Early epigenetic changes of Alzheimer’s disease in the human hippocampus

Figures & data

Table 1. Differentially methylated positions (DMPs) in the hippocampus of early-stage AD in the 450 K microarray.

DMPs	Genomic coordinates		Beta Difference	p-value	Genes
cg16867657	6	11,044,877	0.147	0.020	ELOVL2
cg18121224	5	176,559,564	0.108	0.033	NSD1
cg17448336	3	147,141,589	0.104	0.040	ZIC1
cg05877788	17	27,899,875	0.104	0.042	GIT1/TP53I13
cg07816556	6	26,017,281	0.102	0.014	HIST1H1A
cg13836098	6	26,225,269	0.101	0.047	HIST1H3E/HIST1H3 F
cg01566965	4	174,447,847	0.088	0.018	HAND2/SCRG1
cg10373891	13	52,338,758	−0.090	0.039	DHRS12/WDFY2

The table shows eight DMPs prioritized by beta difference (delta) criteria. Abbreviations: ID: identification, each CpG site was annotated by UCSC hg19 build.

Figure 1. Early epigenetic marks of AD validated by bisulphite pyrosequencing results. DNA methylation levels in AD stages vs. control samples at validated CpG sites ELOVL2-cg16867657 (a), GIT1/TP53I13-cg05877788 (b), HIST1H1A-cg07816556 (c) and HIST1H3E/HIST1H3 F- cg13836098 (d). *p-value<0.05; **p-value<0.01; ***p-value <0.001, ****p-value <0.0001. Grey dots: outlier samples.

Table 2. Correlation between DNA methylation levels at each validated DMP and tau burden.

DMPs	Genes	Correlation coefficient	p-Value
cg16867657	ELOVL2	0.350*	0.017
cg05877788	GIT1/TP53I13	0.274	0.068
cg07816556	HIST1H1A	0.272	0.085
cg13836098	HIST1H3E/HIST1H3 F	0.469**	0.001

* p-value<0.05; ** p-value<0.01.

Figure 2. Scatter plots graphs of correlation analysis result for DNA methylation levels at each validated DMP and tau burden. Correlation between validated epigenetic marks and p-tau protein burden is graphically showed for ELOVL2 (a), GIT1/TP53I13 (b), HIST1H1A (c) and HIST1H3E/HIST1H3 F (d) genes. A significant positive correlation was found for ELOVL2 [r = 0.350; p-value < 0.05] and HIST1H3E/HIST1H3 F [r = 0.469; p-value < 0.01] genes.