title: DNA methylation dynamics in human carotid plaques after cerebrovascular events.
abstract: OBJECTIVE
  To understand whether cerebrovascular events, a major complication of atherosclerosis, are associated with any specific DNA methylation changes in the carotid plaque.
  
  
  RESULTS
  We profiled the DNA methylomes of human symptomatic carotid plaques obtained from patients who had cerebrovascular events (n=19) and asymptomatic counterparts (n=19) with a high-density microarray (≈485 000 CpG sites, Illumina), and crossed DNA methylation data with RNAseq-based expression data from an independent symptomatic carotid plaque set (n=8). Few (30) CpGs showed a significant (P<0.05; absolute Delta-Beta, >0.20) differential methylation between the 2 groups. Within symptomatic carotid plaques, DNA methylation correlated significantly with postcerebrovascular event time (range, 3-45 days; r-value range, -0.926 to 0.857; P<0.05) for ≈45 000 CpGs, the vast majority of which became hypomethylated with increasing postcerebrovascular event time. Hypomethylation was not due to erasure of the gene-body and CG-poor region hypermethylation that accompany the progression of stable lesions, but rather targeted promoters and CpG islands. Noticeably, promoter hypomethylation and increased expression of genes involved in the inhibition of the inflammatory response, defense against oxidative stress, and active DNA demethylation were observed with increasing postcerebrovascular event time. Concomitantly, histological changes consistent with phagocyte-driven plaque healing were observed.
  
  
  CONCLUSIONS
  Weak changes in the DNA methylome distinguish symptomatic from asymptomatic plaques, but a widespread demethylation resulting in permissive transcriptional marks at atheroprotective gene promoters is established in plaques after a cerebrovascular event, thus mirroring previous observations that ruptured plaques tend to revert to a stable structure. The identified loci are candidate targets to accelerate the pace of carotid plaque stabilization.
authors.affiliation: From the Division of Health Sciences, Department of Medical Sciences, León Campus, University of Guanajuato, León, Gto., Mexico (S.Z.); Experimental Cardiovascular Research and Department of Cardiology, Clinical Sciences Malmö, Lund University, Sweden (I.G.); Department of Clinical Sciences, Lund University, Malmö, Sweden (I.G.M.); Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain (F.J.C., A.G., H.H., S.M., N.V., M.E., S.Z.); Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain (M.E.); and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain (M.E.). mesteller@idibell.cat szaina@ugto.mx.
authors.forename: Silvio
authors.initials: S
authors.lastname: Zaina
authors.affiliation: From the Division of Health Sciences, Department of Medical Sciences, León Campus, University of Guanajuato, León, Gto., Mexico (S.Z.); Experimental Cardiovascular Research and Department of Cardiology, Clinical Sciences Malmö, Lund University, Sweden (I.G.); Department of Clinical Sciences, Lund University, Malmö, Sweden (I.G.M.); Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain (F.J.C., A.G., H.H., S.M., N.V., M.E., S.Z.); Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain (M.E.); and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain (M.E.).
authors.forename: Isabel
authors.initials: I
authors.lastname: Gonçalves
authors.affiliation: From the Division of Health Sciences, Department of Medical Sciences, León Campus, University of Guanajuato, León, Gto., Mexico (S.Z.); Experimental Cardiovascular Research and Department of Cardiology, Clinical Sciences Malmö, Lund University, Sweden (I.G.); Department of Clinical Sciences, Lund University, Malmö, Sweden (I.G.M.); Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain (F.J.C., A.G., H.H., S.M., N.V., M.E., S.Z.); Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain (M.E.); and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain (M.E.).
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Carmona
authors.affiliation: From the Division of Health Sciences, Department of Medical Sciences, León Campus, University of Guanajuato, León, Gto., Mexico (S.Z.); Experimental Cardiovascular Research and Department of Cardiology, Clinical Sciences Malmö, Lund University, Sweden (I.G.); Department of Clinical Sciences, Lund University, Malmö, Sweden (I.G.M.); Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain (F.J.C., A.G., H.H., S.M., N.V., M.E., S.Z.); Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain (M.E.); and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain (M.E.).
authors.forename: Antonio
authors.initials: A
authors.lastname: Gomez
authors.affiliation: From the Division of Health Sciences, Department of Medical Sciences, León Campus, University of Guanajuato, León, Gto., Mexico (S.Z.); Experimental Cardiovascular Research and Department of Cardiology, Clinical Sciences Malmö, Lund University, Sweden (I.G.); Department of Clinical Sciences, Lund University, Malmö, Sweden (I.G.M.); Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain (F.J.C., A.G., H.H., S.M., N.V., M.E., S.Z.); Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain (M.E.); and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain (M.E.).
authors.forename: Holger
authors.initials: H
authors.lastname: Heyn
authors.affiliation: From the Division of Health Sciences, Department of Medical Sciences, León Campus, University of Guanajuato, León, Gto., Mexico (S.Z.); Experimental Cardiovascular Research and Department of Cardiology, Clinical Sciences Malmö, Lund University, Sweden (I.G.); Department of Clinical Sciences, Lund University, Malmö, Sweden (I.G.M.); Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain (F.J.C., A.G., H.H., S.M., N.V., M.E., S.Z.); Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain (M.E.); and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain (M.E.).
authors.forename: Inês G
authors.initials: IG
authors.lastname: Mollet
authors.affiliation: From the Division of Health Sciences, Department of Medical Sciences, León Campus, University of Guanajuato, León, Gto., Mexico (S.Z.); Experimental Cardiovascular Research and Department of Cardiology, Clinical Sciences Malmö, Lund University, Sweden (I.G.); Department of Clinical Sciences, Lund University, Malmö, Sweden (I.G.M.); Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain (F.J.C., A.G., H.H., S.M., N.V., M.E., S.Z.); Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain (M.E.); and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain (M.E.).
authors.forename: Sebastian
authors.initials: S
authors.lastname: Moran
authors.affiliation: From the Division of Health Sciences, Department of Medical Sciences, León Campus, University of Guanajuato, León, Gto., Mexico (S.Z.); Experimental Cardiovascular Research and Department of Cardiology, Clinical Sciences Malmö, Lund University, Sweden (I.G.); Department of Clinical Sciences, Lund University, Malmö, Sweden (I.G.M.); Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain (F.J.C., A.G., H.H., S.M., N.V., M.E., S.Z.); Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain (M.E.); and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain (M.E.).
authors.forename: Nuray
authors.initials: N
authors.lastname: Varol
authors.affiliation: From the Division of Health Sciences, Department of Medical Sciences, León Campus, University of Guanajuato, León, Gto., Mexico (S.Z.); Experimental Cardiovascular Research and Department of Cardiology, Clinical Sciences Malmö, Lund University, Sweden (I.G.); Department of Clinical Sciences, Lund University, Malmö, Sweden (I.G.M.); Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain (F.J.C., A.G., H.H., S.M., N.V., M.E., S.Z.); Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain (M.E.); and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain (M.E.). mesteller@idibell.cat szaina@ugto.mx.
authors.forename: Manel
authors.initials: M
authors.lastname: Esteller
mesh_terms: D020757:Amaurosis Fugax / Q000175:diagnosis / Q000235:genetics*; D058070:Asymptomatic Diseases; D002339:Carotid Arteries / Q000473:pathology*; D016893:Carotid Stenosis / Q000150:complications / Q000175:diagnosis / Q000235:genetics*; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D006801:Humans; D002546:Ischemic Attack, Transient / Q000175:diagnosis / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D058226:Plaque, Atherosclerotic; D011401:Promoter Regions, Genetic; D012422:Rupture, Spontaneous; D020521:Stroke / Q000175:diagnosis / Q000235:genetics*; D014158:Transcription, Genetic
keywords: CpG islands; DNA methylation; atherosclerosis; human; oxidative stress