Ítem
Acceso Abierto

Identification of transcriptomic responses related to normal, healthy and accelerated aging

Mostrar el registro sencillo de la publicación
dc.contributor.advisorRamírez Clavijo, Sandra Rocío
dc.creatorPayan-Gomez, Cesar
dc.creator.degreeDoctor en Ciencias Biomédicasspa
dc.creator.degreetypeFull timespa
dc.date.accessioned2019-02-18T22:27:12Z
dc.date.available2019-02-18T22:27:12Z
dc.date.created2018-12-14
dc.date.issued2018
dc.descriptionEl envejecimiento es la reducción de las capacidades fisiológicas y adaptativas del organismo con el paso del tiempo. La acumulación de daño en el ADN podría ser el evento central desencadenante del proceso de envejecimiento. Los síndromes progeroides causados por una deficiencia de la sub-vía de reparación de escisión de nucleótidos acoplada a transcripción (TCR-NER) presentan un vínculo directo entre daño en el ADN y envejecimiento. Hay un paralelo entre la respuesta transcripcional de ratones progeroides y ratones sometidos a restricción dietética (DR) (una intervención que prolonga la vida). La DR aumenta la resistencia a diferentes formas de estrés. Ratones deficientes en TCR-NER también son menos susceptibles a un tipo de estrés agudo. El paralelo entre las respuestas transcriptómicas de los animales en dos extremos de esperanza de vida se ha explicado por la existencia de una respuesta de supervivencia programada. Esta tesis aborda varias cuestiones relacionadas con la respuesta de supervivencia utilizando principalmente el análisis de datos transcriptómicos. Primero, se estableció que los ratones viejos activan una respuesta de supervivencia incompleta después de tres días de DR, en segundo lugar, se describió un mecanismo común de activación de la respuesta protectora. En tercer lugar, se proporcionó una conexión entre la acumulación de daño en el ADN y la neurodegeneración. Finalmente, por medio de una metodología de análisis integrador sobre datos de transcriptómica de cerebro humano se encontró que en envejecimiento normal los astrocitos desarrollan dos fenotipos opuestos.spa
dc.description.abstractAging is defined as the reduction in the physiological and adaptive capabilities of organisms with the passage of time. The accumulation of DNA damage could be the central event on which other factors related to the aging process coalesce. One of the links connecting DNA damage to aging are the progeroid syndromes caused by a deficiency of DNA transcription-coupled nucleotide excision repair (TCR-NER) subpathway. There is a parallel between the transcriptional response of progeroid mice and mice on a dietary restriction (DR) regimen (an intervention that extend the lifespan). DR increased resistance to different forms of acute stress. Corroborating that TCR-NER deficiency induces activation of similar protective mechanisms, Csb-/- and Csa-/- mice are less susceptible to renal ischemia-reperfusion injury. The parallel between the transcriptomic responses of animals at two life expectancy extremes, in addition to the shared increase in resistance to ischemia-reperfusion injury, has been explained by the existence of a programmed survival response. This thesis addresses several questions related with the survival response, the mechanism of neurodegeneration and normal aging using mainly analysis of transcriptomic data. First, it was established that old mice activate an incomplete survival response after three days of DR, second, a common mechanism of activation of the protective response was described. Third, a connection between the accumulation of DNA damage and neurodegeneration was provided. Finally, an integrative methodology of analysis was used over brain human transcriptomic data, the result was the identification of an opposite activation of astrocytes in the human aged prefrontal cortex.spa
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.48713/10336_19101
dc.identifier.urihttp://repository.urosario.edu.co/handle/10336/19101
dc.language.isospa
dc.publisherUniversidad del Rosariospa
dc.publisher.departmentFacultad de Ciencias Naturales y Matemáticasspa
dc.publisher.programDoctorado en Ciencias Biomédicasspa
dc.rightsAtribución-NoComercial-SinDerivadas 2.5 Colombiaspa
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.rights.accesoAbierto (Texto Completo)spa
dc.rights.licenciaEL AUTOR, manifiesta que la obra objeto de la presente autorización es original y la realizó sin violar o usurpar derechos de autor de terceros, por lo tanto la obra es de exclusiva autoría y tiene la titularidad sobre la misma. PARGRAFO: En caso de presentarse cualquier reclamación o acción por parte de un tercero en cuanto a los derechos de autor sobre la obra en cuestión, EL AUTOR, asumirá toda la responsabilidad, y saldrá en defensa de los derechos aquí autorizados; para todos los efectos la universidad actúa como un tercero de buena fe. EL AUTOR, autoriza a LA UNIVERSIDAD DEL ROSARIO, para que en los términos establecidos en la Ley 23 de 1982, Ley 44 de 1993, Decisión andina 351 de 1993, Decreto 460 de 1995 y demás normas generales sobre la materia, utilice y use la obra objeto de la presente autorización. -------------------------------------- POLITICA DE TRATAMIENTO DE DATOS PERSONALES. Declaro que autorizo previa y de forma informada el tratamiento de mis datos personales por parte de LA UNIVERSIDAD DEL ROSARIO para fines académicos y en aplicación de convenios con terceros o servicios conexos con actividades propias de la academia, con estricto cumplimiento de los principios de ley. Para el correcto ejercicio de mi derecho de habeas data cuento con la cuenta de correo habeasdata@urosario.edu.co, donde previa identificación podré solicitar la consulta, corrección y supresión de mis datos.spa
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/2.5/co/
dc.source.bibliographicCitationMendonca GV, Pezarat-Correia P, Vaz JR, Silva L, Heffernan KS. Impact of Aging on Endurance and Neuromuscular Physical Performance: The Role of Vascular Senescence. Sports Med. 2017;47(4):583-98.spa
dc.source.bibliographicCitationVermeij WP, Hoeijmakers JH, Pothof J. Aging: not all DNA damage is equal. Curr Opin Genet Dev. 2014;26:124-30.spa
dc.source.bibliographicCitationHoeijmakers JH. DNA damage, aging, and cancer. N Engl J Med. 2009;361(15):1475-85.spa
dc.source.bibliographicCitationBrown-Borg HM. Longevity in mice: is stress resistance a common factor? Age (Dordr). 2006;28(2):145-62spa
dc.source.bibliographicCitationMitchell JR, Verweij M, Brand K, van de Ven M, Goemaere N, van den Engel S, et al. Short-term dietary restriction and fasting precondition against ischemia reperfusion injury in mice. Aging Cell. 2010;9(1):40-53.spa
dc.source.bibliographicCitationSusa D, Mitchell JR, Verweij M, van de Ven M, Roest H, van den Engel S, et al. Congenital DNA repair deficiency results in protection against renal ischemia reperfusion injury in mice. Aging Cell. 2009;8(2):192-200spa
dc.source.bibliographicCitationSchumacher B, van der Pluijm I, Moorhouse MJ, Kosteas T, Robinson AR, Suh Y, et al. Delayed and accelerated aging share common longevity assurance mechanisms. PLoS Genet. 2008;4(8):e1000161spa
dc.source.bibliographicCitationCole JH, Franke K. Predicting Age Using Neuroimaging: Innovative Brain Ageing Biomarkers. Trends Neurosci. 2017;40(12):681-90spa
dc.source.bibliographicCitationLópez-Otín C, Blasco MA, Partridge L, Serrano M, Kroemer G. The hallmarks of aging. Cell. 2013;153(6):1194-217spa
dc.source.bibliographicCitationBjorksten J, Tenhu H. The crosslinking theory of aging--added evidence. Exp Gerontol. 1990;25(2):91-5spa
dc.source.bibliographicCitationAfanas'ev I. Signaling and Damaging Functions of Free Radicals in Aging-Free Radical Theory, Hormesis, and TOR. Aging Dis. 2010;1(2):75-88spa
dc.source.bibliographicCitationWei W, Ji S. Cellular senescence: Molecular mechanisms and pathogenicity. J Cell Physiol. 2018;233(12):9121-35spa
dc.source.bibliographicCitationRoche Y, Zhang D, Segers-Nolten GM, Vermeulen W, Wyman C, Sugasawa K, et al. Fluorescence correlation spectroscopy of the binding of nucleotide excision repair protein XPC-hHr23B with DNA substrates. J Fluoresc. 2008;18(5):987-95spa
dc.source.bibliographicCitationMitchell JR, Hoeijmakers JH, Niedernhofer LJ. Divide and conquer: nucleotide excision repair battles cancer and ageing. Curr Opin Cell Biol. 2003;15(2):232-40spa
dc.source.bibliographicCitationDiderich KE, Nicolaije C, Priemel M, Waarsing JH, Day JS, Brandt RM, et al. Bone fragility and decline in stem cells in prematurely aging DNA repair deficient trichothiodystrophy mice. Age (Dordr). 2012;34(4):845-61spa
dc.source.bibliographicCitationNagtegaal AP, Rainey RN, van der Pluijm I, Brandt RM, van der Horst GT, Borst JG, et al. Cockayne syndrome group B (Csb) and group a (Csa) deficiencies predispose to hearing loss and cochlear hair cell degeneration in mice. J Neurosci. 2015;35(10):4280-6spa
dc.source.bibliographicCitationJaarsma D, van der Pluijm I, van der Horst GT, Hoeijmakers JH. Cockayne syndrome pathogenesis: lessons from mouse models. Mech Ageing Dev. 2013;134(5-6):180-95spa
dc.source.bibliographicCitationvan der Pluijm I, Garinis GA, Brandt RM, Gorgels TG, Wijnhoven SW, Diderich KE, et al. Impaired genome maintenance suppresses the growth hormone--insulin-like growth factor 1 axis in mice with Cockayne syndrome. PLoS Biol. 2007;5(1):e2spa
dc.source.bibliographicCitationNiedernhofer LJ, Garinis GA, Raams A, Lalai AS, Robinson AR, Appeldoorn E, et al. A new progeroid syndrome reveals that genotoxic stress suppresses the somatotroph axis. Nature. 2006;444(7122):1038-43.spa
dc.source.bibliographicCitationSpoor M, Nagtegaal AP, Ridwan Y, Borgesius NZ, van Alphen B, van der Pluijm I, et al. Accelerated loss of hearing and vision in the DNA-repair deficient Ercc1(δ/-) mouse. Mech Ageing Dev. 2012;133(2-3):59-67spa
dc.source.bibliographicCitationVo N, Seo HY, Robinson A, Sowa G, Bentley D, Taylor L, et al. Accelerated aging of intervertebral discs in a mouse model of progeria. J Orthop Res. 2010;28(12):1600-7spa
dc.source.bibliographicCitationSchermer B, Bartels V, Frommolt P, Habermann B, Braun F, Schultze JL, et al. Transcriptional profiling reveals progeroid Ercc1(-/Δ) mice as a model system for glomerular aging. BMC Genomics. 2013;14:559spa
dc.source.bibliographicCitationGarinis GA, Uittenboogaard LM, Stachelscheid H, Fousteri M, van Ijcken W, Breit TM, et al. Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity. Nat Cell Biol. 2009;11(5):604-15spa
dc.source.bibliographicCitationMadabhushi R, Pan L, Tsai LH. DNA damage and its links to neurodegeneration. Neuron. 2014;83(2):266-82spa
dc.source.bibliographicCitationMartin LJ. DNA damage and repair: relevance to mechanisms of neurodegeneration. J Neuropathol Exp Neurol. 2008;67(5):377-87spa
dc.source.bibliographicCitationSepe S, Payan-Gomez C, Milanese C, Hoeijmakers JH, Mastroberardino PG. Nucleotide excision repair in chronic neurodegenerative diseases. DNA Repair (Amst). 2013;12(8):568-77spa
dc.source.bibliographicCitationBorgesius NZ, de Waard MC, van der Pluijm I, Omrani A, Zondag GC, van der Horst GT, et al. Accelerated age-related cognitive decline and neurodegeneration, caused by deficient DNA repair. J Neurosci. 2011;31(35):12543-53spa
dc.source.bibliographicCitationHirsch E, Graybiel AM, Agid YA. Melanized dopaminergic neurons are differentially susceptible to degeneration in Parkinson's disease. Nature. 1988;334(6180):345-8spa
dc.source.bibliographicCitationFerrante RJ, Kowall NW, Beal MF, Richardson EP, Bird ED, Martin JB. Selective sparing of a class of striatal neurons in Huntington's disease. Science. 1985;230(4725):561-3spa
dc.source.bibliographicCitationBraak H, Alafuzoff I, Arzberger T, Kretzschmar H, Del Tredici K. Staging of Alzheimer disease-associated neurofibrillary pathology using paraffin sections and immunocytochemistry. Acta Neuropathol. 2006;112(4):389-404.spa
dc.source.bibliographicCitationFontana L, Partridge L, Longo VD. Extending healthy life span--from yeast to humans. Science. 2010;328(5976):321-6.spa
dc.source.bibliographicCitationFontana L, Nehme J, Demaria M. Caloric restriction and cellular senescence. Mech Ageing Dev. 2018;176:19-23.spa
dc.source.bibliographicCitationLópez-Lluch G, Navas P. Calorie restriction as an intervention in ageing. J Physiol. 2016;594(8):2043-60.spa
dc.source.bibliographicCitationOmodei D, Licastro D, Salvatore F, Crosby SD, Fontana L. Serum from humans on long-term calorie restriction enhances stress resistance in cell culture. Aging (Albany NY). 2013;5(8):599-606. 35. Huisman SA, de Bruijn P, Ghobadi Moghaddam-Helmantel IM, IJzermans JN, Wiemer EA, Mathijssen RH, et al. Fasting protects against the side effects of irinotecan treatment but does not affect anti-tumour activity in mice. Br J Pharmacol. 2016;173(5):804-14spa
dc.source.bibliographicCitationAntoine DJ, Williams DP, Kipar A, Laverty H, Park BK. Diet restriction inhibits apoptosis and HMGB1 oxidation and promotes inflammatory cell recruitment during acetaminophen hepatotoxicity. Mol Med. 2010;16(11-12):479-90spa
dc.source.bibliographicCitationVerweij M, van de Ven M, Mitchell JR, van den Engel S, Hoeijmakers JH, Ijzermans JN, et al. Glucose supplementation does not interfere with fasting-induced protection against renal ischemia/reperfusion injury in mice. Transplantation. 2011;92(7):752-8spa
dc.source.bibliographicCitationIsenberg JS, Roberts DD. The role of CD47 in pathogenesis and treatment of renal ischemia reperfusion injury. Pediatr Nephrol. 2018spa
dc.source.bibliographicCitationSitumorang GR, Sheerin NS. Ischaemia reperfusion injury: mechanisms of progression to chronic graft dysfunction. Pediatr Nephrol. 2018.spa
dc.source.bibliographicCitationKezić A, Stajic N, Thaiss F. Innate Immune Response in Kidney Ischemia/Reperfusion Injury: Potential Target for Therapy. J Immunol Res. 2017;2017:6305439.spa
dc.source.bibliographicCitationBarin-Le Guellec C, Largeau B, Bon D, Marquet P, Hauet T. Ischemia/reperfusion-associated tubular cells injury in renal transplantation: Can metabolomics inform about mechanisms and help identify new therapeutic targets? Pharmacol Res. 2018;129:34-43spa
dc.source.bibliographicCitationBonventre JV, Yang L. Cellular pathophysiology of ischemic acute kidney injury. J Clin Invest. 2011;121(11):4210-21spa
dc.source.bibliographicCitationJongbloed F, de Bruin RW, Pennings JL, Payán-Gómez C, van den Engel S, van Oostrom CT, et al. Preoperative fasting protects against renal ischemia-reperfusion injury in aged and overweight mice. PLoS One. 2014;9(6):e100853spa
dc.source.bibliographicCitationJongbloed F, Saat TC, Verweij M, Payan-Gomez C, Hoeijmakers JH, van den Engel S, et al. A signature of renal stress resistance induced by short-term dietary restriction, fasting, and protein restriction. Sci Rep. 2017;7:40901spa
dc.source.bibliographicCitationKilkenny C, Browne WJ, Cuthill IC, Emerson M, Altman DG. Improving bioscience research reporting: the ARRIVE guidelines for reporting animal research. PLoS Biol. 2010;8(6):e1000412. 46. Ringnér M. What is principal component analysis? Nat Biotechnol. 2008;26(3):303-4spa
dc.source.bibliographicCitationHuber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015;12(2):115-21spa
dc.source.bibliographicCitationXia J, Fjell CD, Mayer ML, Pena OM, Wishart DS, Hancock RE. INMEX--a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res. 2013;41(Web Server issue):W63-70spa
dc.source.bibliographicCitationSinclair DA. Toward a unified theory of caloric restriction and longevity regulation. Mech Ageing Dev. 2005;126(9):987-1002spa
dc.source.bibliographicCitationEstrela GR, Wasinski F, Batista RO, Hiyane MI, Felizardo RJ, Cunha F, et al. Caloric Restriction Is More Efficient than Physical Exercise to Protect from Cisplatin Nephrotoxicity via PPAR-Alpha Activation. Front Physiol. 2017;8:116spa
dc.source.bibliographicCitationMartinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, et al. Aging increases cell-to-cell transcriptional variability upon immune stimulation. Science. 2017;355(6332):1433-6spa
dc.source.bibliographicCitationEnge M, Arda HE, Mignardi M, Beausang J, Bottino R, Kim SK, et al. Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns. Cell. 2017;171(2):321-30.e14spa
dc.source.bibliographicCitationEin-Dor L, Zuk O, Domany E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci U S A. 2006;103(15):5923-8spa
dc.source.bibliographicCitationHong G, Zhang W, Li H, Shen X, Guo Z. Separate enrichment analysis of pathways for up- and downregulated genes. J R Soc Interface. 2014;11(92):20130950spa
dc.source.bibliographicCitationGoldstein JL, Zhao TJ, Li RL, Sherbet DP, Liang G, Brown MS. Surviving starvation: essential role of the ghrelin-growth hormone axis. Cold Spring Harb Symp Quant Biol. 2011;76:121-7. 56. Wu G, Fang YZ, Yang S, Lupton JR, Turner ND. Glutathione metabolism and its implications for health. J Nutr. 2004;134(3):489-92spa
dc.source.bibliographicCitationChen Y, Dong H, Thompson DC, Shertzer HG, Nebert DW, Vasiliou V. Glutathione defense mechanism in liver injury: insights from animal models. Food Chem Toxicol. 2013;60:38-44spa
dc.source.bibliographicCitationLou Z, Wang AP, Duan XM, Hu GH, Song GL, Zuo ML, et al. Upregulation of NOX2 and NOX4 Mediated by TGF-β Signaling Pathway Exacerbates Cerebral Ischemia/Reperfusion Oxidative Stress Injury. Cell Physiol Biochem. 2018;46(5):2103-13spa
dc.source.bibliographicCitationMartinez BA, Petersen DA, Gaeta AL, Stanley SP, Caldwell GA, Caldwell KA. Dysregulation of the Mitochondrial Unfolded Protein Response Induces Non-Apoptotic Dopaminergic Neurodegeneration in. J Neurosci. 2017;37(46):11085-100spa
dc.source.bibliographicCitationOlivera-Perez HM, Lam L, Dang J, Jiang W, Rodriguez F, Rigali E, et al. Omega-3 fatty acids increase the unfolded protein response and improve amyloid-β phagocytosis by macrophages of patients with mild cognitive impairment. FASEB J. 2017;31(10):4359-69spa
dc.source.bibliographicCitationPeng W, Robertson L, Gallinetti J, Mejia P, Vose S, Charlip A, et al. Surgical stress resistance induced by single amino acid deprivation requires Gcn2 in mice. Sci Transl Med. 2012;4(118):118ra11. 62. Longo VD, Antebi A, Bartke A, Barzilai N, Brown-Borg HM, Caruso C, et al. Interventions to Slow Aging in Humans: Are We Ready? Aging Cell. 2015;14(4):497-510spa
dc.source.bibliographicCitationMasoro EJ. Caloric restriction and aging: controversial issues. J Gerontol A Biol Sci Med Sci. 2006;61(1):14-9spa
dc.source.bibliographicCitationDang W. The controversial world of sirtuins. Drug Discov Today Technol. 2014;12:e9-e17spa
dc.source.bibliographicCitationMeijer AJ, Lorin S, Blommaart EF, Codogno P. Regulation of autophagy by amino acids and MTOR-dependent signal transduction. Amino Acids. 2015;47(10):2037-63spa
dc.source.bibliographicCitationValente E, Rocha M. Integrating data from heterogeneous DNA microarray platforms. J Integr Bioinform. 2015;12(4):281spa
dc.source.bibliographicCitationMcCall MN, Jaffee HA, Irizarry RA. fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays. Bioinformatics. 2012;28(23):3153-4spa
dc.source.bibliographicCitationCarty CL, Kooperberg C, Neuhouser ML, Tinker L, Howard B, Wactawski-Wende J, et al. Low-fat dietary pattern and change in body-composition traits in the Women's Health Initiative Dietary Modification Trial. Am J Clin Nutr. 2011;93(3):516-24spa
dc.source.bibliographicCitationBeresford SA, Johnson KC, Ritenbaugh C, Lasser NL, Snetselaar LG, Black HR, et al. Low-fat dietary pattern and risk of colorectal cancer: the Women's Health Initiative Randomized Controlled Dietary Modification Trial. JAMA. 2006;295(6):643-54spa
dc.source.bibliographicCitationPrentice RL, Caan B, Chlebowski RT, Patterson R, Kuller LH, Ockene JK, et al. Low-fat dietary pattern and risk of invasive breast cancer: the Women's Health Initiative Randomized Controlled Dietary Modification Trial. JAMA. 2006;295(6):629-42spa
dc.source.bibliographicCitationHuang dW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37(1):1-13. 72. Tseng GC, Ghosh D, Feingold E. Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res. 2012;40(9):3785-99spa
dc.source.bibliographicCitationSeo J, Gordish-Dressman H, Hoffman EP. An interactive power analysis tool for microarray hypothesis testing and generation. Bioinformatics. 2006;22(7):808-14spa
dc.source.bibliographicCitationLee SE, Koo YD, Lee JS, Kwak SH, Jung HS, Cho YM, et al. Retinoid X receptor α overexpression alleviates mitochondrial dysfunction-induced insulin resistance through transcriptional regulation of insulin receptor substrate 1. Mol Cells. 2015;38(4):356-61spa
dc.source.bibliographicCitationAmigo I, Kowaltowski AJ. Dietary restriction in cerebral bioenergetics and redox state. Redox Biol. 2014;2:296-304spa
dc.source.bibliographicCitationChoi BK, Kim JH, Jung JS, Lee YS, Han ME, Baek SY, et al. Reduction of ischemia-induced cerebral injury by all-trans-retinoic acid. Exp Brain Res. 2009;193(4):581-9spa
dc.source.bibliographicCitationShen H, Luo Y, Kuo CC, Deng X, Chang CF, Harvey BK, et al. 9-Cis-retinoic acid reduces ischemic brain injury in rodents via bone morphogenetic protein. J Neurosci Res. 2009;87(2):545-55spa
dc.source.bibliographicCitationFusco S, Pani G. Brain response to calorie restriction. Cell Mol Life Sci. 2013;70(17):3157-70spa
dc.source.bibliographicCitationAli AH, Carey EJ, Lindor KD. Recent advances in the development of farnesoid X receptor agonists. Ann Transl Med. 2015;3(1):5spa
dc.source.bibliographicCitationMellon I. Transcription-coupled repair: a complex affair. Mutat Res. 2005;577(1-2):155-61spa
dc.source.bibliographicCitationJaarsma D, van der Pluijm I, de Waard MC, Haasdijk ED, Brandt R, Vermeij M, et al. Age-related neuronal degeneration: complementary roles of nucleotide excision repair and transcription-coupled repair in preventing neuropathology. PLoS Genet. 2011;7(12):e1002405spa
dc.source.bibliographicCitationKraemer KH, Patronas NJ, Schiffmann R, Brooks BP, Tamura D, DiGiovanna JJ. Xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome: a complex genotype-phenotype relationship. Neuroscience. 2007;145(4):1388-96spa
dc.source.bibliographicCitationDelleDonne A, Klos KJ, Fujishiro H, Ahmed Z, Parisi JE, Josephs KA, et al. Incidental Lewy body disease and preclinical Parkinson disease. Arch Neurol. 2008;65(8):1074-80spa
dc.source.bibliographicCitationSepe S, Milanese C, Gabriels S, Derks KW, Payan-Gomez C, van IJcken WF, et al. Inefficient DNA Repair Is an Aging-Related Modifier of Parkinson's Disease. Cell Rep. 2016;15(9):1866-75spa
dc.source.bibliographicCitationAhmad A, Robinson AR, Duensing A, van Drunen E, Beverloo HB, Weisberg DB, et al. ERCC1-XPF endonuclease facilitates DNA double-strand break repair. Mol Cell Biol. 2008;28(16):5082-92spa
dc.source.bibliographicCitationBrouwer RW, van den Hout MC, Grosveld FG, van Ijcken WF. NARWHAL, a primary analysis pipeline for NGS data. Bioinformatics. 2012;28(2):284-5spa
dc.source.bibliographicCitationXu G, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D. SAMMate: a GUI tool for processing short read alignments in SAM/BAM format. Source Code Biol Med. 2011;6(1):2spa
dc.source.bibliographicCitationZheng B, Liao Z, Locascio JJ, Lesniak KA, Roderick SS, Watt ML, et al. PGC-1α, a potential therapeutic target for early intervention in Parkinson's disease. Sci Transl Med. 2010;2(52):52ra73spa
dc.source.bibliographicCitationXiao Y, Hsiao TH, Suresh U, Chen HI, Wu X, Wolf SE, et al. A novel significance score for gene selection and ranking. Bioinformatics. 2014;30(6):801-7spa
dc.source.bibliographicCitationSubramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP. GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics. 2007;23(23):3251-3spa
dc.source.bibliographicCitationVivar JC, Pemu P, McPherson R, Ghosh S. Redundancy control in pathway databases (ReCiPa): an application for improving gene-set enrichment analysis in Omics studies and "Big data" biology. OMICS. 2013;17(8):414-22spa
dc.source.bibliographicCitationMutez E, Nkiliza A, Belarbi K, de Broucker A, Vanbesien-Mailliot C, Bleuse S, et al. Involvement of the immune system, endocytosis and EIF2 signaling in both genetically determined and sporadic forms of Parkinson's disease. Neurobiol Dis. 2014;63:165-70spa
dc.source.bibliographicCitationMootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34(3):267-73spa
dc.source.bibliographicCitationEden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics. 2009;10:48spa
dc.source.bibliographicCitationMilanese C, Cerri S, Ulusoy A, Gornati SV, Plat A, Gabriels S, et al. Activation of the DNA damage response in vivo in synucleinopathy models of Parkinson's disease. Cell Death Dis. 2018;9(8):818spa
dc.source.bibliographicCitationVermeij WP, Dollé ME, Reiling E, Jaarsma D, Payan-Gomez C, Bombardieri CR, et al. Restricted diet delays accelerated ageing and genomic stress in DNA-repair-deficient mice. Nature. 2016;537(7620):427-31spa
dc.source.bibliographicCitationCaspers S, Moebus S, Lux S, Pundt N, Schütz H, Mühleisen TW, et al. Studying variability in human brain aging in a population-based German cohort-rationale and design of 1000BRAINS. Front Aging Neurosci. 2014;6:149spa
dc.source.bibliographicCitationLemaitre H, Goldman AL, Sambataro F, Verchinski BA, Meyer-Lindenberg A, Weinberger DR, et al. Normal age-related brain morphometric changes: nonuniformity across cortical thickness, surface area and gray matter volume? Neurobiol Aging. 2012;33(3):617.e1-9spa
dc.source.bibliographicCitationlarke LE, Liddelow SA, Chakraborty C, Münch AE, Heiman M, Barres BA. Normal aging induces A1-like astrocyte reactivity. Proc Natl Acad Sci U S A. 2018;115(8):E1896-E905spa
dc.source.bibliographicCitationChen CY, Logan RW, Ma T, Lewis DA, Tseng GC, Sibille E, et al. Effects of aging on circadian patterns of gene expression in the human prefrontal cortex. Proc Natl Acad Sci U S A. 2016;113(1):206-11spa
dc.source.bibliographicCitationRhinn H, Abeliovich A. Differential Aging Analysis in Human Cerebral Cortex Identifies Variants in TMEM106B and GRN that Regulate Aging Phenotypes. Cell Syst. 2017;4(4):404-15.e5spa
dc.source.bibliographicCitationde Magalhães JP, Curado J, Church GM. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics. 2009;25(7):875-81spa
dc.source.bibliographicCitationDillman AA, Majounie E, Ding J, Gibbs JR, Hernandez D, Arepalli S, et al. Transcriptomic profiling of the human brain reveals that altered synaptic gene expression is associated with chronological aging. Sci Rep. 2017;7(1):16890spa
dc.source.bibliographicCitationEijssen LM, Jaillard M, Adriaens ME, Gaj S, de Groot PJ, Müller M, et al. User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org. Nucleic Acids Res. 2013;41(Web Server issue):W71-6spa
dc.source.bibliographicCitationRitchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47spa
dc.source.bibliographicCitationJohnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007;8(1):118-27spa
dc.source.bibliographicCitationWang X, Kang DD, Shen K, Song C, Lu S, Chang LC, et al. An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection. Bioinformatics. 2012;28(19):2534-6spa
dc.source.bibliographicCitationRhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res. 2002;62(15):4427-33spa
dc.source.bibliographicCitationWang J, Duncan D, Shi Z, Zhang B. WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res. 2013;41(Web Server issue):W77-83spa
dc.source.bibliographicCitationLanz TA, Joshi JJ, Reinhart V, Johnson K, Grantham LE, Volfson D. STEP levels are unchanged in pre-frontal cortex and associative striatum in post-mortem human brain samples from subjects with schizophrenia, bipolar disorder and major depressive disorder. PLoS One. 2015;10(3):e0121744spa
dc.source.bibliographicCitationSomel M, Franz H, Yan Z, Lorenc A, Guo S, Giger T, et al. Transcriptional neoteny in the human brain. Proc Natl Acad Sci U S A. 2009;106(14):5743-8spa
dc.source.bibliographicCitationMaycox PR, Kelly F, Taylor A, Bates S, Reid J, Logendra R, et al. Analysis of gene expression in two large schizophrenia cohorts identifies multiple changes associated with nerve terminal function. Mol Psychiatry. 2009;14(12):1083-94spa
dc.source.bibliographicCitationSomel M, Guo S, Fu N, Yan Z, Hu HY, Xu Y, et al. MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. Genome Res. 2010;20(9):1207-18spa
dc.source.bibliographicCitationWalsh CJ, Hu P, Batt J, Santos CC. Microarray Meta-Analysis and Cross-Platform Normalization: Integrative Genomics for Robust Biomarker Discovery. Microarrays (Basel). 2015;4(3):389-406spa
dc.source.bibliographicCitationHeberle H, Meirelles GV, da Silva FR, Telles GP, Minghim R. InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics. 2015;16:169spa
dc.source.bibliographicCitationCahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, Christopherson KS, et al. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci. 2008;28(1):264-78spa
dc.source.bibliographicCitationZamanian JL, Xu L, Foo LC, Nouri N, Zhou L, Giffard RG, et al. Genomic analysis of reactive astrogliosis. J Neurosci. 2012;32(18):6391-410spa
dc.source.bibliographicCitationLiddelow SA, Guttenplan KA, Clarke LE, Bennett FC, Bohlen CJ, Schirmer L, et al. Neurotoxic reactive astrocytes are induced by activated microglia. Nature. 2017;541(7638):481-7spa
dc.source.bibliographicCitationAstarita G, Avanesian A, Grimaldi B, Realini N, Justinova Z, Panlilio LV, et al. Methamphetamine accelerates cellular senescence through stimulation of de novo ceramide biosynthesis. PLoS One. 2015;10(2):e0116961spa
dc.source.bibliographicCitationBortell N, Basova L, Semenova S, Fox HS, Ravasi T, Marcondes MC. Astrocyte-specific overexpressed gene signatures in response to methamphetamine exposure in vitro. J Neuroinflammation. 2017;14(1):49spa
dc.source.bibliographicCitationUgbode CI, Smith I, Whalley BJ, Hirst WD, Rattray M. Sonic hedgehog signalling mediates astrocyte crosstalk with neurons to confer neuroprotection. J Neurochem. 2017;142(3):429-43spa
dc.source.bibliographicCitationPujato M, Kieken F, Skiles AA, Tapinos N, Fiser A. Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. Nucleic Acids Res. 2014;42(22):13500-12spa
dc.source.bibliographicCitationLee JS, Ward WO, Ren H, Vallanat B, Darlington GJ, Han ES, et al. Meta-analysis of gene expression in the mouse liver reveals biomarkers associated with inflammation increased early during aging. Mech Ageing Dev. 2012;133(7):467-78spa
dc.source.bibliographicCitationHarris SE, Riggio V, Evenden L, Gilchrist T, McCafferty S, Murphy L, et al. Age-related gene expression changes, and transcriptome wide association study of physical and cognitive aging traits, in the Lothian Birth Cohort 1936. Aging (Albany NY). 2017;9(12):2489-503spa
dc.source.bibliographicCitationBryois J, Buil A, Ferreira PG, Panousis NI, Brown AA, Viñuela A, et al. Time-dependent genetic effects on gene expression implicate aging processes. Genome Res. 2017;27(4):545-52spa
dc.source.bibliographicCitationReynolds LM, Ding J, Taylor JR, Lohman K, Soranzo N, de la Fuente A, et al. Transcriptomic profiles of aging in purified human immune cells. BMC Genomics. 2015;16:333spa
dc.source.bibliographicCitationVoutetakis K, Chatziioannou A, Gonos ES, Trougakos IP. Comparative Meta-Analysis of Transcriptomics Data during Cellular Senescence and In Vivo Tissue Ageing. Oxid Med Cell Longev. 2015;2015:732914spa
dc.source.bibliographicCitationStranahan AM, Jiam NT, Spiegel AM, Gallagher M. Aging reduces total neuron number in the dorsal component of the rodent prefrontal cortex. J Comp Neurol. 2012;520(6):1318-26spa
dc.source.bibliographicCitationWellman CL, Sengelaub DR. Alterations in dendritic morphology of frontal cortical neurons after basal forebrain lesions in adult and aged rats. Brain Res. 1995;669(1):48-58spa
dc.source.bibliographicCitationDiaz F, Villena A, Gonzalez P, Requena V, Rius F, Perez De Vargas I. Stereological age-related changes in neurons of the rat dorsal lateral geniculate nucleus. Anat Rec. 1999;255(4):396-400spa
dc.source.bibliographicCitationMorterá P, Herculano-Houzel S. Age-related neuronal loss in the rat brain starts at the end of adolescence. Front Neuroanat. 2012;6:45spa
dc.source.bibliographicCitationDi Lorenzo Alho AT, Suemoto CK, Polichiso L, Tampellini E, de Oliveira KC, Molina M, et al. Three-dimensional and stereological characterization of the human substantia nigra during aging. Brain Struct Funct. 2016;221(7):3393-403spa
dc.source.bibliographicCitationMortazavi F, Wang X, Rosene DL, Rockland KS. White Matter Neurons in Young Adult and Aged Rhesus Monkey. Front Neuroanat. 2016;10:15spa
dc.source.bibliographicCitationMohan A, Thalamuthu A, Mather KA, Zhang Y, Catts VS, Weickert CS, et al. Differential expression of synaptic and interneuron genes in the aging human prefrontal cortex. Neurobiol Aging. 2018;70:194-202spa
dc.source.bibliographicCitationFarhy-Tselnicker I, van Casteren ACM, Lee A, Chang VT, Aricescu AR, Allen NJ. Astrocyte-Secreted Glypican 4 Regulates Release of Neuronal Pentraxin 1 from Axons to Induce Functional Synapse Formation. Neuron. 2017;96(2):428-45.e13spa
dc.source.bibliographicCitationKucukdereli H, Allen NJ, Lee AT, Feng A, Ozlu MI, Conatser LM, et al. Control of excitatory CNS synaptogenesis by astrocyte-secreted proteins Hevin and SPARC. Proc Natl Acad Sci U S A. 2011;108(32):E440-9spa
dc.source.bibliographicCitationRothstein JD, Dykes-Hoberg M, Pardo CA, Bristol LA, Jin L, Kuncl RW, et al. Knockout of glutamate transporters reveals a major role for astroglial transport in excitotoxicity and clearance of glutamate. Neuron. 1996;16(3):675-86spa
dc.source.bibliographicCitationFabricius K, Jacobsen JS, Pakkenberg B. Effect of age on neocortical brain cells in 90+ year old human females--a cell counting study. Neurobiol Aging. 2013;34(1):91-9spa
dc.source.bibliographicCitationWalløe S, Pakkenberg B, Fabricius K. Stereological estimation of total cell numbers in the human cerebral and cerebellar cortex. Front Hum Neurosci. 2014;8:508spa
dc.source.bibliographicCitationMelo P, Magalhães A, Alves CJ, Tavares MA, de Sousa L, Summavielle T, et al. Methamphetamine mimics the neurochemical profile of aging in rats and impairs recognition memory. Neurotoxicology. 2012;33(3):491-9spa
dc.source.bibliographicCitationVašák M, Meloni G. Mammalian Metallothionein-3: New Functional and Structural Insights. Int J Mol Sci. 2017;18(6)spa
dc.source.bibliographicCitationChung RS, Adlard PA, Dittmann J, Vickers JC, Chuah MI, West AK. Neuron-glia communication: metallothionein expression is specifically up-regulated by astrocytes in response to neuronal injury. J Neurochem. 2004;88(2):454-61spa
dc.source.bibliographicCitationWest AK, Hidalgo J, Eddins D, Levin ED, Aschner M. Metallothionein in the central nervous system: Roles in protection, regeneration and cognition. Neurotoxicology. 2008;29(3):489-503spa
dc.source.bibliographicCitationSwindell WR. Metallothionein and the biology of aging. Ageing Res Rev. 2011;10(1):132-45spa
dc.source.bibliographicCitationLeung YK, Pankhurst M, Dunlop SA, Ray S, Dittmann J, Eaton ED, et al. Metallothionein induces a regenerative reactive astrocyte phenotype via JAK/STAT and RhoA signalling pathways. Exp Neurol. 2010;221(1):98-106spa
dc.source.bibliographicCitationTanaka Y, Mizoguchi K. Influence of aging on chondroitin sulfate proteoglycan expression and neural stem/progenitor cells in rat brain and improving effects of a herbal medicine, yokukansan. Neuroscience. 2009;164(3):1224-34spa
dc.source.bibliographicCitationFehon RG, McClatchey AI, Bretscher A. Organizing the cell cortex: the role of ERM proteins. Nat Rev Mol Cell Biol. 2010;11(4):276-87spa
dc.source.bibliographicCitationLavialle M, Aumann G, Anlauf E, Pröls F, Arpin M, Derouiche A. Structural plasticity of perisynaptic astrocyte processes involves ezrin and metabotropic glutamate receptors. Proc Natl Acad Sci U S A. 2011;108(31):12915-9spa
dc.source.bibliographicCitationFreymuth PS, Fitzsimons HL. The ERM protein Moesin is essential for neuronal morphogenesis and long-term memory in Drosophila. Mol Brain. 2017;10(1):41spa
dc.source.bibliographicCitationPersson A, Lindberg OR, Kuhn HG. Radixin inhibition decreases adult neural progenitor cell migration and proliferation in vitro and in vivo. Front Cell Neurosci. 2013;7:161spa
dc.source.bibliographicCitationMoon Y, Kim JY, Kim WR, Kim HJ, Jang MJ, Nam Y, et al. Function of ezrin-radixin-moesin proteins in migration of subventricular zone-derived neuroblasts following traumatic brain injury. Stem Cells. 2013;31(8):1696-705spa
dc.source.bibliographicCitationMatsui T, Yonemura S, Tsukita S. Activation of ERM proteins in vivo by Rho involves phosphatidyl-inositol 4-phosphate 5-kinase and not ROCK kinases. Curr Biol. 1999;9(21):1259-62spa
dc.source.bibliographicCitationShaw RJ, Henry M, Solomon F, Jacks T. RhoA-dependent phosphorylation and relocalization of ERM proteins into apical membrane/actin protrusions in fibroblasts. Mol Biol Cell. 1998;9(2):403-19spa
dc.source.bibliographicCitationYonemura S, Matsui T, Tsukita S. Rho-dependent and -independent activation mechanisms of ezrin/radixin/moesin proteins: an essential role for polyphosphoinositides in vivo. J Cell Sci. 2002;115(Pt 12):2569-80spa
dc.source.bibliographicCitationBriscoe J, Thérond PP. The mechanisms of Hedgehog signalling and its roles in development and disease. Nat Rev Mol Cell Biol. 2013;14(7):416-29spa
dc.source.bibliographicCitationFarmer WT, Abrahamsson T, Chierzi S, Lui C, Zaelzer C, Jones EV, et al. Neurons diversify astrocytes in the adult brain through sonic hedgehog signaling. Science. 2016;351(6275):849-54spa
dc.source.bibliographicCitationChechneva OV, Deng W. Empowering sonic hedgehog to rescue brain cells after ischemic stroke. Neural Regen Res. 2015;10(3):360-2spa
dc.source.bibliographicCitationChechneva OV, Deng W. Empowering sonic hedgehog to rescue brain cells after ischemic stroke. Neural Regen Res. 2015;10(3):360-2spa
dc.source.bibliographicCitationBaruch K, Deczkowska A, David E, Castellano JM, Miller O, Kertser A, et al. Aging. Aging-induced type I interferon response at the choroid plexus negatively affects brain function. Science. 2014;346(6205):89-93spa
dc.source.bibliographicCitationZhang G, Li J, Purkayastha S, Tang Y, Zhang H, Yin Y, et al. Hypothalamic programming of systemic ageing involving IKK-β, NF-κB and GnRH. Nature. 2013;497(7448):211-6spa
dc.source.bibliographicCitationPayán-Gómez, C.; Rodríguez, D.; Amador-Muñoz, D.; Ramírez-Clavijo, S. Integrative Analysis of Global Gene Expression Identifies Opposite Patterns of Reactive Astrogliosis in Aged Human Prefrontal Cortex. Brain Sci. 2018, 8, 227spa
dc.source.bibliographicCitationKrstic D, Madhusudan A, Doehner J, Vogel P, Notter T, Imhof C, et al. Systemic immune challenges trigger and drive Alzheimer-like neuropathology in mice. J Neuroinflammation. 2012;9:151spa
dc.source.bibliographicCitationJongbloed F, de Bruin RW, Klaassen RA, Beekhof P, van Steeg H, Dor FJ, et al. Short-Term Preoperative Calorie and Protein Restriction Is Feasible in Healthy Kidney Donors and Morbidly Obese Patients Scheduled for Surgery. Nutrients. 2016;8(5)spa
dc.source.instnameinstname:Universidad del Rosariospa
dc.source.reponamereponame:Repositorio Institucional EdocURspa
dc.subjectEnvejecimientospa
dc.subjectTranscriptomicaspa
dc.subjectExpectativa de vidaspa
dc.subjectRespuesta protectoraspa
dc.subjectEstrés agudospa
dc.subjectDaño en el ADNspa
dc.subjectParkinsonspa
dc.subject.ddcFisiología humanaspa
dc.subject.keywordAgingspa
dc.subject.keywordDNA damagespa
dc.subject.keywordlifespanspa
dc.subject.keywordprotective responsespa
dc.subject.keywordParkinsonspa
dc.subject.lembEnvejecimientospa
dc.subject.lembADNspa
dc.subject.lembExpectativa de vidaspa
dc.titleIdentification of transcriptomic responses related to normal, healthy and accelerated agingspa
dc.typedoctoralThesiseng
dc.type.documentTesisspa
dc.type.hasVersioninfo:eu-repo/semantics/acceptedVersion
dc.type.spaTesis de doctoradospa
local.department.reportEscuela de Medicina y Ciencias de la Saludspa
Archivos
Bloque original
Mostrando1 - 1 de 1
Miniatura
Nombre:
DocumentoTesisCPayan_AprobadoSRamirez.pdf
Tamaño:
2 MB
Formato:
Adobe Portable Document Format
Descripción:
Descargar
Colecciones
Doctorado en Ciencias Biomédicas