Epigenetics of chronic inflammatory diseases

References

• DeansCMaggertKAWhat do you mean, “epigenetic”?Genetics2015199488789625855649
   PubMed Web of Science ®Google Scholar
• ShoemakerRDengJWangWZhangKAllele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genomeGenome Res201020788388920418490
   PubMed Web of Science ®Google Scholar
• NathanCDingANonresolving inflammationCell2010140687188220303877
   PubMed Web of Science ®Google Scholar
• MedzhitovRInflammation 2010: new adventures of an old flameCell2010140677177620303867
   PubMed Web of Science ®Google Scholar
• PerkinsDJPatelMCBlancoJCVogelSNEpigenetic mechanisms governing innate inflammatory responsesJ Interferon Cytokine Res201636745446127379867
   PubMed Web of Science ®Google Scholar
• SugimotoMASousaLPPinhoVPerrettiMTeixeiraMMResolution of inflammation: what controls its onset?Front Immunol2016716027199985
   PubMed Web of Science ®Google Scholar
• SerhanCNSavillJResolution of inflammation: the beginning programs the endNat Immunol20056121191119716369558
   PubMed Web of Science ®Google Scholar
• NewtonKDixitVMSignaling in innate immunity and inflammationCold Spring Harb Perspect Biol201243a00604922296764
   PubMed Web of Science ®Google Scholar
• TabasIGlassCKAnti-inflammatory therapy in chronic disease: challenges and opportunitiesScience2013339611616617223307734
   PubMed Web of Science ®Google Scholar
• BuckleyCDGilroyDWSerhanCNProresolving lipid mediators and mechanisms in the resolution of acute inflammationImmunity201440331532724656045
   PubMed Web of Science ®Google Scholar
• ZhouVWGorenABernsteinBECharting histone modifications and the functional organization of mammalian genomesNat Rev Genet201112171821116306
   PubMed Web of Science ®Google Scholar
• FeinbergAPIrizarryRAEvolution in health and medicine Sackler colloquium: stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and diseaseProc Natl Acad Sci U S A2010107Suppl 11757176420080672
   PubMed Web of Science ®Google Scholar
• BenayounBAPollinaEABrunetAEpigenetic regulation of ageing: linking environmental inputs to genomic stabilityNat Rev Mol Cell Biol2015161059361026373265
   PubMed Web of Science ®Google Scholar
• PalSTylerJKEpigenetics and agingSci Adv201627e160058427482540
   PubMed Web of Science ®Google Scholar
• StylianouEEpigenetics: the fine-tuner in inflammatory bowel disease?Curr Opin Gastroenterol201329437037723743674
   PubMed Web of Science ®Google Scholar
• StrickerSHKöferleABeckSFrom profiles to function in epigenomicsNat Rev Genet2017181516627867193
   PubMed Web of Science ®Google Scholar
• JonesPAFunctions of DNA methylation: islands, start sites, gene bodies and beyondNat Rev Genet201213748449222641018
   PubMed Web of Science ®Google Scholar
• MorrisKVMattickJSThe rise of regulatory RNANat Rev Genet201415642343724776770
   PubMed Web of Science ®Google Scholar
• WangSWuWClaretFXMutual regulation of microRNAs and DNA methylation in human cancersEpigenetics201712318719728059592
   PubMed Web of Science ®Google Scholar
• HanYHeXIntegrating epigenomics into the understanding of biomedical insightBioinform Biol Insights20161026728927980397
   PubMedGoogle Scholar
• MaozRGarfinkelBPSoreqHAlzheimer’s disease and ncRNAsAdv Exp Med Biol201797833736128523555
   PubMed Web of Science ®Google Scholar
• WierdaRJGeutskensSBJukemaJWQuaxPHvan den ElsenPJEpigenetics in atherosclerosis and inflammationJ Cell Mol Med2010146A1225124020132414
   PubMed Web of Science ®Google Scholar
• BentzonJFTargeting inflammation in atherosclerosisJ Am Coll Cardiol201668252794279628007142
   PubMed Web of Science ®Google Scholar
• YurdagulADoranACCaiBFredmanGTabasIAMechanisms and consequences of defective efferocytosis in atherosclerosisFront Cardiovasc Med201748629379788
   PubMed Web of Science ®Google Scholar
• KasikaraCDoranACCaiBTabasIThe role of non-resolving inflammation in atherosclerosisJ Clin Invest201812872713272330108191
   PubMed Web of Science ®Google Scholar
• OrdovásJMSmithCEEpigenetics and cardiovascular diseaseNat Rev Cardiol20107951051920603647
   PubMed Web of Science ®Google Scholar
• JoehanesRJustACMarioniREEpigenetic signatures of cigarette smokingCirc Cardiovasc Genet20169543644727651444
   PubMed Web of Science ®Google Scholar
• Fernández-SanlésASayols-BaixerasSSubiranaIDeganoIRElosuaRAssociation between DNA methylation and coronary heart disease or other atherosclerotic events: a systematic reviewAtherosclerosis201726332533328577936
   PubMed Web of Science ®Google Scholar
• Valencia-MoralesMPZainaSHeynHThe DNA methylation drift of the atherosclerotic aorta increases with lesion progressionBMC Med Genomics20158725881171
   PubMed Web of Science ®Google Scholar
• ZhangCAdamosCOhMJOxLDL induces endothelial cell proliferation via Rho/ROCK/Akt/p27kip1 signaling: opposite effects of oxLDL and cholesterol loadingAm J Physiol Cell Physiol20173133C340C35128701359
   PubMed Web of Science ®Google Scholar
• SmithJAZhaoWWangXNeighborhood characteristics influence DNA methylation of genes involved in stress response and inflammation: The Multi-Ethnic Study of AtherosclerosisEpigenetics201712866267328678593
   PubMed Web of Science ®Google Scholar
• DunnJThabetSJoHFlow-dependent epigenetic DNA methylation in endothelial gene expression and atherosclerosisArterioscler Thromb Vasc Biol20153571562156925953647
   PubMed Web of Science ®Google Scholar
• LiuYPengWQuKTET2: a novel epigenetic regulator and potential intervention target for atherosclerosisDNA Cell Biol201837651752329653065
   PubMed Web of Science ®Google Scholar
• JiangWAgrawalDKBoosaniCSCell-specific histone modifications in atherosclerosis (Review)Mol Med Rep20181821215122429901135
   PubMed Web of Science ®Google Scholar
• GreißelACulmesMBurgkartRHistone acetylation and methylation significantly change with severity of atherosclerosis in human carotid plaquesCardiovasc Pathol2016252798626764138
   PubMed Web of Science ®Google Scholar
• BekkeringSQuintinJJoostenLAvan der MeerJWNeteaMGRiksenNPOxidized low-density lipoprotein induces long-term proinflammatory cytokine production and foam cell formation via epigenetic reprogramming of monocytesArterioscler Thromb Vasc Biol20143481731173824903093
   PubMed Web of Science ®Google Scholar
• HoeksemaMAGijbelsMJvan den BosscheJTargeting macrophage histone deacetylase 3 stabilizes atherosclerotic lesionsEMBO Mol Med2014691124113225007801
   PubMed Web of Science ®Google Scholar
• AlkemadeFEvan VlietPHennemanPPrenatal exposure to apoE deficiency and postnatal hypercholesterolemia are associated with altered cell-specific lysine methyltransferase and histone methylation patterns in the vasculatureAm J Pathol2010176254254820035052
   PubMed Web of Science ®Google Scholar
• LucasTBonauerADimmelerSRNA therapeutics in cardiovascular diseaseCirc Res2018123220522029976688
   PubMed Web of Science ®Google Scholar
• KimSHKimGJUmemuraTLeeSGChoKJAberrant expression of plasma microRNA-33a in an atherosclerosis-risk groupMol Biol Rep2017441798827664032
   PubMed Web of Science ®Google Scholar
• SchoberANazari-JahantighMWeiYMicroRNA-126-5p promotes endothelial proliferation and limits atherosclerosis by suppressing Dlk1Nat Med201420436837624584117
   PubMed Web of Science ®Google Scholar
• PriceNLRotllanNCanfrán-DuqueAGenetic dissection of the impact of miR-33a and miR-33b during the progression of atherosclerosisCell Rep20172151317133029091769
   PubMed Web of Science ®Google Scholar
• LiuKXuekelatiSZhouKExpression profiles of six atherosclerosis-associated microRNAs that cluster in patients with hyperhomocysteinemia: a clinical studyDNA Cell Biol201837318919829461880
   PubMed Web of Science ®Google Scholar
• BellRDLongXLinMIdentification and initial functional characterization of a human vascular cell-enriched long noncoding RNAArterioscler Thromb Vasc Biol20143461249125924578380
   PubMed Web of Science ®Google Scholar
• LiuYReynoldsLMDingJBlood monocyte transcriptome and epigenome analyses reveal loci associated with human atherosclerosisNat Commun20178139328855511
   PubMed Web of Science ®Google Scholar
• MillerCLPjanicMWangTIntegrative functional genomics identifies regulatory mechanisms at coronary artery disease lociNat Commun201671209227386823
   PubMed Web of Science ®Google Scholar
• ZainaSUnraveling the DNA methylome of atherosclerosisCurr Opin Lipidol201425214815324535282
   PubMed Web of Science ®Google Scholar
• SkylerJSBakrisGLBonifacioEDifferentiation of diabetes by pathophysiology, natural history, and prognosisDiabetes201766224125527980006
   PubMed Web of Science ®Google Scholar
• LumengCNBodzinJLSaltielARObesity induces a phenotypic switch in adipose tissue macrophage polarizationJ Clin Invest2007117117518417200717
   PubMed Web of Science ®Google Scholar
• SaltielAROlefskyJMInflammatory mechanisms linking obesity and metabolic diseaseJ Clin Invest201712711428045402
   PubMed Web of Science ®Google Scholar
• KraniotouCKaradimaVBellosGTsangarisGTPredictive biomarkers for type 2 of diabetes mellitus: bridging the gap between systems research and personalized medicineJ Proteomics2018188596229518575
   PubMed Web of Science ®Google Scholar
• FuchsbergerCFlannickJTeslovichTMThe genetic architecture of type 2 diabetesNature20165367614414727398621
   PubMed Web of Science ®Google Scholar
• KeatingSTEl-OstaAEpigenetics and metabolismCirc Res2015116471573625677519
   PubMed Web of Science ®Google Scholar
• LawlorNKhetanSUcarDStitzelMLGenomics of islet (Dys) function and type 2 diabetesTrends Genet201733424425528245910
   PubMed Web of Science ®Google Scholar
• DayehTVolkovPSalöSGenome-wide DNA methylation analysis of human pancreatic islets from type 2 diabetic and non-diabetic donors identifies candidate genes that influence insulin secretionPLoS Genet2014103e100416024603685
   PubMed Web of Science ®Google Scholar
• PasqualiLGaultonKJRodríguez-SeguíSAPancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variantsNat Genet201446213614324413736
   PubMed Web of Science ®Google Scholar
• StitzelMLSethupathyPPearsonDSGlobal epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility lociCell Metab201012544345521035756
   PubMed Web of Science ®Google Scholar
• KwakSHParkKSRecent progress in genetic and epigenetic research on type 2 diabetesExp Mol Med201648e22026964836
   PubMed Web of Science ®Google Scholar
• VolkovPBacosKOforiJKWhole-genome bisulfite sequencing of human pancreatic islets reveals novel differentially methylated regions in type 2 diabetes pathogenesisDiabetes20176641074108528052964
   PubMed Web of Science ®Google Scholar
• PheifferCErasmusRTKengneAPMatshaTEDifferential DNA methylation of microRNAs within promoters, intergenic and intragenic regions of type 2 diabetic, pre-diabetic and non-diabetic individualsClin Biochem201649643343826656639
   PubMed Web of Science ®Google Scholar
• HallEDekker NitertMVolkovPThe effects of high glucose exposure on global gene expression and DNA methylation in human pancreatic isletsMol Cell Endocrinol2018472576729183809
   PubMed Web of Science ®Google Scholar
• WahlSDrongALehneBEpigenomewide association study of body mass index, and the adverse outcomes of adiposityNature20175417635818628002404
   PubMed Web of Science ®Google Scholar
• BacosKGillbergLVolkovPBlood-based biomarkers of age-associated epigenetic changes in human islets associate with insulin secretion and diabetesNat Commun201671108927029739
   PubMed Web of Science ®Google Scholar
• ElliottHRShihabHALockettGARole of DNA methylation in type 2 diabetes etiology: using genotype as a causal anchorDiabetes20176661713172228246294
   PubMed Web of Science ®Google Scholar
• BhandareRSchugJLe LayJGenome-wide analysis of histone modifications in human pancreatic isletsGenome Res201020442843320181961
   PubMed Web of Science ®Google Scholar
• HuypensPSassSWuMEpigenetic germline inheritance of diet-induced obesity and insulin resistanceNat Genet201648549749926974008
   PubMed Web of Science ®Google Scholar
• SchroederJWConneelyKNCubellsJCNeonatal DNA methylation patterns associate with gestational ageEpigenetics20116121498150422139580
   PubMed Web of Science ®Google Scholar
• LeungATracCduJNatarajanRSchonesDEPersistent chromatin modifications induced by high fat dietJ Biol Chem201629120104461045527006400
   PubMed Web of Science ®Google Scholar
• FengJXingWXieLRegulatory roles of microRNAs in diabetesInt J Mol Sci201617101729
   PubMed Web of Science ®Google Scholar
• KirbyTJWaltonRGFinlinBIntegrative mRNA-microRNA analyses reveal novel interactions related to insulin sensitivity in human adipose tissuePhysiol Genomics201648214515326672043
   PubMed Web of Science ®Google Scholar
• ChengMLiuXYangMHanLXuAHuangQComputational analyses of type 2 diabetes-associated loci identified by genome-wide association studiesJ Diabetes20179436237727121852
   PubMed Web of Science ®Google Scholar
• GoyalNKesharwaniDDattaMLncing non-coding RNAs with metabolism and diabetes: roles of lncRNAsCell Mol Life Sci201875101827183729387902
   PubMed Web of Science ®Google Scholar
• KuGMKimHVaughnIWResearch resource: RNA-Seq reveals unique features of the pancreatic β-cell transcriptomeMol Endocrinol201226101783179222915829
   PubMedGoogle Scholar
• MoranIAkermanIvan de BuntMHuman beta cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetesCell Metab20121643544823040067
   PubMed Web of Science ®Google Scholar
• AkermanITuZBeucherAHuman pancreatic β cell lncRNAs control cell-specific regulatory networksCell Metab201725240041128041957
   PubMed Web of Science ®Google Scholar
• FadistaJVikmanPLaaksoEOGlobal genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolismProc Natl Acad Sci U S A201411138139241392925201977
   PubMed Web of Science ®Google Scholar
• ParkerSCStitzelMLTaylorDLChromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variantsProc Natl Acad Sci U S A201311044179211792624127591
   PubMed Web of Science ®Google Scholar
• HenekaMTO’BanionMKInflammatory processes in Alzheimer’s diseaseJ Neuroimmunol20071841–2699117222916
   PubMed Web of Science ®Google Scholar
• JohanssonJUWoodlingNSShiJAndreassonKIInflammatory cyclooxygenase activity and PGE2 signaling in models of Alzheimer’s diseaseCurr Immunol Rev201511212513128413375
   PubMedGoogle Scholar
• WangJGuBJMastersCLWangYJA systemic view of Alzheimer disease - insights from amyloid-β metabolism beyond the brainNat Rev Neurol2017131061262328960209
   PubMed Web of Science ®Google Scholar
• HardyJSelkoeDJThe amyloid hypothesis of Alzheimer’s disease: progress and problems on the road to therapeuticsScience2002297558035335612130773
   PubMed Web of Science ®Google Scholar
• FragaVGCarvalhoMDGCaramelliPde SousaLPGomesKBResolution of inflammation, n-3 fatty acid supplementation and Alzheimer disease: a narrative reviewJ Neuroimmunol201731011111928778434
   PubMed Web of Science ®Google Scholar
• RidgePGMukherjeeSCranePKKauweJSAlzheimer’s Disease Genetics ConsortiumAlzheimer’s disease: analyzing the missing heritabilityPLoS One20138e7977124244562
   PubMed Web of Science ®Google Scholar
• QaziTJQuanZMirAQingHEpigenetics in Alzheimer’s disease: perspective of DNA methylationMol Neurobiol20185521026104428092081
   PubMed Web of Science ®Google Scholar
• LordJCruchagaCThe epigenetic landscape of Alzheimer’s diseaseNat Neurosci20141791138114025157507
   PubMed Web of Science ®Google Scholar
• LunnonKSmithRHannonEMethylomic profiling implicates cortical deregulation of ANK1 in Alzheimer’s diseaseNat Neurosci20141791164117025129077
   PubMed Web of Science ®Google Scholar
• de JagerPLSrivastavaGLunnonKAlzheimer’s disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other lociNat Neurosci20141791156116325129075
   PubMed Web of Science ®Google Scholar
• ChibnikLBYuLEatonMLAlzheimer’s loci: epigenetic associations and interaction with genetic factorsAnn Clin Transl Neurol20152663664726125039
   PubMed Web of Science ®Google Scholar
• WatsonCTRoussosPGargPGenome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer’s diseaseGenome Med201681526803900
   PubMed Web of Science ®Google Scholar
• di FrancescoAArosioBFalconiAGlobal changes in DNA methylation in Alzheimer’s disease peripheral blood mononuclear cellsBrain Behav Immun20154513914425452147
   PubMed Web of Science ®Google Scholar
• LunnonKHannonESmithRGVariation in 5-hydroxymethylcytosine across human cortex and cerebellumGenome Biol2016172726883014
   PubMed Web of Science ®Google Scholar
• EllisonEMBradley-WhitmanMALovellMASingle-base resolution mapping of 5-hydroxymethylcytosine modifications in hippocampus of Alzheimer’s disease subjectsJ Mol Neurosci201763218519728866733
   PubMed Web of Science ®Google Scholar
• ZhaoJZhuYYangJA genome-wide profiling of brain DNA hydroxymethylation in Alzheimer’s diseaseAlzheimers Dement201713667468828089213
   PubMed Web of Science ®Google Scholar
• NarayanPJLillCFaullRCurtisMADragunowMIncreased acetyl and total histone levels in post-mortem Alzheimer’s disease brainNeurobiol Dis20157428129425484284
   PubMed Web of Science ®Google Scholar
• NarayanPDragunowMAlzheimer’s disease and histone code alterationsAdv Exp Med Biol201797832133628523554
   PubMed Web of Science ®Google Scholar
• GräffJReiDGuanJSAn epigenetic blockade of cognitive functions in the neurodegenerating brainNature2012483738822222622388814
   PubMed Web of Science ®Google Scholar
• VillelaDRamalhoRFSilvaARDifferential DNA methylation of microRNA genes in temporal cortex from Alzheimer’s disease individualsNeural Plast20162016258494027213057
   PubMed Web of Science ®Google Scholar
• HébertSSHorréKNicolaïLLoss of microRNA cluster miR-29a/b-1 in sporadic Alzheimer’s disease correlates with increased BACE1/beta-secretase expressionProc Natl Acad Sci U S A2008105176415642018434550
   PubMed Web of Science ®Google Scholar
• DenkJBoelmansKSiegismundCLassnerDArltSJahnHMicroRNA profiling of CSF reveals potential biomarkers to detect Alzheimer’s diseasePLoS One2015105e012642325992776
   PubMed Web of Science ®Google Scholar
• LauPBossersKJankyRAlteration of the microRNA network during the progression of Alzheimer’s diseaseEMBO Mol Med20135101613163424014289
   PubMed Web of Science ®Google Scholar
• ManasseroGGuglielmottoMZamfirRBeta-amyloid 1-42 monomers, but not oligomers, produce PHF-like conformation of Tau proteinAging Cell201615591492327406053
   PubMed Web of Science ®Google Scholar
• MagistriMVelmeshevDMakhmutovaMFaghihiMATranscriptomics profiling of Alzheimer’s disease reveal neurovascular defects, altered amyloid-β homeostasis, and deregulated expression of long noncoding RNAsJ Alzheimers Dis201548364766526402107
   PubMed Web of Science ®Google Scholar
• HansenTBJensenTIClausenBHNatural RNA circles function as efficient microRNA spongesNature2013495744138438823446346
   PubMed Web of Science ®Google Scholar