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Morello G, La Cognata V, Guarnaccia M, D’Agata V, Cavallaro S. Cracking the Code of Neuronal Cell Fate. Cells 2023; 12:1057. [PMID: 37048129 PMCID: PMC10093029 DOI: 10.3390/cells12071057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Transcriptional regulation is fundamental to most biological processes and reverse-engineering programs can be used to decipher the underlying programs. In this review, we describe how genomics is offering a systems biology-based perspective of the intricate and temporally coordinated transcriptional programs that control neuronal apoptosis and survival. In addition to providing a new standpoint in human pathology focused on the regulatory program, cracking the code of neuronal cell fate may offer innovative therapeutic approaches focused on downstream targets and regulatory networks. Similar to computers, where faults often arise from a software bug, neuronal fate may critically depend on its transcription program. Thus, cracking the code of neuronal life or death may help finding a patch for neurodegeneration and cancer.
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Affiliation(s)
- Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Velia D’Agata
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95124 Catania, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
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2
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Chromatin compaction precedes apoptosis in developing neurons. Commun Biol 2022; 5:797. [PMID: 35941180 PMCID: PMC9359995 DOI: 10.1038/s42003-022-03704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
While major changes in cellular morphology during apoptosis have been well described, the subcellular changes in nuclear architecture involved in this process remain poorly understood. Imaging of nucleosomes in cortical neurons in vitro before and during apoptosis revealed that chromatin compaction precedes the activation of caspase-3 and nucleus shrinkage. While this early chromatin compaction remained unaffected by pharmacological blockade of the final execution of apoptosis through caspase-3 inhibition, interfering with the chromatin dynamics by modulation of actomyosin activity prevented apoptosis, but resulted in necrotic-like cell death instead. With super-resolution imaging at different phases of apoptosis in vitro and in vivo, we demonstrate that chromatin compaction occurs progressively and can be classified into five stages. In conclusion, we show that compaction of chromatin in the neuronal nucleus precedes apoptosis execution. These early changes in chromatin structure critically affect apoptotic cell death and are not part of the final execution of the apoptotic process in developing cortical neurons. Single-molecule imaging in developing cortical neurons shows that chromatin compaction precedes apoptosis and is an essential part of it, but can be uncoupled from the following apoptotic process.
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3
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Morello G, Villari A, Spampinato AG, La Cognata V, Guarnaccia M, Gentile G, Ciotti MT, Calissano P, D’Agata V, Severini C, Cavallaro S. Transcriptional Profiles of Cell Fate Transitions Reveal Early Drivers of Neuronal Apoptosis and Survival. Cells 2021; 10:3238. [PMID: 34831459 PMCID: PMC8620386 DOI: 10.3390/cells10113238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/23/2022] Open
Abstract
Neuronal apoptosis and survival are regulated at the transcriptional level. To identify key genes and upstream regulators primarily responsible for these processes, we overlayed the temporal transcriptome of cerebellar granule neurons following induction of apoptosis and their rescue by three different neurotrophic factors. We identified a core set of 175 genes showing opposite expression trends at the intersection of apoptosis and survival. Their functional annotations and expression signatures significantly correlated to neurological, psychiatric and oncological disorders. Transcription regulatory network analysis revealed the action of nine upstream transcription factors, converging pro-apoptosis and pro-survival-inducing signals in a highly interconnected functionally and temporally ordered manner. Five of these transcription factors are potential drug targets. Transcriptome-based computational drug repurposing produced a list of drug candidates that may revert the apoptotic core set signature. Besides elucidating early drivers of neuronal apoptosis and survival, our systems biology-based perspective paves the way to innovative pharmacology focused on upstream targets and regulatory networks.
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Affiliation(s)
- Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Ambra Villari
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Antonio Gianmaria Spampinato
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Giulia Gentile
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Maria Teresa Ciotti
- Institute of Biochemistry and Cell Biology, National Research Council (IBBC-CNR), Via E. Ramarini, 32, Monterotondo Scalo, 00015 Rome, Italy; (M.T.C.); (C.S.)
| | - Pietro Calissano
- European Brain Research Institute (EBRI Foundation), Viale Regina Elena, 295, 00161 Rome, Italy;
| | - Velia D’Agata
- Department of Biomedical and Biotechnological Sciences, Section of Human Anatomy and Histology, University of Catania, Via Santa Sofia, 87, 95123 Catania, Italy;
| | - Cinzia Severini
- Institute of Biochemistry and Cell Biology, National Research Council (IBBC-CNR), Via E. Ramarini, 32, Monterotondo Scalo, 00015 Rome, Italy; (M.T.C.); (C.S.)
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
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4
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La Cognata V, Golini E, Iemmolo R, Balletta S, Morello G, De Rosa C, Villari A, Marinelli S, Vacca V, Bonaventura G, Dell'Albani P, Aronica E, Mammano F, Mandillo S, Cavallaro S. CXCR2 increases in ALS cortical neurons and its inhibition prevents motor neuron degeneration in vitro and improves neuromuscular function in SOD1G93A mice. Neurobiol Dis 2021; 160:105538. [PMID: 34743985 DOI: 10.1016/j.nbd.2021.105538] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/13/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disease characterized by depletion of motor neurons (MNs), for which effective medical treatments are still required. Previous transcriptomic analysis revealed the up-regulation of C-X-C motif chemokine receptor 2 (CXCR2)-mRNA in a subset of sporadic ALS patients and SOD1G93A mice. Here, we confirmed the increase of CXCR2 in human ALS cortex, and showed that CXCR2 is mainly localized in cell bodies and axons of cortical neurons. We also investigated the effects of reparixin, an allosteric inhibitor of CXCR2, in degenerating human iPSC-derived MNs and SOD1G93A mice. In vitro, reparixin rescued MNs from apoptotic cell death, preserving neuronal morphology, mitochondrial membrane potential and cytoplasmic membrane integrity, whereas in vivo it improved neuromuscular function of SOD1G93A mice. Altogether, these data suggest a role for CXCR2 in ALS pathology and support its pharmacological inhibition as a candidate therapeutic strategy against ALS at least in a specific subgroup of patients.
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Affiliation(s)
- Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Elisabetta Golini
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Rosario Iemmolo
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Sara Balletta
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Carla De Rosa
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Ambra Villari
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Sara Marinelli
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Valentina Vacca
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Gabriele Bonaventura
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Paola Dell'Albani
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 Amsterdam, the Netherlands.
| | - Fabio Mammano
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy; Department of Physics and Astronomy "G. Galilei", University of Padua, Padova, Italy.
| | - Silvia Mandillo
- Institute of Biochemistry and Cell Biology, National Research Council, Via E. Ramarini 32, 00015 Monterotondo Scalo, RM, Italy.
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, CT, Italy.
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5
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Schaffner SL, Lussier AA, Baker JA, Goldowitz D, Hamre KM, Kobor MS. Neonatal Alcohol Exposure in Mice Induces Select Differentiation- and Apoptosis-Related Chromatin Changes Both Independent of and Dependent on Sex. Front Genet 2020; 11:35. [PMID: 32117449 PMCID: PMC7026456 DOI: 10.3389/fgene.2020.00035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/13/2020] [Indexed: 01/08/2023] Open
Abstract
Prenatal alcohol exposure (PAE) affects many aspects of physiology and behavior, including brain development. Specifically, ethanol can influence expression of genes important for brain growth, including chromatin modifiers. Ethanol can also increase apoptotic cell death in the brain and alter epigenetic profiles such as modifications to histones and DNA methylation. Although differential sex outcomes and disruptions to the function of multiple brain regions have been reported in fetal alcohol spectrum disorder (FASD), the majority of our knowledge on molecular epigenetic and apoptotic dysregulation in PAE is based on data from males and is sometimes limited to assessments of the whole brain or one brain region. Here, we examined histone modifications, DNA methylation, and expression of genes involved in differentiation and proliferation related-chromatin modifications and apoptosis in the cerebral cortex and cerebellum of C57BL/6J mice exposed to an acute alcohol challenge on postnatal day 7, with a focus on differential outcomes between sexes and brain regions. We found that neonatal alcohol exposure altered histone modifications, and impacted expression of a select few chromatin modifier and apoptotic genes in both the cortex and cerebellum. The results were observed primarily in a sex-independent manner, although some additional trends toward sexual dimorphisms were observed. Alcohol exposure induced trends toward increased bulk H3K4me3 levels, increased Kmt2e expression, and elevated levels of Casp6 mRNA and bulk γH2A.X. Additional trends indicated that ethanol may impact Kdm4a promoter DNA methylation levels and bulk levels of the histone variant H2A.Z, although further studies are needed. We comprehensively examined effects of ethanol exposure across different sexes and brain regions, and our results suggest that major impacts of ethanol on bulk chromatin modifications underlying differentiation and apoptosis may be broadly applicable across the rodent cortex and cerebellum in both sexes.
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Affiliation(s)
- Samantha L. Schaffner
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute – Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Alexandre A. Lussier
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute – Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jessica A. Baker
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Dan Goldowitz
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute – Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Kristin M. Hamre
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute – Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Human Early Learning Partnership, School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
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6
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Bonaventura G, La Cognata V, Iemmolo R, Zimbone M, Contino A, Maccarrone G, Failla B, Barcellona ML, Conforti FL, D’Agata V, Cavallaro S. Ag-NPs induce apoptosis, mitochondrial damages and MT3/OSGIN2 expression changes in an in vitro model of human dental-pulp-stem-cells-derived neurons. Neurotoxicology 2018; 67:84-93. [DOI: 10.1016/j.neuro.2018.04.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 01/09/2023]
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7
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Maino B, Spampinato AG, Severini C, Petrella C, Ciotti MT, D'Agata V, Calissano P, Cavallaro S. The trophic effect of nerve growth factor in primary cultures of rat hippocampal neurons is associated to an anti-inflammatory and immunosuppressive transcriptional program. J Cell Physiol 2018; 233:7178-7187. [PMID: 29741791 DOI: 10.1002/jcp.26744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/06/2018] [Indexed: 12/20/2022]
Abstract
Nerve growth factor, the prototype of a family of neurotrophins, elicits differentiation and survival of peripheral and central neuronal cells. Although its neural mechanisms have been studied extensively, relatively little is known about the transcriptional regulation governing its effects. We have previously observed that in primary cultures of rat hippocampal neurons treatment with nerve growth factor for 72 hr increases neurite outgrowth and cell survival. To obtain a comprehensive view of the underlying transcriptional program, we performed whole-genome expression analysis by microarray technology. We identified 541 differentially expressed genes and characterized dysregulated pathways related to innate immunity: the complement system and neuro-inflammatory signaling. The exploitation of such genes and pathways may help interfering with the intracellular mechanisms involved in neuronal survival and guide novel therapeutic strategies for neurodegenerative diseases.
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Affiliation(s)
- Barbara Maino
- Institute of Neurological Sciences, Italian National Research Council, Catania, Italy
| | - Antonio G Spampinato
- Institute of Neurological Sciences, Italian National Research Council, Catania, Italy
| | - Cinzia Severini
- Institute of Cell Biology and Neurobiology, Italian National Research Council, Roma, Italy.,European Brain Research Institute, Roma, Italy
| | - Carla Petrella
- Institute of Cell Biology and Neurobiology, Italian National Research Council, Roma, Italy
| | | | - Velia D'Agata
- Department of Biomedical and Biotechnological Sciences, Section of Human Anatomy and Histology, University of Catania, Catania, Italy
| | | | - Sebastiano Cavallaro
- Institute of Neurological Sciences, Italian National Research Council, Catania, Italy
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8
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D'Amico AG, Maugeri G, Rasà DM, La Cognata V, Saccone S, Federico C, Cavallaro S, D'Agata V. NAP counteracts hyperglycemia/hypoxia induced retinal pigment epithelial barrier breakdown through modulation of HIFs and VEGF expression. J Cell Physiol 2017; 233:1120-1128. [DOI: 10.1002/jcp.25971] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 04/21/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Agata G. D'Amico
- Department of Human Science and Promotion of Quality of LifeSan Raffaele Open University of RomeItaly
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological SciencesUniversity of CataniaItaly
| | - Grazia Maugeri
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological SciencesUniversity of CataniaItaly
| | - Daniela M. Rasà
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological SciencesUniversity of CataniaItaly
| | | | - Salvatore Saccone
- Section of Animal Biology, Department of Biological, Geological and Environmental SciencesUniversity of CataniaItaly
| | - Concetta Federico
- Section of Animal Biology, Department of Biological, Geological and Environmental SciencesUniversity of CataniaItaly
| | | | - Velia D'Agata
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological SciencesUniversity of CataniaItaly
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Selection and Prioritization of Candidate Drug Targets for Amyotrophic Lateral Sclerosis Through a Meta-Analysis Approach. J Mol Neurosci 2017; 61:563-580. [PMID: 28236105 PMCID: PMC5359376 DOI: 10.1007/s12031-017-0898-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/08/2017] [Indexed: 02/06/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive and incurable neurodegenerative disease. Although several compounds have shown promising results in preclinical studies, their translation into clinical trials has failed. This clinical failure is likely due to the inadequacy of the animal models that do not sufficiently reflect the human disease. Therefore, it is important to optimize drug target selection by identifying those that overlap in human and mouse pathology. We have recently characterized the transcriptional profiles of motor cortex samples from sporadic ALS (SALS) patients and differentiated these into two subgroups based on differentially expressed genes, which encode 70 potential therapeutic targets. To prioritize drug target selection, we investigated their degree of conservation in superoxide dismutase 1 (SOD1) G93A transgenic mice, the most widely used ALS animal model. Interspecies comparison of our human expression data with those of eight different SOD1G93A datasets present in public repositories revealed the presence of commonly deregulated targets and related biological processes. Moreover, deregulated expression of the majority of our candidate targets occurred at the onset of the disease, offering the possibility to use them for an early and more effective diagnosis and therapy. In addition to highlighting the existence of common key drivers in human and mouse pathology, our study represents the basis for a rational preclinical drug development.
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Maino B, Paparone S, Severini C, Ciotti MT, D'agata V, Calissano P, Cavallaro S. Drug target identification at the crossroad of neuronal apoptosis and survival. Expert Opin Drug Discov 2017; 12:249-259. [PMID: 28067072 DOI: 10.1080/17460441.2017.1280023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Inappropriate activation of apoptosis may contribute to neurodegeneration, a multifaceted process that results in various chronic disorders, including Alzheimer's and Parkinson's diseases. Several in vitro and in vivo studies demonstrated that neuronal apoptosis is a multi-pathway cell-death program that requires RNA synthesis. Thus, transcriptionally activated genes whose products induce cell death can be triggered by different stimuli and antagonized by neurotrophic factors. Systems biology is now unveiling the series of intracellular signaling pathways and key drug targets at the intersection of neuronal apoptosis and survival. Areas covered: This review introduces a genomic approach that can be used to elucidate the systems biology of neuronal apoptosis and survival, and to rationally select drug targets, no longer oriented to emulate the action of growth factors at the membrane receptor level, but rather to modulate their downstream signals. Expert opinion: The advent of genomics is offering an unprecedented opportunity to explore how the delicate balance between apoptosis and survival-inducing signals triggers a transcriptional program. Characterization of this program can be useful to identify potential pharmacological targets for existing drugs. Such knowledge might pave the way towards an innovative pharmacology.
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Affiliation(s)
- Barbara Maino
- a Institute of Neurological Sciences , Italian National Research Council , Catania , Italy
| | - Simona Paparone
- a Institute of Neurological Sciences , Italian National Research Council , Catania , Italy
| | - Cinzia Severini
- b Institute of Cell Biology and Neurobiology , Italian National Research Council , Roma , Italy.,c European Brain Research Institute , 00143 Roma , Italy
| | - Maria Teresa Ciotti
- b Institute of Cell Biology and Neurobiology , Italian National Research Council , Roma , Italy
| | - Velia D'agata
- d Department of Biomedical and Biotechnological Sciences, Section of Human Anatomy and Histology , University of Catania , 95125 Catania , Italy
| | | | - Sebastiano Cavallaro
- a Institute of Neurological Sciences , Italian National Research Council , Catania , Italy
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Paparone S, Severini C, Ciotti MT, D'Agata V, Calissano P, Cavallaro S. Transcriptional landscapes at the intersection of neuronal apoptosis and substance P-induced survival: exploring pathways and drug targets. Cell Death Discov 2016; 2:16050. [PMID: 27551538 PMCID: PMC4979452 DOI: 10.1038/cddiscovery.2016.50] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 05/20/2016] [Accepted: 05/25/2016] [Indexed: 12/29/2022] Open
Abstract
A change in the delicate equilibrium between apoptosis and survival regulates the neurons fate during the development of nervous system and its homeostasis in adulthood. Signaling pathways promoting or protecting from apoptosis are activated by multiple signals, including those elicited by neurotrophic factors, and depend upon specific transcriptional programs. To decipher the rescue program induced by substance P (SP) in cerebellar granule neurons, we analyzed their whole-genome expression profiles after induction of apoptosis and treatment with SP. Transcriptional pathways associated with the survival effect of SP included genes encoding for proteins that may act as pharmacological targets. Inhibition of one of these, the Myc pro-oncogene by treatment with 10058-F4, reverted in a dose-dependent manner the rescue effect of SP. In addition to elucidate the transcriptional mechanisms at the intersection of neuronal apoptosis and survival, our systems biology-based perspective paves the way towards an innovative pharmacology based on targets downstream of neurotrophic factor receptors.
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Affiliation(s)
- S Paparone
- Institute of Neurological Sciences, Italian National Research Council , Via Paolo Gaifami, 18, Catania 95125, Italy
| | - C Severini
- Institute of Cell Biology and Neurobiology, Italian National Research Council, Via del Fosso di Fiorano 64, Roma 00143, Italy; European Brain Research Institute, Via del Fosso di Fiorano 64, Roma 00143, Italy
| | - M T Ciotti
- Institute of Cell Biology and Neurobiology, Italian National Research Council , Via del Fosso di Fiorano 64, Roma 00143, Italy
| | - V D'Agata
- Department of Biomedical and Biotechnological Sciences, Section of Human Anatomy and Histology, University of Catania , Catania 95125, Italy
| | - P Calissano
- European Brain Research Institute , Via del Fosso di Fiorano 64, Roma 00143, Italy
| | - S Cavallaro
- Institute of Neurological Sciences, Italian National Research Council , Via Paolo Gaifami, 18, Catania 95125, Italy
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12
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Maino B, D'Agata V, Severini C, Ciotti MT, Calissano P, Copani A, Chang YC, DeLisi C, Cavallaro S. Igf1 and Pacap rescue cerebellar granule neurons from apoptosis via a common transcriptional program. Cell Death Discov 2015; 1. [PMID: 26941962 PMCID: PMC4773033 DOI: 10.1038/cddiscovery.2015.29] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A shift of the delicate balance between apoptosis and survival-inducing signals determines the fate of neurons during the development of the central nervous system and its homeostasis throughout adulthood. Both pathways, promoting or protecting from apoptosis, trigger a transcriptional program. We conducted whole-genome expression profiling to decipher the transcriptional regulatory elements controlling the apoptotic/survival switch in cerebellar granule neurons following the induction of apoptosis by serum and potassium deprivation or their rescue by either insulin-like growth factor-1 (Igf1) or pituitary adenylyl cyclase-activating polypeptide (Pacap). Although depending on different upstream signaling pathways, the survival effects of Igf1 and Pacap converged into common transcriptional cascades, thus suggesting the existence of a general transcriptional program underlying neuronal survival.
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Affiliation(s)
- Barbara Maino
- Institute of Neurological Sciences, Italian National Research Council, 95126 Catania, Italy
| | - Velia D'Agata
- Department of Biomedical and Biotechnological Sciences, Section of Human Anatomy and Histology, University of Catania, 95123 Catania, Italy
| | - Cinzia Severini
- Institute of Neurobiology and Molecular Medicine, Italian National Research Council, 00143 Roma, Italy
| | | | | | - Agata Copani
- Department of Drug Sciences, University of Catania, 95125 Catania, Italy
| | - Yi-Chien Chang
- Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA
| | - Charles DeLisi
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Sebastiano Cavallaro
- Institute of Neurological Sciences, Italian National Research Council, 95126 Catania, Italy
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13
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Abstract
Neuronal apoptosis represents an intrinsic «suicide» program, by which a neuron orchestrates its own destruction. Although engagement of apoptosis requires transcription and protein synthesis, the complete spectrum of genes involved in distinct temporal domains remained unknown until the advent of genomics. In the last 10 years, the genome sequences and the development of high-throughput genomic technologies, such as DNA microarrays, have offered the unprecedented experimental opportunities to explore the transcriptional mechanisms underlying apoptosis from a new systems-level perspective. This review goes over this genomic approach and illustrates the use of microarray methodology to dissecting the multigenic program underlying neuronal apoptosis.
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Affiliation(s)
- Sebastiano Cavallaro
- Functional Genomics Center, Institute of Neurological Sciences, Italian National Research Council (CNR), Via Paolo Gaifami 18, Catania, 95126, Italy,
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14
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Deighton RF, Kerr LE, Short DM, Allerhand M, Whittle IR, McCulloch J. Network generation enhances interpretation of proteomic data from induced apoptosis. Proteomics 2010; 10:1307-15. [DOI: 10.1002/pmic.200900112] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Yeste-Velasco M, Folch J, Pallàs M, Camins A. The p38(MAPK) signaling pathway regulates neuronal apoptosis through the phosphorylation of the retinoblastoma protein. Neurochem Int 2008; 54:99-105. [PMID: 19007833 DOI: 10.1016/j.neuint.2008.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 10/13/2008] [Accepted: 10/14/2008] [Indexed: 01/21/2023]
Abstract
We investigated the role of SB202190, a selective p38 mitogen-activated protein kinase (MAPK) inhibitor in cerebellar granule neurons (CGC) in response to serum potassium deprivation (S/K deprivation), an apoptotic stimulus. CGC apoptosis after S/K deprivation was shown to be mediated through cell cycle re-entry and the induction of transcription factor E2F-1. We found that SB 202190 (10muM) inhibits retinoblastoma protein (pRb) phosphorylation, in response to S/K deprivation. Moreover, the expression of cyclin E and E2F-1 were also significantly decreased. Interestingly, SB202190 did not affect or modulate the increase in the protein expression levels of cyclin D1. Similarly, p-Akt and p-GSK3 protein levels, measured after 12h S/K deprivation, did not appear to be regulated by SB 202190 (10muM). These data indicate that the neuroprotective effects of the p38 inhibitor were not mediated via Akt activation. In conclusion, these results suggest that p38MAPK converged with the cell cycle in S/K deprivation-induced apoptosis through pRb phosphorylation.
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Affiliation(s)
- Marc Yeste-Velasco
- Unitat de Farmacologia i Farmacognòsia, Facultat de Farmàcia, Institut de Biomedicina (IBUB), Centros de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain
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16
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Cavallaro S. Neuronal apoptosis revealed by genomic analysis: integrating gene expression profiles with functional information. Neuroinformatics 2007; 5:115-26. [PMID: 17873373 DOI: 10.1007/s12021-007-0006-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/28/2022]
Abstract
Apoptosis is a key physiological response that occurs during development of the nervous system, resulting in the death of nearly half of the embryonic neuronal population. Aberrant apoptotic mechanisms are thought to contribute significantly to many neurological disorders including Alzheimer's disease. Although many experiments in the past have demonstrated the requirement of de novo gene expression during neuronal apoptosis, the complete spectrum of genes involved in distinct temporal domains is mostly unknown. To begin a comprehensive survey of the gene-based molecular mechanisms that underlie neuronal apoptosis, we have used the unprecedented experimental opportunities that genome sequences and the development of DNA microarray technology now provide to perform genome-wide expression analysis in different paradigms of neuronal apoptosis. In order to extract knowledge from gene expression information we have developed new informatics applications that enable clustering methods based on semantic characteristics, such as gene ontologies. This review will highlight the use of a genomic approach to identify the molecular program underlying neuronal apoptosis and illustrate how a semantic clustering method can be useful to extract more knowledge from microarray data.
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Affiliation(s)
- Sebastiano Cavallaro
- Istituto di Scienze Neurologiche, CNR, Viale Regina Margherita 6, Catania, Italy.
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Yeste-Velasco M, Folch J, Trullàs R, Abad MA, Enguita M, Pallàs M, Camins A. Glycogen synthase kinase-3 is involved in the regulation of the cell cycle in cerebellar granule cells. Neuropharmacology 2007; 53:295-307. [PMID: 17612578 DOI: 10.1016/j.neuropharm.2007.05.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Revised: 04/02/2007] [Accepted: 05/16/2007] [Indexed: 01/17/2023]
Abstract
Recent studies have demonstrated that neuronal reentry in the cell cycle and specifically the expression of the transcription factor E2F-1, constitutes a pathway that may be involved in neuronal apoptosis after serum and potassium withdrawal. Other enzymes such as glycogen synthase kinase-3beta (GSK-3beta) are also involved in this apoptotic stimulus, and thus in the process of neuronal cell death. Primary cerebellar granule cells (CGNs) were used in this study to determine whether pharmacological inhibition of GSK-3beta is involved in neuronal modulation of the cell cycle, and specifically in the regulation of E2F-1 and retinoblastoma protein (Rb). CGNs showed a dramatic increase in GSK-3beta activity after 2h of serum and potassium deprivation. Immunoblot and activity assays revealed that lithium and SB415286 inhibit fully the activation of GSK-3beta and attenuate the expression of cyclin D, cyclin E, pRb phosphorylation and the transcription factor E2F-1. These data were confirmed using AR-014418, a selective GSK-3beta inhibitor that prevents the expression of cell-cycle proteins. Our data indicate that GSK-3beta inhibition regulates, in part, the cell cycle in CGNs by inhibiting Rb phosphorylation and thus inhibiting E2F-1 activity. However, the selective inhibition of GSK-3beta with AR-A014418 had not effect on cell viability or apoptosis mediated by S/K withdrawal. Furthermore, our results suggest that selective GSK-3beta inhibition is not sufficient to protect against apoptosis in this S/K withdrawal model, indicating that Li(+) and SB415286 neuroprotective effects are mediated by the inhibition of additional targets to GSK3beta. Therefore, there is a connection between cell cycle and GSK-3beta activation and that these, along with other mechanisms, are involved in the molecular paths leading to the apoptotic process of rat CGNs triggered by S/K withdrawal.
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Affiliation(s)
- M Yeste-Velasco
- Unitat de Farmacologia, Facultat de Farmàcia Universitat de Barcelona, Nucli Universitari de Pedralbes, E-08028 Barcelona, Spain
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18
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Heinitz K, Beck M, Schliebs R, Perez-Polo JR. Toxicity mediated by soluble oligomers of beta-amyloid(1-42) on cholinergic SN56.B5.G4 cells. J Neurochem 2006; 98:1930-45. [PMID: 16945109 DOI: 10.1111/j.1471-4159.2006.04015.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease (AD) is characterized by cholinergic dysfunction and progressive basal forebrain cell loss which has been assumed to be as a result of the extensive accumulation of beta-amyloid (Abeta). In addition to Abeta fibrillar assemblies, there are pre-fibrillar forms that have been shown to be neurotoxic, although their role in cholinergic degeneration is still not known. Using the cholinergic cell line SN56.B5.G4, we investigated the effect of different Abeta(1-42) aggregates on cell viability. In our model, only soluble oligomeric but not fibrillar Abeta(1-42) forms induced toxicity in cholinergic cells. To determine whether the neurotoxicity of oligomeric Abeta(1-42) was caused by its oxidative potential, we performed microarray analysis of SN56.B5.G4 cells treated either with oligomeric Abeta(1-42) or H(2)O(2). We showed that genes affected by Abeta(1-42) differed from those affected by non-specific oxidative stress. Many of the genes affected by Abeta(1-42) were present in the endoplasmic reticulum (ER), Golgi apparatus and/or otherwise involved in protein modification and degradation (chaperones, ATF6), indicating a possible role for ER-mediated stress in Abeta-mediated toxicity. Moreover, a number of genes, which are known to be involved in AD (clusterin, Slc18a3), were identified. This study provides important leads for the understanding of oligomeric Abeta(1-42) toxicity in cholinergic cells, which may account in part for cholinergic degeneration in AD.
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Affiliation(s)
- Katrin Heinitz
- Paul Flechsig Institute for Brain Research, Department of Neurochemistry, University of Leipzig, Leipzig, Germany
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Alberghina L, Colangelo AM. The modular systems biology approach to investigate the control of apoptosis in Alzheimer's disease neurodegeneration. BMC Neurosci 2006; 7 Suppl 1:S2. [PMID: 17118156 PMCID: PMC1775042 DOI: 10.1186/1471-2202-7-s1-s2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Apoptosis is a programmed cell death that plays a critical role during the development of the nervous system and in many chronic neurodegenerative diseases, including Alzheimer's disease (AD). This pathology, characterized by a progressive degeneration of cholinergic function resulting in a remarkable cognitive decline, is the most common form of dementia with high social and economic impact. Current therapies of AD are only symptomatic, therefore the need to elucidate the mechanisms underlying the onset and progression of the disease is surely needed in order to develop effective pharmacological therapies. Because of its pivotal role in neuronal cell death, apoptosis has been considered one of the most appealing therapeutic targets, however, due to the complexity of the molecular mechanisms involving the various triggering events and the many signaling cascades leading to cell death, a comprehensive understanding of this process is still lacking. Modular systems biology is a very effective strategy in organizing information about complex biological processes and deriving modular and mathematical models that greatly simplify the identification of key steps of a given process. This review aims at describing the main steps underlying the strategy of modular systems biology and briefly summarizes how this approach has been successfully applied for cell cycle studies. Moreover, after giving an overview of the many molecular mechanisms underlying apoptosis in AD, we present both a modular and a molecular model of neuronal apoptosis that suggest new insights on neuroprotection for this disease.
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Affiliation(s)
- Lilia Alberghina
- Department of Biotechnology and Biosciences, Laboratory of Neuroscience R. Levi-Montalcini, University of Milano-Bicocca, 20126 Milan, Italy.
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Paratore S, Parenti R, Torrisi A, Copani A, Cicirata F, Cavallaro S. Genomic profiling of cortical neurons following exposure to beta-amyloid. Genomics 2006; 88:468-79. [PMID: 16904863 DOI: 10.1016/j.ygeno.2006.06.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Revised: 06/12/2006] [Accepted: 06/16/2006] [Indexed: 10/24/2022]
Abstract
In vitro and in vivo studies have shown that beta-amyloid peptide induces neuronal cell death. To explore the molecular basis underlying beta-amyloid-induced toxicity, we analyzed gene expression profiles of cultured rat cortical neurons treated for 24 and 48 h with synthetic beta-amyloid peptide. From the 8740 genes interrogated by oligonucleotide microarray analysis, 241 genes were found to be differentially expressed and segregated into distinct clusters. Functional clustering based on gene ontologies showed coordinated expression of genes with common biological functions and metabolic pathways. The comparison with genes differentially expressed in cerebellar granule neurons following serum and potassium deprivation indicates the existence of common regulatory mechanisms underlying neuronal cell death. Our results offer a genomic view of the changes that accompany beta-amyloid-induced neurodegeneration.
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Affiliation(s)
- Sabrina Paratore
- Functional Genomics Center, Institute of Neurological Sciences, Italian National Research Council, Italy
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21
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2448604 DOI: 10.1002/cfg.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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