Epigenome-wide profiling identifies significant differences in DNA methylation between matched-pairs of T- and B-lymphocytes from healthy individuals
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 identifi...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
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Taylor & Francis
2013
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| Online Access: | https://eprints.nottingham.ac.uk/31132/ |
| _version_ | 1848794132806369280 |
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| author | Glossop, John R. Nixon, Nicola B. Emes, Richard D. Haworth, Kim E. Packham, Jon C. Dawes, Peter T. Fryer, Anthony A. Mattey, Derek L. Farrell, William E. |
| author_facet | Glossop, John R. Nixon, Nicola B. Emes, Richard D. Haworth, Kim E. Packham, Jon C. Dawes, Peter T. Fryer, Anthony A. Mattey, Derek L. Farrell, William E. |
| author_sort | Glossop, John R. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T19:11:20Z |
| format | Article |
| id | nottingham-31132 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:11:20Z |
| publishDate | 2013 |
| publisher | Taylor & Francis |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-311322020-05-04T20:20:15Z https://eprints.nottingham.ac.uk/31132/ Epigenome-wide profiling identifies significant differences in DNA methylation between matched-pairs of T- and B-lymphocytes from healthy individuals Glossop, John R. Nixon, Nicola B. Emes, Richard D. Haworth, Kim E. Packham, Jon C. Dawes, Peter T. Fryer, Anthony A. Mattey, Derek L. Farrell, William E. 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. Taylor & Francis 2013 Article PeerReviewed Glossop, John R., Nixon, Nicola B., Emes, Richard D., Haworth, Kim E., Packham, Jon C., Dawes, Peter T., Fryer, Anthony A., Mattey, Derek L. and Farrell, William E. (2013) Epigenome-wide profiling identifies significant differences in DNA methylation between matched-pairs of T- and B-lymphocytes from healthy individuals. Epigenetics, 8 (11). pp. 1188-1197. ISSN 1559-2294 http://www.tandfonline.com/doi/abs/10.4161/epi.26265 doi:10.4161/epi.26265 doi:10.4161/epi.26265 |
| spellingShingle | Glossop, John R. Nixon, Nicola B. Emes, Richard D. Haworth, Kim E. Packham, Jon C. Dawes, Peter T. Fryer, Anthony A. Mattey, Derek L. Farrell, William E. Epigenome-wide profiling identifies significant differences in DNA methylation between matched-pairs of T- and B-lymphocytes from healthy individuals |
| title | Epigenome-wide profiling identifies significant differences in DNA methylation between matched-pairs of T- and B-lymphocytes from healthy individuals |
| title_full | Epigenome-wide profiling identifies significant differences in DNA methylation between matched-pairs of T- and B-lymphocytes from healthy individuals |
| title_fullStr | Epigenome-wide profiling identifies significant differences in DNA methylation between matched-pairs of T- and B-lymphocytes from healthy individuals |
| title_full_unstemmed | Epigenome-wide profiling identifies significant differences in DNA methylation between matched-pairs of T- and B-lymphocytes from healthy individuals |
| title_short | Epigenome-wide profiling identifies significant differences in DNA methylation between matched-pairs of T- and B-lymphocytes from healthy individuals |
| title_sort | epigenome-wide profiling identifies significant differences in dna methylation between matched-pairs of t- and b-lymphocytes from healthy individuals |
| url | https://eprints.nottingham.ac.uk/31132/ https://eprints.nottingham.ac.uk/31132/ https://eprints.nottingham.ac.uk/31132/ |