Table 2.
Overview of studies investigating DNA hydroxymethylation in AD.
| Epigenetic Mechanism | Effect | Gene/Target Pathway Involved | Study Model 1 | Tissue/Study Design | Main Results | Ref. |
|---|---|---|---|---|---|---|
| 5hmC | ↓ | FBXL16, ANK1 | AD (n = 96/104) | CNS (ECx)/methylation array technology and pyrosequencing | Decreased levels of 5hmC in FBXL16 (four probes). Decreased levels of 5hmC in ANK1 (4 CpGs). |
[50] |
| 5hmC | ↑↓ |
BIN1 Signaling, energy metabolism, cell function processes, gene expression, protein degradation, and cell structure and stabilization |
LOAD (n =3), Ctrl (n = 2) | CNS (HPC)/RRHP | Identification of 15.158 (DhMR), majority hyperhydroxymetylated. | [70] |
| 5hmC | ↑↓ |
ABAT, CAMK1D, HTRA3, LRRN1 Long term memory and neurotrophin signaling pathway |
AD (n = 20), MCI (n = 4), Ctrl (n = 6) | CNS (DLPFC)/NGS | Identification of 517 DhMRs, associated with neuritic plaques, and of 60 DhMRs, associated with neurofibrillary tangles. Correlation between 5hmC and gene expression. |
[71] |
| 5hmC | ↑↓ | Neuron projection development, neurogenesis | AD (n = 3/2), Ctrl (n = 3/2) | CNS (PFC)/NGS | Identification of 7601 DhMR in the discovery set. Identification of 2351 DhMR in the replication set. | [72] |
| 5hmC | ↓↑ | 5hmC cell subtype localization | EOAD (n = 5), LOAD (n = 5), Ctrl (n = 5) | CNS (ITG)/immunohistochemistry | Decreased localization of nuclear 5hmC marks in AD cases compared to controls. No differences in localization of 5hmC in neurofilament-positive pyramidal neurons, disease-resistant calretinin-interneurons, microglia in AD cases compared to control subjects. |
[63] |
| 5hmC | None | None | AD (n = 12; 10 sporadic + 2 familial), Ctrl (n = 14) | CNS (ECx, CB)/immunohistochemistry | No significant difference in 5hmC levels between studied groups. | [69] |
| 5hmC | ↓ | None stated | AD (n = 13), Ctrl (n = 8) | CNS (ECx, CB)/immunohistochemistry | Decreased levels of 5hmC in both ECx and CB of AD patients compared to control group subjects. | [68] |
| 5hmC | ↑ | 5hmC cell subtype localization | EOAD and LOAD (n = 29), Ctrl (n = 29) | CNS (MFG, MTG)/immunohistochemistry | Increased levels of 5hmC in MFG and MTG of AD patients. Positive correlation of 5hmC with 5mC and AD markers (Aβ, tau, and ubiquitin loads). Differences in cell subtype 5hmC distribution (lower levels in astrocytes and microglia, higher levels in neurons). |
[64] |
| 5hmC | ↑ | None stated | preclinical AD (n = 5), AD (n = 7), Ctrl (n = 5) | CNS (HPG, CB)/immunohistochemistry | Increased levels of 5hmC in HPG of both AD patients and preclinical AD cases compared to control group subjects. | [65] |
| 5hmC | ↓ | 5hmC cell subtype localization | AD (n = 10), Ctrl (n = 10) monozygotic twins (AD twin and non-AD affected twin) |
CNS (HPC)/immunohistochemistry | Decreased levels of 5hmC in AD. Decreased levels of 5hmC in CA3 HPC region glial cells and overall decrease in neuronal cells in AD. Negative correlation between 5hmC and amyloid plaque load. Decreased levels of in 5hmC of the AD twin compared to the non-AD affected twin. |
[66] |
| 5hmC | None | TREM2 | AD (n = 12), Ctrl (n = 5) | CNS (HPC) 5hmC DNA immunoprecipitation/RT-qPCR |
No significant difference in TREM2 5hmC levels between studied groups. | [73] |
↓—decreased levels; ↑—increased levels; 5hmC—5-hydroxymethylated cytosine; AD—Alzheimer’s disease; CB—cerebellum; CNS—central nervous system; Ctrl—control subjects; DhMRs—differentially hydroxymethylated regions; DLPFC—dorsolateral prefrontal cortex; ECx—entorhinal cortex; EOAD—early onset Alzheimer’s disease; HPC—hippocampus; HPG—hippocampus/parahippocampal gyrus; ITG—inferior temporal gyrus; LOAD—late onset Alzheimer’s disease; MCI—mild cognitive impairment; MFG—middle frontal gyrus; MTG—middle temporal gyrus; NGS—next-generation sequencing; RRHP—reduced representation 5-hydroxymethylcytosine profiling; RT-qPCR—reverse transcription quantitative real-time PCR; TREM2—triggering receptor expressed on myeloid cell gene. 1 Number of subjects per group is presented as discovery cohort/validation cohort.