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| Status |
Public on Oct 19, 2020 |
| Title |
Altered DNA methylation profiles in blood from patients with sporadic Creutzfeldt-Jakob disease |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
Prion diseases are fatal and transmissible neurodegenerative disorders caused by the misfolding and aggregation of prion protein. Although recent studies have implicated epigenetic variation in common neurodegenerative disorders, no study has yet explored their role in human prion diseases. Here we profiled genome-wide blood DNA methylation in the most common human prion disease, sporadic Creutzfeldt-Jakob disease (sCJD). Our case-control study (n=219), when accounting for differences in cell type composition between individuals, identified 38 probes at genome-wide significance (p < 1.24x10-7). Nine of these sites were taken forward in a replication study, performed in an independent case-control (n=186) cohort using pyrosequencing. Sites in or close to FKBP5, AIM2 (2 probes), UHRF1, KCNAB2, PRNP, ANK1 successfully replicated. The blood-based DNA methylation signal was tissue- and disease-specific, in that the replicated probe signals were unchanged in case-control studies using sCJD frontal-cortex (n=84), blood samples from patients with Alzheimer’s disease, and from inherited and acquired prion diseases. Machine learning algorithms using blood DNA methylation array profiles accurately distinguished sCJD patients and controls. Finally, we identified sites whose methylation levels associated with prolonged survival in sCJD patients. Altogether, this study has identified a peripheral DNA methylation signature of sCJD with a variety of potential biomarker applications.
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| Overall design |
106 Control and 114 sCJD blood-derived DNA samples were bisulfite converted, sent to UCL Genomics for amplification and hybridization to the Illumina Infinium 450 Beadchip Array. iDAT files were analyzed using ChAMP and one sample (Control 52) was excluded from analysis due to poor detection p-value.
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| Contributor(s) |
Dabin LC, Guntoro F, Campbell T, Bélicard T, Smith AR, Smith RG, Raybould R, Schott JM, Lunnon K, Sarkies P, Collinge J, Mead S, Viré E |
| Citation(s) |
32918118 |
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| Submission date |
Aug 27, 2020 |
| Last update date |
Oct 24, 2020 |
| Contact name |
Luke Child Dabin |
| Organization name |
Indiana University
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| Department |
Medical and Molecular Genetics
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| Lab |
Jungsu Kim
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| Street address |
320 W 15th St #414
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| City |
Indianapolis |
| State/province |
Indiana |
| ZIP/Postal code |
46202 |
| Country |
USA |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (219)
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| Relations |
| BioProject |
PRJNA659744 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE156994_Control52_3998426115_R04C02_Grn.idat.gz |
3.1 Mb |
(ftp)(http) |
IDAT |
| GSE156994_Control52_3998426115_R04C02_Red.idat.gz |
3.2 Mb |
(ftp)(http) |
IDAT |
| GSE156994_RAW.tar |
1.9 Gb |
(http)(custom) |
TAR (of IDAT) |
| GSE156994_sCJDvsCtrl_ChAMP_SampleSheet.csv.gz |
2.0 Kb |
(ftp)(http) |
CSV |
| Processed data included within Sample table |
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