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| Status |
Public on Dec 16, 2022 |
| Title |
Comparative analysis of the DNA methylation landscape in CD4, CD8, and B memory lineages |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
There is considerable evidence that epigenetic mechanisms and DNA methylation are critical drivers of immune cell lineage differentiation and activation. However, there has been limited coordinated investigation of common pathways in distinct cell types for immunological processes such as immune activation. Further, it remains unclear if the memory cell subtypes differentiate distinctly by cell lineages. We used the Illumina EPIC array to characterize the DNA methylation similarities and differences in B cell, CD4 T, and CD8 T naïve and memory cells states. Our data describe considerable overlap in CpG dinucleotides and genes with altered DNA methylation in the process of naïve to memory activation across the three lineages, clearly suggesting that common pathways exist for immune memory generation. Further, our analyses revealed specific CpG dinucleotides and genes in CD4 T and CD8 T central to effector memory differentiation. Finally, we identified unique DNA methylation patterns in TEMRA CD8 T cells compared to other CD8 T memory cell subtypes.
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| Overall design |
Bisulphite converted, EPIC arrayed DNA from naïve and memory B and T lymphocytes: B naïve (n=6), B memory (n=7), CD4 naïve (n=6), CD4 central memory (n=6), CD4 effector memory (n=6), CD8 naïve (n=12), CD8 central memory (n=5), CD8 effector memory (n=4), CD8 TEMRA (n=5).
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| Contributor(s) |
Zhang Z, Butler RA, Koestler DC, Bell-Glenn S, Warrier G, Molinaro AM, Christensen BC, Wiencke JK, Kelsey KT, Salas LA |
| Citation(s) |
36522672 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| P30 CA168524 |
Cancer Center Support Grant |
UNIVERSITY OF KANSAS MEDICAL CENTER RESEARCH INSTITUTE INC |
ROY A. JENSEN |
| R01 CA216265 |
(PQ3) Immune epigenetic biomarkers of bladder cancer outcomes |
DARTMOUTH COLLEGE |
Brock Clarke Christensen |
| R01 CA253976 |
DNA-based Immune Phenotyping in HNSCC for Biomarkers of Response to Immunotherapy |
BROWN UNIVERSITY |
Brock Clarke Christensen |
| R01 CA253976 |
DNA-based Immune Phenotyping in HNSCC for Biomarkers of Response to Immunotherapy |
BROWN UNIVERSITY |
Karl Timothy Kelsey |
| P20 GM104416 |
Center for Molecular Epidemiology |
DARTMOUTH COLLEGE |
MARGARET Rita KARAGAS |
| P20 GM130423 |
The Kansas Institute for Precision Medicine |
UNIVERSITY OF KANSAS MEDICAL CENTER RESEARCH INSTITUTE INC |
ANDREW K. GODWIN |
| R01 CA207360 |
Immune epigenetic biomarkers of survival in glioma epidemiology |
University of California San Francisco |
John K. Wiencke |
| P50 CA097257 |
Brain Tumor SPORE Grant |
University of California San Francisco |
MITCHEL S. BERGER |
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| Submission date |
May 18, 2021 |
| Last update date |
Dec 19, 2022 |
| Contact name |
Lucas A. Salas |
| E-mail(s) |
[email protected]
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| Organization name |
Geisel School of Medicine at Dartmouth
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| Department |
Epidemiology
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| Lab |
Salas Lab
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| Street address |
1 Medical Center Dr, DHMC
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| City |
Lebanon |
| State/province |
NH |
| ZIP/Postal code |
03756 |
| Country |
USA |
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| Platforms (1) |
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| Samples (57)
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| Relations |
| BioProject |
PRJNA730922 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE174666_RAW.tar |
965.9 Mb |
(http)(custom) |
TAR (of IDAT) |
| GSE174666_processed.txt.gz |
667.7 Mb |
(ftp)(http) |
TXT |
| GSE174666_signal_intensities.txt.gz |
992.2 Mb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
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