title: Epigenome-wide profiling identifies significant differences in DNA methylation between matched-pairs of T- and B-lymphocytes from healthy individuals.
abstract: Multiple reports now describe changes to the DNA methylome in rheumatoid arthritis and in many cases have analyzed methylation in mixed cell populations from whole blood. However, these approaches may preclude the identification of cell type-specific methylation, which may subsequently bias identification of disease-specific changes. To address this possibility, we conducted genome-wide DNA methylation profiling using HumanMethylation450 BeadChips to identify differences within matched pairs of T-lymphocytes and B-lymphocytes isolated from the peripheral blood of 10 healthy females. Array data were processed and differential methylation identified using NIMBL software. Validation of array data was performed by bisulfite pyrosequencing. Genome-wide DNA methylation was initially determined by analysis of LINE-1 sequences and was higher in B-lymphocytes than matched T-lymphocytes (69.8% vs. 65.2%, P ≤ 0.01). Pairwise analysis identified 679 CpGs, representing 250 genes, which were differentially methylated between T-lymphocytes and B-lymphocytes. The majority of sites (76.6%) were hypermethylated in B-lymphocytes. Pyrosequencing of selected candidates confirmed the array data in all cases. Hierarchical clustering revealed perfect segregation of samples into two distinct clusters based on cell type. Differentially methylated genes showed enrichment for biological functions/pathways associated with leukocytes and T-lymphocytes. Our work for the first time shows that T-lymphocytes and B-lymphocytes possess intrinsic differences in DNA methylation within a restricted set of functionally related genes. These data provide a foundation for investigating DNA methylation in diseases in which these cell types play important and distinct roles.
authors.affiliation: Institute for Science and Technology in Medicine; Keele University; Guy Hilton Research Centre; Staffordshire, UK; Haywood Rheumatology Centre; Haywood Hospital; Staffordshire, UK.
authors.forename: John R
authors.initials: JR
authors.lastname: Glossop
authors.affiliation: Haywood Rheumatology Centre; Haywood Hospital; Staffordshire, UK.
authors.forename: Nicola B
authors.initials: NB
authors.lastname: Nixon
authors.affiliation: School of Veterinary Medicine and Science; University of Nottingham; Leicestershire, UK.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Emes
authors.affiliation: Institute for Science and Technology in Medicine; Keele University; Guy Hilton Research Centre; Staffordshire, UK.
authors.forename: Kim E
authors.initials: KE
authors.lastname: Haworth
authors.affiliation: Haywood Rheumatology Centre; Haywood Hospital; Staffordshire, UK.
authors.forename: Jon C
authors.initials: JC
authors.lastname: Packham
authors.affiliation: Haywood Rheumatology Centre; Haywood Hospital; Staffordshire, UK.
authors.forename: Peter T
authors.initials: PT
authors.lastname: Dawes
authors.affiliation: Institute for Science and Technology in Medicine; Keele University; Guy Hilton Research Centre; Staffordshire, UK.
authors.forename: Anthony A
authors.initials: AA
authors.lastname: Fryer
authors.affiliation: Institute for Science and Technology in Medicine; Keele University; Guy Hilton Research Centre; Staffordshire, UK; Haywood Rheumatology Centre; Haywood Hospital; Staffordshire, UK.
authors.forename: Derek L
authors.initials: DL
authors.lastname: Mattey
authors.affiliation: Institute for Science and Technology in Medicine; Keele University; Guy Hilton Research Centre; Staffordshire, UK.
authors.forename: William E
authors.initials: WE
authors.lastname: Farrell
mesh_terms: D001402:B-Lymphocytes / Q000378:metabolism*; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D020869:Gene Expression Profiling; D015894:Genome, Human; D006801:Humans; D008875:Middle Aged; D013601:T-Lymphocytes / Q000378:metabolism*
keywords: B-lymphocyte; CpG; DNA methylation; Illumina 450K array; T-lymphocyte; genome-wide; rheumatoid arthritis