Mostrar el registro sencillo del ítem

dc.contributor.authorNavarro Quiroz, Elkin
dc.contributor.authorNavarro Quiroz, Roberto
dc.contributor.authorPacheco Lugo, Lisandro
dc.contributor.authorAroca Martínez, Gustavo
dc.contributor.authorGómez Escorcia, Lorena
dc.contributor.authorGonzalez Torres, Henry
dc.contributor.authorCadena Bonfanti, Andres
dc.contributor.authorMarmolejo, Maria del Carmen
dc.contributor.authorSanchez, Eduardo
dc.contributor.authorVillarreal Camacho, Jose Luis
dc.contributor.authorLorenzi, Hernan
dc.contributor.authorTorres, Augusto
dc.contributor.authorNavarro, Kelvin Fernando
dc.contributor.authorNavarro Rodriguez, Pablo
dc.contributor.authorVilla, Joe Luis
dc.contributor.authorFernández- Ponce, Cecilia
dc.date.accessioned2019-06-26T14:34:14Z
dc.date.available2019-06-26T14:34:14Z
dc.date.issued2019
dc.identifier.issn19326203
dc.identifier.urihttps://hdl.handle.net/20.500.12442/3358
dc.description.abstractThe aim of this study was to identity in silico the relationships among microRNAs (miRNAs) and genes encoding transcription factors, ubiquitylation, DNA methylation, and histone modifications in systemic lupus erythematosus (SLE). To identify miRNA dysregulation in SLE, we used miR2Disease and PhenomiR for information about miRNAs exhibiting differential regulation in disease and other biological processes, and HMDD for information about experimentally supported human miRNA–disease association data from genetics, epigenetics, circulating miRNAs, and miRNA–target interactions. This information was incorporated into the miRNA analysis. High-throughput sequencing revealed circulating miRNAs associated with kidney damage in patients with SLE. As the main finding of our in silico analysis of miRNAs differentially expressed in SLE and their interactions with disease-susceptibility genes, post-translational modifications, and transcription factors; we highlight 226 miRNAs associated with genes and processes. Moreover, we highlight that alterations of miRNAs such as hsa-miR-30a-5p, hsa-miR-16-5p, hsa-miR-142-5p, and hsa-miR-324-3p are most commonly associated with post-translational modifications. In addition, altered miRNAs that are most frequently associated with susceptibility-related genes are hsa-miR-16-5p, hsamiR- 374a-5p, hsa-miR-34a-5p, hsa-miR-31-5p, and hsa-miR-1-3p.eng
dc.language.isoengeng
dc.publisherPublic Library of Scienceeng
dc.publisherFacultad de Ciencias Básicas y Biomédicas
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 Internacional*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.sourcePLoS ONEeng
dc.source.urihttps://doi.org/10.1371/journal.pone.0218116eng
dc.subjectMicroRNAseng
dc.subjectSystemic lupus erythematosuseng
dc.subjectDNA methylationeng
dc.subjectPost-translational modificationeng
dc.subjectEpigeneticseng
dc.subjectTranscription factorseng
dc.subjectGene regulationeng
dc.titleIntegrated analysis of microRNA regulation and its interaction with mechanisms of epigenetic regulation in the etiology of systemic lupus erythematosuseng
dc.typearticleeng
dcterms.referencesBanchereau R, Hong S, Cantarel B, Baldwin N, Baisch J, Edens M, et al. Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients. Cell. Elsevier Inc.; 2016; 165: 551–565. https://doi.org/10.1016/j.cell.2016.03.008 PMID: 27040498eng
dcterms.referencesPacheco-Lugo L, Sáenz-García J, Navarro Quiroz E, González Torres H, Fang L, Díaz-Olmos Y, et al. Plasma cytokines as potential biomarkers of kidney damage in patients with systemic lupus erythematosus. Lupus. SAGE PublicationsSage UK: London, England; 2019; 28: 34–43. https://doi.org/10.1177/ 0961203318812679 PMID: 30453818eng
dcterms.referencesWeinhold B. Epigenetics: the science of change. Environ Health Perspect. National Institute of Environmental Health Science; 2006; 114: A160—7. Available: http://www.ncbi.nlm.nih.gov/pubmed/16507447 https://doi.org/10.1289/ehp.114-a160 PMID: 16507447eng
dcterms.referencesMoore LD, Le T, Fan G. DNA methylation and its basic function. Neuropsychopharmacology. Nature Publishing Group; 2013; 38: 23–38. https://doi.org/10.1038/npp.2012.112 PMID: 22781841eng
dcterms.referencesLong MD, Smiraglia DJ, Campbell MJ. The genomic impact of DNA CpG methylation on gene expression; relationships in prostate cancer [Internet]. Biomolecules. Multidisciplinary Digital Publishing Institute (MDPI); 2017. https://doi.org/10.3390/biom7010015 PMID: 28216563eng
dcterms.referencesHe L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet. Nature Publishing Group; 2004; 5: 522–531. https://doi.org/10.1038/nrg1379 PMID: 15211354eng
dcterms.referencesMaison C, Bailly D, Peters AHFMFM, Quivy J-P, Roche D, Taddei A, et al. Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nat Genet. Nature Publishing Group; 2002; 30: 329–334. https://doi.org/10.1038/ng843 PMID: 11850619eng
dcterms.referencesFukagawa T, Nogami M, Yoshikawa M, Ikeno M, Okazaki T, Takami Y, et al. Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nat Cell Biol. Nature Publishing Group; 2004; 6: 784–791. https://doi.org/10.1038/ncb1155 PMID: 15247924eng
dcterms.referencesZhao S, Long H, Lu Q. Epigenetic perspectives in systemic lupus erythematosus: pathogenesis, biomarkers, and therapeutic potentials. Clin Rev Allergy Immunol. 2010; 39: 3–9. https://doi.org/10.1007/ s12016-009-8165-7 PMID: 19639427eng
dcterms.referencesZhao M, Liu S, Luo S, Wu H, Tang M, Cheng W, et al. DNA methylation and mRNA and microRNA expression of SLE CD4+ T cells correlate with disease phenotype. J Autoimmun. Academic Press; 2014; 54: 127–136. https://doi.org/10.1016/j.jaut.2014.07.002 PMID: 25091625eng
dcterms.referencesPan W, Zhu S, Yuan M, Cui H, Wang L, Luo X, et al. MicroRNA-21 and microRNA-148a contribute to DNA hypomethylation in lupus CD4+ T cells by directly and indirectly targeting DNA methyltransferase 1. J Immunol. American Association of Immunologists; 2010; 184: 6773–6781. https://doi.org/10.4049/ jimmunol.0904060 PMID: 20483747eng
dcterms.referencesJiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, et al. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 2009; 37: D98–104. https://doi.org/ 10.1093/nar/gkn714 PMID: 18927107eng
dcterms.referencesRuepp A, Kowarsch A, Schmidl D, Bruggenthin F, Brauner B, Dunger I, et al. PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol. BioMed Central; 2010; 11: R6. https://doi.org/10.1186/gb-2010-11-1-r6 PMID: 20089154eng
dcterms.referencesLi Y, Qiu C, Tu J, Geng B, Yang J, Jiang T, et al. HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res. Oxford University Press; 2014; 42: D1070–4. https://doi.org/10.1093/nar/gkt1023 PMID: 24194601eng
dcterms.referencesNavarro-Quiroz E, Pacheco-Lugo L, Navarro-Quiroz R, Lorenzi H, España-Puccini P, Díaz-Olmos Y, et al. Profiling analysis of circulating microRNA in peripheral blood of patients with class IV lupus nephritis. PLoS One. 2017; 12. https://doi.org/10.1371/journal.pone.0187973 PMID: 29136041eng
dcterms.referencesNavarro-Quiroz E, Pacheco-Lugo L, Lorenzi H, Díaz-Olmos Y, Almendrales L, Rico E, et al. Highthroughput sequencing reveals circulating miRNAs as potential biomarkers of kidney damage in patients with systemic lupus erythematosus. Zhou X, editor. PLoS One. Public Library of Science; 2016; 11: e0166202. https://doi.org/10.1371/journal.pone.0166202 PMID: 27835701eng
dcterms.referencesVlachos IS, Zagganas K, Paraskevopoulou MD, Georgakilas G, Karagkouni D, Vergoulis T, et al. DIANA-miRPath v3.0: deciphering microRNA function with experimental support. Nucleic Acids Res. Oxford University Press; 2015; 43: W460–W466. https://doi.org/10.1093/nar/gkv403 PMID: 25977294eng
dcterms.referencesKanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. Oxford University Press; 2000; 28: 27–30. https://doi.org/10.1093/nar/28.1.27 PMID: 10592173eng
dcterms.referencesArtimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, et al. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. England; 2012; 40: W597–603. https://doi.org/10.1093/nar/ gks400 PMID: 22661580eng
dcterms.referencesBairoch A. The ENZYME database in 2000. Nucleic Acids Res. 2000;28: 304–305. Available: http:// www.ncbi.nlm.nih.gov/pubmed/10592255%0Ahttp://www.pubmedcentral.nih.gov/articlerender.fcgi? artid=PMC102465eng
dcterms.referencesWang J, Lu M, Qiu C, Cui Q. TransmiR: a transcription factor–microRNA regulation database. Nucleic Acids Res. Narnia; 2010; 38: D119—D122. https://doi.org/10.1093/nar/gkp803 PMID: 19786497eng
dcterms.referencesChien CH, Sun YM, Chang WC, Chiang-Hsieh PY, Lee TY, Tsai WC, et al. Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res. 2011; 39: 9345–9356. https://doi.org/10.1093/nar/gkr604 PMID: 21821656eng
dcterms.referencesShannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. Cold Spring Harbor Laboratory Press; 2003; 13: 2498–504. https://doi.org/10.1101/gr.1239303 PMID: 14597658eng
dcterms.referencesWang S, Adrianto I, Wiley GB, Lessard CJ, Kelly JA, Adler AJ, et al. A functional haplotype of UBE2L3 confers risk for systemic lupus erythematosus. Genes Immun. NIH Public Access; 2012; 13: 380–387. https://doi.org/10.1038/gene.2012.6 PMID: 22476155eng
dcterms.referencesWertz IE, Dixit VM. Signaling to NF- B: Regulation by Ubiquitination. Cold Spring Harb Perspect Biol. 2010; 2: a003350–a003350. https://doi.org/10.1101/cshperspect.a003350 PMID: 20300215eng
dcterms.referencesOrian A, Whiteside S, Israël A, Stancovski I, Schwartz AL, Ciechanover A. Ubiquitin-mediated processing of NF-kappa B transcriptional activator precursor p105. Reconstitution of a cell-free system and identification of the ubiquitin-carrier protein, E2, and a novel ubiquitin-protein ligase, E3, involved in conjugation. J Biol Chem. 1995; 270: 21707–21714. Available: http://www.ncbi.nlm.nih.gov/pubmed/ 7665588 https://doi.org/10.1074/jbc.270.37.21707 PMID: 7665588eng
dcterms.referencesJavierre BM, Hernando H, Ballestar E. Environmental triggers and epigenetic deregulation in autoimmune disease. Discov Med. 2011; 12: 535–545. Available: http://www.ncbi.nlm.nih.gov/pubmed/ 22204770 PMID: 22204770eng
dcterms.referencesAbd-Elkareem MI, Al Tamimy HM, Khamis OA, Abdellatif SS, Hussein MRA. Increased urinary levels of the leukocyte adhesion molecules ICAM-1 and VCAM-1 in human lupus nephritis with advanced renal histological changes: preliminary findings. Clin Exp Nephrol. 2010; 14: 548–557. https://doi.org/10. 1007/s10157-010-0322-z PMID: 20714774eng
dcterms.referencesPerl A. Oxidative stress in the pathology and treatment of systemic lupus erythematosus. Nat Rev Rheumatol. 2013; 9: 674–686. https://doi.org/10.1038/nrrheum.2013.147 PMID: 24100461eng
dcterms.referencesCoit P, Jeffries M, Altorok N, Dozmorov MG, Koelsch KA, Wren JD, et al. Genome-wide DNA methylation study suggests epigenetic accessibility and transcriptional poising of interferon-regulated genes in naïve CD4+ T cells from lupus patients. J Autoimmun. 2013; 43: 78–84. https://doi.org/10.1016/j.jaut. 2013.04.003 PMID: 23623029eng
dcterms.referencesAbsher DM, Li X, Waite LL, Gibson A, Roberts K, Edberg J, et al. Genome-Wide DNA Methylation Analysis of Systemic Lupus Erythematosus Reveals Persistent Hypomethylation of Interferon Genes and Compositional Changes to CD4+ T-cell Populations. O’Shea J, editor. PLoS Genet. 2013; 9: e1003678. https://doi.org/10.1371/journal.pgen.1003678 PMID: 23950730eng
dcterms.referencesMazari L, Ouarzane M, Zouali M. Subversion of B lymphocyte tolerance by hydralazine, a potential mechanism for drug-induced lupus. Proc Natl Acad Sci U S A. National Academy of Sciences; 2007; 104: 6317–22. https://doi.org/10.1073/pnas.0610434104 PMID: 17404230eng
dcterms.referencesWilson AS, Power BE, Molloy PL. DNA hypomethylation and human diseases. Biochim Biophys Acta— Rev Cancer. 2007; 1775: 138–162. https://doi.org/10.1016/j.bbcan.2006.08.007 PMID: 17045745eng
dcterms.referencesWaterland RA, Kellermayer R, Laritsky E, Rayco-Solon P, Harris RA, Travisano M, et al. Season of Conception in Rural Gambia Affects DNA Methylation at Putative Human Metastable Epialleles. Whitelaw E, editor. PLoS Genet. Public Library of Science; 2010; 6: e1001252. https://doi.org/10.1371/ journal.pgen.1001252 PMID: 21203497eng
dcterms.referencesJavierre BM, Fernandez AF, Richter J, Al-Shahrour F, Martin-Subero JI, Rodriguez-Ubreva J, et al. Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome Res. 2010; 20: 170–179. https://doi.org/10.1101/gr.100289.109 PMID: 20028698eng
dcterms.referencesVučković F, Krisˇtić J, Gudelj I, Teruel M, Keser T, Pezer M, et al. Association of Systemic Lupus Erythematosus With Decreased Immunosuppressive Potential of the IgG Glycome. Arthritis Rheumatol. 2015; 67: 2978–2989. https://doi.org/10.1002/art.39273 PMID: 26200652eng
dcterms.referencesKarsten CM, Pandey MK, Figge J, Kilchenstein R, Taylor PR, Rosas M, et al. Anti-inflammatory activity of IgG1 mediated by Fc galactosylation and association of FcγRIIB and dectin-1. Nat Med. 2012; 18: 1401–1406. https://doi.org/10.1038/nm.2862 PMID: 22922409eng
dcterms.referencesZhu S, Pan W, Song X, Liu Y, Shao X, Tang Y, et al. The microRNA miR-23b suppresses IL-17-associated autoimmune inflammation by targeting TAB2, TAB3 and IKK-α. Nat Med. 2012; 18: 1077–1086. https://doi.org/10.1038/nm.2815 PMID: 22660635eng
dcterms.referencesZhao X, Tang Y, Qu B, Cui H, Wang S, Wang L, et al. MicroRNA-125a contributes to elevated inflammatory chemokine RANTES levels via targeting KLF13 in systemic lupus erythematosus. Arthritis Rheum. 2010; 62: 3425–3435. https://doi.org/10.1002/art.27632 PMID: 20589685eng
dcterms.referencesTe JL, Dozmorov IM, Guthridge JM, Nguyen KL, Cavett JW, Kelly JA, et al. Identification of Unique MicroRNA Signature Associated with Lupus Nephritis. Means T, editor. PLoS One. Public Library of Science; 2010; 5: e10344. https://doi.org/10.1371/journal.pone.0010344 PMID: 20485490eng
dcterms.referencesWang Z, Chang C, Peng M, Lu Q. Translating epigenetics into clinic: focus on lupus. Clin Epigenetics. BioMed Central; 2017; 9: 78. https://doi.org/10.1186/s13148-017-0378-7 PMID: 28785369eng
dcterms.referencesHu N, Qiu X, Luo Y, Yuan J, Li Y, Lei W, et al. Abnormal histone modification patterns in lupus CD4+ T cells. J Rheumatol. The Journal of Rheumatology; 2008; 35: 804–810. Available: http://www.ncbi.nlm. nih.gov/pubmed/18398941 PMID: 18398941eng
dcterms.referencesRougeulle C, Chaumeil J, Sarma K, Allis CD, Reinberg D, Avner P, et al. Differential Histone H3 Lys-9 and Lys-27 Methylation Profiles on the X Chromosome. Mol Cell Biol. 2004; 24: 5475–5484. https://doi. org/10.1128/MCB.24.12.5475-5484.2004 PMID: 15169908eng
dcterms.referencesMohammadoo-Khorasani M, Musavi M, Mousavi M, Moossavi M, Khoddamian M, Sandoughi M, et al. Deoxyribonuclease I gene polymorphism and susceptibility to systemic lupus erythematosus. Clin Rheumatol. 2016; 35: 101–105. https://doi.org/10.1007/s10067-015-3111-y PMID: 26547219eng
dcterms.referencesChitrabamrung S, Rubin RL, Tan EM. Serum deoxyribonuclease I and clinical activity in systemic lupus erythematosus. Rheumatol Int. Springer-Verlag; 1981; 1: 55–60. https://doi.org/10.1007/BF00541153 PMID: 6287560eng
dcterms.referencesRice GI, Rodero MP, Crow YJ. Human Disease Phenotypes Associated With Mutations in TREX1. J Clin Immunol. 2015; 35: 235–243. https://doi.org/10.1007/s10875-015-0147-3 PMID: 25731743eng
sb.sedeSede Barranquilla
sb.programaMaestría en Genética
dc.rights.accessrightsinfo:eu-repo/semantics/openAccessspa


Ficheros en el ítem

Thumbnail
Thumbnail

Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del ítem

Attribution-NonCommercial-NoDerivatives 4.0 Internacional
Excepto si se señala otra cosa, la licencia del ítem se describe como Attribution-NonCommercial-NoDerivatives 4.0 Internacional