Integration of DNA Methylation & Health Scores Identifies Subtypes in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

References

• Jason LA , PorterN , HunnellJ , RademakerA , RichmanJA . CFS prevalence and risk factors over time . J. Health Psychol.16 ( 3 ), 445 – 456 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Reyes M , NisenbaumR , HoaglinDCet al. Prevalence and incidence of chronic fatigue syndrome in Wichita, Kansas . Arch. Intern. Med.163 ( 13 ), 1530 – 1536 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Brown MM , BellDS , JasonLA , ChristosC , BellDE . Understanding long-term outcomes of chronic fatigue syndrome . J. Clin. Psychol.68 ( 9 ), 1028 – 1035 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Johnston SC , BrenuEW , HardcastleSL , HuthTK , StainesDR , Marshall-GradisnikSM . A comparison of health status in patients meeting alternative definitions for chronic fatigue syndrome/myalgic encephalomyelitis . Health Qual. Life Outcomes12 , 64 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Hatcher S , HouseA . Life events, difficulties and dilemmas in the onset of chronic fatigue syndrome: a case–control study . Psychol. Med.33 ( 7 ), 1185 – 1192 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Lin JS , ReschSC , BrimmerDJet al. The economic impact of chronic fatigue syndrome in Georgia: direct and indirect costs . Cost Eff. Resour. Alloc.9 ( 1 ), 1 ( 2011 ).
   PubMedGoogle Scholar
• Reynolds KJ , VernonSD , BoucheryE , ReevesWC . The economic impact of chronic fatigue syndrome . Cost Eff. Resour. Alloc.2 ( 1 ), 4 ( 2004 ).
   PubMedGoogle Scholar
• Jones JF , LinJM , MaloneyEMet al. An evaluation of exclusionary medical/psychiatric conditions in the definition of chronic fatigue syndrome . BMC Med.7 , 57 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Nater UM , LinJM , MaloneyEMet al. Psychiatric comorbidity in persons with chronic fatigue syndrome identified from the Georgia population . Psychosom. Med.71 ( 5 ), 557 – 565 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Carruthers BM , Van De SandeMI , De MeirleirKLet al. Myalgic encephalomyelitis: international consensus criteria . J. Intern. Med.270 ( 4 ), 327 – 338 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Fukuda K , StrausSE , HickieI , SharpeMC , DobbinsJG , KomaroffA . The chronic fatigue syndrome: a comprehensive approach to its definition and study. International Chronic Fatigue Syndrome Study Group . Ann. Intern. Med.121 ( 12 ), 953 – 959 ( 1994 ).
   PubMed Web of Science ®Google Scholar
• Jason LA , RichmanJA , RademakerAWet al. A community-based study of chronic fatigue syndrome . Arch. Intern. Med.159 ( 18 ), 2129 – 2137 ( 1999 ).
   PubMed Web of Science ®Google Scholar
• Bansal AS , BradleyAS , BishopKN , Kiani-AlikhanS , FordB . Chronic fatigue syndrome, the immune system and viral infection . Brain Behav. Immun.26 ( 1 ), 24 – 31 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• De Vega WC , HerreraS , VernonSD , McGowanPO . Epigenetic modifications and glucocorticoid sensitivity in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) . BMC Med. Genomics10 ( 1 ), 11 ( 2017 ).
   PubMedGoogle Scholar
• De Vega WC , VernonSD , McGowanPO . DNA methylation modifications associated with chronic fatigue syndrome . PLoS ONE9 ( 8 ), e104757 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Naviaux RK , NaviauxJC , LiKet al. Metabolic features of chronic fatigue syndrome . Proc. Natl Acad. Sci. USA113 ( 37 ), e5472 – e5480 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Costa V , AprileM , EspositoR , CiccodicolaA . RNA-Seq and human complex diseases: recent accomplishments and future perspectives . Eur. J. Hum. Genet.21 ( 2 ), 134 – 142 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Stessman HA , BernierR , EichlerEE . A genotype-first approach to defining the subtypes of a complex disease . Cell156 ( 5 ), 872 – 877 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Jones PA . Functions of DNA methylation: islands, start sites, gene bodies and beyond . Nat. Rev. Genet.13 ( 7 ), 484 – 492 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Lam LL , EmberlyE , FraserHBet al. Factors underlying variable DNA methylation in a human community cohort . Proc. Natl Acad. Sci. USA109 ( Suppl. 2 ), 17253 – 17260 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Ernst C , McGowanPO , DelevaV , MeaneyMJ , SzyfM , TureckiG . The effects of pH on DNA methylation state: in vitro and post-mortem brain studies . J. Neurosci. Methods174 ( 1 ), 123 – 125 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Vilahur N , BaccarelliAA , BustamanteMet al. Storage conditions and stability of global DNA methylation in placental tissue . Epigenomics5 ( 3 ), 341 – 348 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Hebels DG , GeorgiadisP , KeunHCet al. Performance in omics analyses of blood samples in long-term storage: opportunities for the exploitation of existing biobanks in environmental health research . Environ. Health Perspect.121 ( 4 ), 480 – 487 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Tost J . DNA methylation: an introduction to the biology and the disease-associated changes of a promising biomarker . Mol. Biotechnol.44 ( 1 ), 71 – 81 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Kerr JR , PettyR , BurkeBet al. Gene expression subtypes in patients with chronic fatigue syndrome/myalgic encephalomyelitis . J. Infect. Dis.197 ( 8 ), 1171 – 1184 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Zhang L , GoughJ , ChristmasDet al. Microbial infections in eight genomic subtypes of chronic fatigue syndrome/myalgic encephalomyelitis . J. Clin. Pathol.63 ( 2 ), 156 – 164 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Shimosako N , KerrJR . Use of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) . J. Clin. Pathol.67 ( 12 ), 1078 – 1083 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Aslakson E , Vollmer-ConnaU , WhitePD . The validity of an empirical delineation of heterogeneity in chronic unexplained fatigue . Pharmacogenomics7 ( 3 ), 365 – 373 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Vollmer-Conna U , AslaksonE , WhitePD . An empirical delineation of the heterogeneity of chronic unexplained fatigue in women . Pharmacogenomics7 ( 3 ), 355 – 364 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Aslakson E , Vollmer-ConnaU , ReevesWC , WhitePD . Replication of an empirical approach to delineate the heterogeneity of chronic unexplained fatigue . Popul. Health Metr.7 , 17 ( 2009 ).
   PubMedGoogle Scholar
• Wang B , MezliniAM , DemirFet al. Similarity network fusion for aggregating data types on a genomic scale . Nat. Methods11 ( 3 ), 333 – 337 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Xu T , LeTD , LiuL , WangR , SunB , LiJ . Identifying cancer subtypes from miRNA-TF-mRNA regulatory networks and expression data . PLoS ONE11 ( 4 ), e0152792 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Zhang D , ChenP , ZhengCH , XiaJ . Identification of ovarian cancer subtype-specific network modules and candidate drivers through an integrative genomics approach . Oncotarget7 ( 4 ), 4298 – 4309 ( 2016 ).
   PubMedGoogle Scholar
• Wen H , LiuY , RekikIet al. Combining disrupted and discriminative topological properties of functional connectivity networks as neuroimaging biomarkers for accurate diagnosis of early Tourette syndrome children . Mol. Neurobiol.55 ( 4 ), 3251 – 3269 ( 2017 ).
   PubMed Web of Science ®Google Scholar
• Jason LA , SoS , BrownAA , SunnquistM , EvansM . Test-retest reliability of the DePaul symptom questionnaire . Fatigue3 ( 1 ), 16 – 32 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• De Vega WC , McGowanPO . The epigenetic landscape of myalgic encephalomyelitis/chronic fatigue syndrome: deciphering complex phenotypes . Epigenomics9 ( 11 ), 1337 – 1340 ( 2017 ).
   PubMed Web of Science ®Google Scholar
• Hays RD , MoralesLS . The RAND-36 measure of health-related quality of life . Ann. Med.33 ( 5 ), 350 – 357 ( 2001 ).
   PubMed Web of Science ®Google Scholar
• Wang D , YanL , HuQet al. IMA: an R package for high-throughput analysis of Illumina’s 450 K Infinium methylation data . Bioinformatics28 ( 5 ), 729 – 730 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Aryee MJ , JaffeAE , Corrada-BravoHet al. Minfi: a flexible and comprehensive bioconductor package for the analysis of Infinium DNA methylation microarrays . Bioinformatics30 ( 10 ), 1363 – 1369 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Maksimovic J , GordonL , OshlackA . SWAN: subset-quantile within array normalization for Illumina Infinium HumanMethylation450 BeadChips . Genome Biol.13 ( 6 ), R44 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Sandoval J , HeynH , MoranSet al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome . Epigenetics6 ( 6 ), 692 – 702 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Houseman EA , AccomandoWP , KoestlerDCet al. DNA methylation arrays as surrogate measures of cell mixture distribution . BMC Bioinformatics13 , 86 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Johnson WE , LiC , RabinovicA . Adjusting batch effects in microarray expression data using empirical Bayes methods . Biostatistics8 ( 1 ), 118 – 127 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Dick KJ , NelsonCP , TsaprouniLet al. DNA methylation and body-mass index: a genome-wide analysis . Lancet383 ( 9933 ), 1990 – 1998 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Fraga MF , BallestarE , PazMFet al. Epigenetic differences arise during the lifetime of monozygotic twins . Proc. Natl Acad. Sci. USA102 ( 30 ), 10604 – 10609 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Chen YA , LemireM , ChoufaniSet al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray . Epigenetics8 ( 2 ), 203 – 209 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Morris TJ , BeckS . Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450 k) data . Methods72 , 3 – 8 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Achard S , Delon-MartinC , VertesPEet al. Hubs of brain functional networks are radically reorganized in comatose patients . Proc. Natl Acad. Sci. USA109 ( 50 ), 20608 – 20613 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Shiga M , TakigawaI , MamitsukaH . Annotating gene function by combining expression data with a modular gene network . Bioinformatics23 ( 13 ), i468 – i478 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Subramanian A , TamayoP , MoothaVKet al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles . Proc. Natl Acad. Sci. USA102 ( 43 ), 15545 – 15550 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Buchwald D , GarrityD . Comparison of patients with chronic fatigue syndrome, fibromyalgia, and multiple chemical sensitivities . Arch. Intern. Med.154 ( 18 ), 2049 – 2053 ( 1994 ).
   PubMed Web of Science ®Google Scholar
• Meeus M , NijsJ . Central sensitization: a biopsychosocial explanation for chronic widespread pain in patients with fibromyalgia and chronic fatigue syndrome . Clin. Rheumatol.26 ( 4 ), 465 – 473 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Johnson SK , DelucaJ , NatelsonBH . Personality dimensions in the chronic fatigue syndrome: a comparison with multiple sclerosis and depression . J. Psychiatr. Res.30 ( 1 ), 9 – 20 ( 1996 ).
   PubMed Web of Science ®Google Scholar
• Dancey CP , FriendJ . Symptoms, impairment and illness intrusiveness – their relationship with depression in women with CFS/ME . Psychol. Health23 ( 8 ), 983 – 999 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Maes M . Inflammatory and oxidative and nitrosative stress pathways underpinning chronic fatigue, somatization and psychosomatic symptoms . Curr. Opin. Psychiatry22 ( 1 ), 75 – 83 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Van De Vosse E , HaverkampMH , Ramirez-AlejoNet al. IL-12Rβ1 deficiency: mutation update and description of the IL12RB1 variation database . Hum. Mutat.34 ( 10 ), 1329 – 1339 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Brenu EW , StainesDR , Marshall-GradisbikSM . Methylation profile of CD4+ T cells in chronic fatigue syndrome/myalgic encephalomyelitis . J. Clin. Cell Immunol.5 , 228 ( 2014 ).
   Google Scholar
• Morris G , BerkM , GaleckiP , MaesM . The emerging role of autoimmunity in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) . Mol. Neurobiol.49 ( 2 ), 741 – 756 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Loebel M , StrohscheinK , GianniniCet al. Deficient EBV-specific B- and T-cell response in patients with chronic fatigue syndrome . PLoS ONE9 ( 1 ), e85387 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Mensah F , BansalA , BerkovitzSet al. Extended B cell phenotype in patients with myalgic encephalomyelitis/chronic fatigue syndrome: a cross-sectional study . Clin. Exp. Immunol.184 ( 2 ), 237 – 247 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Bradley AS , FordB , BansalAS . Altered functional B cell subset populations in patients with chronic fatigue syndrome compared with healthy controls . Clin. Exp. Immunol.172 ( 1 ), 73 – 80 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Fluge O , BrulandO , RisaKet al. Benefit from B-lymphocyte depletion using the anti-CD20 antibody rituximab in chronic fatigue syndrome. A double-blind and placebo-controlled study . PLoS ONE6 ( 10 ), e26358 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Gaunt TR , ShihabHA , HemaniGet al. Systematic identification of genetic influences on methylation across the human life course . Genome Biol.17 , 61 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• McRae AF , PowellJE , HendersAKet al. Contribution of genetic variation to transgenerational inheritance of DNA methylation . Genome Biol.15 ( 5 ), R73 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Dowsett EG , RamsayAM , McCartneyRA , BellEJ . Myalgic encephalomyelitis – a persistent enteroviral infection?Postgrad. Med. J.66 ( 777 ), 526 – 530 ( 1990 ).
   PubMed Web of Science ®Google Scholar
• Twisk FNM . An accurate diagnosis of myalgic encephalomyelitis and chronic fatigue syndrome requires strict clinical case definitions and objective test methods . J. Med. Diagnost. Methods5 ( 2 ), 68 – 87 ( 2017 ).
   Google Scholar
• Irlbeck DM , VernonSD , McClearyKKet al. No association found between the detection of either xenotropic murine leukemia virus-related virus or polytropic murine leukemia virus and chronic fatigue syndrome in a blinded, multi-site, prospective study by the establishment and use of the SolveCFS BioBank . BMC Res. Notes7 , 461 ( 2014 ).
   PubMedGoogle Scholar
• Whistler T , TaylorR , CraddockRC , BroderickG , KlimasN , UngerER . Gene expression correlates of unexplained fatigue . Pharmacogenomics7 ( 3 ), 395 – 405 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Vgontzas AN , PapanicolaouDA , BixlerEOet al. Sleep apnea and daytime sleepiness and fatigue: relation to visceral obesity, insulin resistance, and hypercytokinemia . J. Clin. Endocrinol. Metab.85 ( 3 ), 1151 – 1158 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Smith AK , KilaruV , KlengelTet al. DNA extracted from saliva for methylation studies of psychiatric traits: evidence tissue specificity and relatedness to brain . Am. J. Med. Genet. B Neuropsychiatr. Genet.168b ( 1 ), 36 – 44 ( 2015 ).
   PubMedGoogle Scholar
• Cowen L , IdekerT , RaphaelBJ , SharanR . Network propagation: a universal amplifier of genetic associations . Nat. Rev. Genet.18 ( 9 ), 551 – 562 ( 2017 ).
   PubMed Web of Science ®Google Scholar
• Lenzenweger MF . Endophenotype, intermediate phenotype, biomarker: definitions, concept comparisons, clarifications . Depress. Anxiety30 ( 3 ), 185 – 189 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Hallmayer JF , KalaydjievaL , BadcockJet al. Genetic evidence for a distinct subtype of schizophrenia characterized by pervasive cognitive deficit . Am. J. Hum. Genet.77 ( 3 ), 468 – 476 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Morar B , DragovicM , WatersFA , ChandlerD , KalaydjievaL , JablenskyA . Neuregulin 3 (NRG3) as a susceptibility gene in a schizophrenia subtype with florid delusions and relatively spared cognition . Mol. Psychiatry16 ( 8 ), 860 – 866 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Peter B , MatsushitaM , RaskindWH . Motor sequencing deficit as an endophenotype of speech sound disorder: a genome-wide linkage analysis in a multigenerational family . Psychiatr. Genet.22 ( 5 ), 226 – 234 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Mcmanimen SL , JasonLA . Post-exertional malaise in patients with ME and CFS with comorbid fibromyalgia . SRL Neurol. Neurosurg.3 ( 1 ), 22 – 27 ( 2017 ).
   PubMedGoogle Scholar
• White AT , LightAR , HughenRW , VanhaitsmaTA , LightKC . Differences in metabolite-detecting, adrenergic, and immune gene expression after moderate exercise in patients with chronic fatigue syndrome, patients with multiple sclerosis, and healthy controls . Psychosom. Med.74 ( 1 ), 46 – 54 ( 2012 ).
   PubMed Web of Science ®Google Scholar