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Navarro G, Franco N, Martínez-Pinilla E, Franco R. The Epigenetic Cytocrin Pathway to the Nucleus. Epigenetic Factors, Epigenetic Mediators, and Epigenetic Traits. A Biochemist Perspective. Front Genet 2017; 8:179. [PMID: 29230234 PMCID: PMC5711780 DOI: 10.3389/fgene.2017.00179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/06/2017] [Indexed: 12/29/2022] Open
Abstract
A single word, Epigenetics, underlies one exciting subject in today's Science, with different sides and with interactions with philosophy. The apparent trivial description includes everything in between genotype and phenotype that occurs for a given unique DNA sequence/genome. This Perspective article first presents an historical overview and the reasons for the lack of consensus in the field, which derives from different interpretations of the diverse operative definitions of Epigenetics. In an attempt to reconcile the different views, we propose a novel concept, the “cytocrin system.” Secondly, the article questions the inheritability requirement and makes emphasis in the epigenetic mechanisms, known or to be discovered, that provide hope for combating human diseases. Hopes in cancer are at present in deep need of deciphering mechanisms to support ad hoc therapeutic approaches. Better perspectives are for diseases of the central nervous system, in particular to combat neurodegeneration and/or cognitive deficits in Alzheimer's disease. Neurons are post-mitotic cells and, therefore, epigenetic targets to prevent neurodegeneration should operate in non-dividing diseased cells. Accordingly, epigenetic-based human therapy may not need to count much on transmissible potential.
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Affiliation(s)
- Gemma Navarro
- Department of Biochemistry and Physiology, Pharmacy School, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación en Red, Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Eva Martínez-Pinilla
- Departamento de Morfología y Biología Celular, Facultad de Medicina, Instituto de Neurociencias del Principado de Asturias, Universidad de Oviedo, Asturias, Spain
| | - Rafael Franco
- Centro de Investigación en Red, Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain.,Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain
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Oh G, Ebrahimi S, Wang SC, Cortese R, Kaminsky ZA, Gottesman II, Burke JR, Plassman BL, Petronis A. Epigenetic assimilation in the aging human brain. Genome Biol 2016; 17:76. [PMID: 27122015 PMCID: PMC4848814 DOI: 10.1186/s13059-016-0946-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 04/11/2016] [Indexed: 12/22/2022] Open
Abstract
Background Epigenetic drift progressively increases variation in DNA modification profiles of aging cells, but the finale of such divergence remains elusive. In this study, we explored the dynamics of DNA modification and transcription in the later stages of human life. Results We find that brain tissues of older individuals (>75 years) become more similar to each other, both epigenetically and transcriptionally, compared with younger individuals. Inter-individual epigenetic assimilation is concurrent with increasing similarity between the cerebral cortex and the cerebellum, which points to potential brain cell dedifferentiation. DNA modification analysis of twins affected with Alzheimer’s disease reveals a potential for accelerated epigenetic assimilation in neurodegenerative disease. We also observe loss of boundaries and merging of neighboring DNA modification and transcriptomic domains over time. Conclusions Age-dependent epigenetic divergence, paradoxically, changes to convergence in the later stages of life. The newly described phenomena of epigenetic assimilation and tissue dedifferentiation may help us better understand the molecular mechanisms of aging and the origins of diseases for which age is a risk factor. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0946-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriel Oh
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St. R130, Toronto, Ontario, M5T 1R8, Canada
| | - Sasha Ebrahimi
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St. R130, Toronto, Ontario, M5T 1R8, Canada
| | - Sun-Chong Wang
- Institute of Systems Biology and Bioinformatics, National Central University, Chungli, 320, Taiwan
| | - Rene Cortese
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St. R130, Toronto, Ontario, M5T 1R8, Canada.,Department of Pediatrics, University of Chicago, Chicago, Illinois, 60637, USA
| | - Zachary A Kaminsky
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland, 21287, USA
| | - Irving I Gottesman
- Departments of Psychology and Psychiatry, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - James R Burke
- Duke University Medical Center, Duke University, Box 2900, Durham, North Carolina, 27701, USA
| | - Brenda L Plassman
- Duke University Medical Center, Duke University, Box 41, Durham, North Carolina, 27701, USA
| | - Art Petronis
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St. R130, Toronto, Ontario, M5T 1R8, Canada.
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Krubitzer L, Dooley JC. Cortical plasticity within and across lifetimes: how can development inform us about phenotypic transformations? Front Hum Neurosci 2013; 7:620. [PMID: 24130524 PMCID: PMC3793242 DOI: 10.3389/fnhum.2013.00620] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/08/2013] [Indexed: 11/13/2022] Open
Abstract
The neocortex is the part of the mammalian brain that is involved in perception, cognition, and volitional motor control. It is a highly dynamic structure that is dramatically altered within the lifetime of an animal and in different lineages throughout the course of evolution. These alterations account for the remarkable variations in behavior that species exhibit. Of particular interest is how these cortical phenotypes change within the lifetime of the individual and eventually evolve in species over time. Because we cannot study the evolution of the neocortex directly we use comparative analysis to appreciate the types of changes that have been made to the neocortex and the similarities that exist across taxa. Developmental studies inform us about how these phenotypic transitions may arise by alterations in developmental cascades or changes in the physical environment in which the brain develops. Both genes and the sensory environment contribute to aspects of the phenotype and similar features, such as the size of a cortical field, can be altered in a variety of ways. Although both genes and the laws of physics place constraints on the evolution of the neocortex, mammals have evolved a number of mechanisms that allow them to loosen these constraints and often alter the course of their own evolution.
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Affiliation(s)
- Leah Krubitzer
- Center for Neuroscience, University of California Davis, Davis, CA, USA ; Department of Psychology, University of California Davis, Davis, CA, USA
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Burwell RG, Dangerfield PH, Moulton A, Grivas TB. Adolescent idiopathic scoliosis (AIS), environment, exposome and epigenetics: a molecular perspective of postnatal normal spinal growth and the etiopathogenesis of AIS with consideration of a network approach and possible implications for medical therapy. SCOLIOSIS 2011; 6:26. [PMID: 22136338 PMCID: PMC3293085 DOI: 10.1186/1748-7161-6-26] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 12/02/2011] [Indexed: 12/22/2022]
Abstract
Genetic factors are believed to play an important role in the etiology of adolescent idiopathic scoliosis (AIS). Discordant findings for monozygotic (MZ) twins with AIS show that environmental factors including different intrauterine environments are important in etiology, but what these environmental factors may be is unknown. Recent evidence for common chronic non-communicable diseases suggests epigenetic differences may underlie MZ twin discordance, and be the link between environmental factors and phenotypic differences. DNA methylation is one important epigenetic mechanism operating at the interface between genome and environment to regulate phenotypic plasticity with a complex regulation across the genome during the first decade of life. The word exposome refers to the totality of environmental exposures from conception onwards, comprising factors in external and internal environments. The word exposome is used here also in relation to physiologic and etiopathogenetic factors that affect normal spinal growth and may induce the deformity of AIS. In normal postnatal spinal growth we propose a new term and concept, physiologic growth-plate exposome for the normal processes particularly of the internal environments that may have epigenetic effects on growth plates of vertebrae. In AIS, we propose a new term and concept pathophysiologic scoliogenic exposome for the abnormal processes in molecular pathways particularly of the internal environment currently expressed as etiopathogenetic hypotheses; these are suggested to have deforming effects on the growth plates of vertebrae at cell, tissue, structure and/or organ levels that are considered to be epigenetic. New research is required for chromatin modifications including DNA methylation in AIS subjects and vertebral growth plates excised at surgery. In addition, consideration is needed for a possible network approach to etiopathogenesis by constructing AIS diseasomes. These approaches may lead through screening, genetic, epigenetic, biochemical, metabolic phenotypes and pharmacogenomic research to identify susceptible individuals at risk and modulate abnormal molecular pathways of AIS. The potential of epigenetic-based medical therapy for AIS cannot be assessed at present, and must await new research derived from the evaluation of epigenetic concepts of spinal growth in health and deformity. The tenets outlined here for AIS are applicable to other musculoskeletal growth disorders including infantile and juvenile idiopathic scoliosis.
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Affiliation(s)
- R Geoffrey Burwell
- Centre for Spinal Studies and Surgery, Nottingham University Hospitals Trust, Queen's Medical Centre Campus, Derby Road, Nottingham, NG7 2UH, UK
| | - Peter H Dangerfield
- University of Liverpool, Ashton Street, L69 3GE, UK
- Staffordshire University, Leek Road, Stoke-on-Trent, ST4 2DF. UK
- Royal Liverpool Children's Hospital, Eaton Road, Liverpool, L12 2AP, UK
| | - Alan Moulton
- Department of Orthopaedic Surgery, King's Mill Hospital, Sutton Road, Mansfield NG17 4JL, UK
| | - Theodoros B Grivas
- Department of Trauma and Orthopedics, "Tzanio" General Hospital, Tzani and Afendouli 1 st, Piraeus 18536, Greece.co.uk
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Wilkins AS. The enemy within: an epigenetic role of retrotransposons in cancer initiation. Bioessays 2010; 32:856-65. [PMID: 20715060 DOI: 10.1002/bies.201000008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article proposes that cancers can be initiated by retrotransposon (RTN) activation through changes in the transcriptional regulation of nearby genes. I first detail the hypothesis and then discuss the nature of physiological stress(es) in RTN activation; the role of DNA demethylation in the initiation and propagation of new RTN states; the connection between ageing and cancer incidence and the involvement of activated RTNs in the chromosomal aberrations that feature in cancer progression. The hypothesis neither replaces nor invalidates other theories of cancer, in particular the somatic mutation theory, but helps clarify and unify much of the hitherto poorly integrated, complex phenomenology of cancer.
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GORELICK ROOT, CARPINONE JESSICA. Origin and maintenance of sex: the evolutionary joys of self sex. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01334.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Hamlat A, Pasqualini E. Stem cells adaptive network: mechanism and implications for evolution and disease development. Med Hypotheses 2007; 69:610-7. [PMID: 17336463 DOI: 10.1016/j.mehy.2006.12.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 12/21/2006] [Indexed: 10/23/2022]
Abstract
During development, different cells and tissues acquire different programmes of gene expression, so that cells are related to each other through a somatic cells tree or cluster and adult pluripotential stem cells (PSC) may be defined as progenitors that we distinguish in four types according to their biological behaviour. This clustering may segregate specific pathways establishing spatial patterns of cell-cell communications. Thus, we suggest that normal somatic cells renewal is tributary of multipotential stem cells (MSC), while renewal of cells undergoing stress or abnormal death is tributary of PSC through specific pathway(s) from cluster, thus, defining the cell repertoire that will be produced. We also assume that PSC play a pivotal role in evolutionary and propose the theory of "internal clusters competition". According to the functional duality of stem cells (SC) we define a stem cells adaptive network (SCAN) which we believe is linked to the central clock and display two pathways. The diurnal pathway includes SC-somatic cells communications, while the nocturnal pathway includes inter-SC network. These alternate pathways could be activated or repressed as a consequence of change in the biological chirality. This new approach of SC may contribute to our understanding on how some diseases may develop including cancer which could be linked to "cluster illness", while demyelinating and systemic diseases could be related to "PSC locus illness" or "focalised SCAN disturbances" and it explains how any environment stress may act on organism evolution.
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Affiliation(s)
- Abderrahmane Hamlat
- Department of Neurosurgery, CHRU Pontchaillou, Rue Henry Le Guilloux, 35000 Rennes, Cedex 2, France.
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