival. Evolutionary constraints ensure that such pathways are strictly regulated in order to restrain their activation to the appropriate context. We have previously shown that the transmembrane receptor Kremen1 behaves as a dependence receptor, triggering cell death unless bound to its ligand Dickkopf1. In this study, we reveal that Kremen1 apoptotic signaling requires homodimerization of the receptor. Dickkopf1 binding inhibits Kremen1 multimerization and alleviates cell death, whereas forced dimerization increases apoptotic signaling. Furthermore, we show that Kremen2, a paralog of Kremen1, which bears no intrinsic apoptotic activity, binds and competes with Kremen1. Consequently, Kremen2 is a very potent inhibitor of Kremen1-induced cell death. Kremen1 was proposed to act as a tumor suppressor, preventing cancer cell survival in a ligand-poor environment. We found that KREMEN2 expression is increased in a large majority of cancers, suggesting it may confer increased survival capacity. Consistently, low KREMEN2 expression is a good prognostic for patient survival in a variety of cancers.
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Marsolier J, Perichon M, Weitzman JB, Medjkane S. Secreted parasite Pin1 isomerase stabilizes host PKM2 to reprogram host cell metabolism. Commun Biol 2019; 2:152. [PMID: 31044177 PMCID: PMC6491484 DOI: 10.1038/s42003-019-0386-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 03/05/2019] [Indexed: 01/04/2023] Open
Abstract
Metabolic reprogramming is an important feature of host-pathogen interactions and a hallmark of tumorigenesis. The intracellular apicomplexa parasite Theileria induces a Warburg-like effect in host leukocytes by hijacking signaling machineries, epigenetic regulators and transcriptional programs to create a transformed cell state. The molecular mechanisms underlying host cell transformation are unclear. Here we show that a parasite-encoded prolyl-isomerase, TaPin1, stabilizes host pyruvate kinase isoform M2 (PKM2) leading to HIF-1α-dependent regulation of metabolic enzymes, glucose uptake and transformed phenotypes in parasite-infected cells. Our results provide a direct molecular link between the secreted parasite TaPin1 protein and host gene expression programs. This study demonstrates the importance of prolyl isomerization in the parasite manipulation of host metabolism.
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Alese MO, Moodley J, Naicker TA. Signalling of ERK1/2, P38MAPK and P90RSK in HIV-associated pre-eclampsia. J OBSTET GYNAECOL 2019; 39:612-618. [PMID: 30821550 DOI: 10.1080/01443615.2018.1547695] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Due to their significance in trophoblast differentiation and survival, we evaluated the expression of the cell signalling molecules; Extracellular signal-regulated kinase 1/2 (ERK1/2), Mitogen Activated Protein Kinase 38 (MAPK38) and p90 ribosomal protein S6 kinase (p90 RSK) in buffy coat samples. Eighty pregnant women attending a large hospital in Durban, South Africa were assigned into normotensive and pre-eclamptic groups and further stratified by their HIV status. The degree of phosphorylation of the analytes was determined using the Bio-Plex ProTM Cell Signalling Immunoassay. There was a significantly lower protein concentration of the analytes in the pre-eclamptic versus the normotensive patients, irrespective of HIV status (p < .0001). Also, there was no significant difference in expression of ERK1/2 (p = .4369), p38MAPK (p = .4720) and p90 RSK (p = .0188), according to HIV status. This study demonstrates a down-regulation of ERK1/2, p38MAPK and p90RSK prosurvival markers in pre-eclampsia. This implicates the involvement of the MAPK pathway in the pathogenesis of preeclampsia. Activation of these pathways may prove useful in increasing the body of evidence on prevention of placenta dysfunction and apoptosis. Impact statement What is already known on this subject? Preeclampsia occurring in co-morbidity with HIV is a public health problem among pregnant, black South-African women. There have been conflicting theories regarding the predisposition to the development of preeclampsia as a result of compromised immune response due to HIV infection. In normal pregnancies, the MAPK pathway plays a significant role in molecular processes involved in the cells including survival and differentiation of the placental trophoblast. ERK1/2, p38MAPK and p90RSK are members of the MAPK family, which are pro-apoptotic. Inhibition in the signalling of MAPKs has been found to result in oxidative stress, a process which contributes to the defective trophoblast invasion seen in preeclampsia. What do the results of this study add? The results from this study showed that there is no relationship between HIV infection and an increased predisposition to the development of preeclampsia. In addition, this study highlights a downregulation in the expression of ERK1/2, p38 MAPK and p90RSK in preeclampsia. What are the implications of these findings for clinical practice and/or further research? These findings demonstrate the potential of these analytes as biomarkers for the diagnosis of preeclampsia. Also, this may serve as a framework for further research in the prevention of preeclampsia by elucidating more on the pathway.
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