Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer's human brains

Abstract

Accumulation of tau and amyloid-β are two pathologic hallmarks of Alzheimer's disease. We conducted an epigenome-wide association study using the histone 3 lysine 9 acetylation (H3K9ac) mark in 669 aged human prefrontal cortices; in contrast with amyloid-β, tau protein burden had a broad effect on the epigenome, affecting 5,990 of 26,384 H3K9ac domains. Tau-related alterations aggregated in large genomic segments reflecting spatial chromatin organization, and the magnitude of these effects correlated with the segment's nuclear lamina association. Functional relevance of these chromatin changes was demonstrated by (1) consistent transcriptional changes in three independent datasets and (2) similar findings in two mouse models of Alzheimer's disease. Finally, we found that tau overexpression in induced pluripotent stem cell-derived neurons altered chromatin structure and that these effects could be blocked by a small molecule predicted to reverse the tau effect. Thus, we report broad tau-driven chromatin rearrangements in the aging human brain that may be reversible with heat-shock protein 90 (Hsp90) inhibitors.

Figure 1:. The active histone mark H3K9ac is broadly associated with tau pathology in the human cortex.

a, H3K9ac was studied in the prefrontal cortex of 669 subjects. b, Pearson correlation between tau and amyloid-β levels was 0.48 in this cohort. Amyloid-β peptide levels were below the detection threshold for 103 samples. c, Horizontal bars depict the relative frequency of each chromatin state within the H3K9ac domains (97 Mbp) and the whole genome (3.1 Gbp). Chromatin states were obtained from a DLPFC sample with minimal neuropathology (E073) included in the Roadmap Epigenomics Project. For better clarity, the respective upper bars depict the relative frequencies without the quiescent state. d, Median H3K9ac ChIP-seq read coverage is shown on the y-axis for highly transcribed, lowly transcribed and not detectable RefSeq transcripts within ±3 kb around the transcription start site. Transcripts were grouped by median transcription values (high: x > 22 rpkm (0.95 quantile), low: 1 rpkm < x < 1.5 rpkm (0.6 – 0.65 quantiles), not detectable: x = 0). The median of the H3K9ac read density across all samples was calculated for each transcript. Then, the median of all transcripts within each of the three groups was calculated and plotted as solid line. The 25% and 75% quantiles for each group are depicted by the transparent bands. e, Bars depict the number of H3K9ac domains that were significantly associated at an FDR of 0.05 with age, gender, tau levels and amyloid-β levels. f, Bars depict the number of H3K9ac domains stratified by promoter, enhancer and other domains. Dark shading indicates the number of domains whose H3K9ac levels were significantly associated with tau or amyloid-β.

Figure 2:. Tau-related chromatin alterations show spatial patterns.

a, Manhattan plot depicts log-transformed unadjusted p-values for the tau coefficients of all H3K9ac domains along chromosome 1 (two-sided Wald tests; n=669 subjects). Transformed p-values were plotted with the sign of the respective coefficient to distinguish between positive and negative associations. Red dashed lines indicate FDR threshold of 0.05 when adjusting for all 26,384 domains. Broad genomic segments covering H3K9ac domains showing associations with tau similar in direction and strength are depicted as orange line segments. The gray polygon represents the chromsome’s centromere. Two ribbons at the bottom show chromatin structure related annotation. The first ribbon indicates A and B compartments. The second ribbon indicates lamina-associated domains. b, Boxplot shows larger mean tau-related changes in H3K9ac levels in A compartments (n=284) than in B compartments (n=223) (Mann-Whitney-Wilcoxon test, p=8×10⁻¹³). The center line of the boxplot shows the median, the outer hinges correspond to the lower and upper quartiles, and the whiskers extend to the most extreme observed value within 1.5×IQR from the hinges. Compartments with no or a very few H3K9ac domains (< 5) were discarded. c-d, Scatter plots show the association between segments’ mean tau-related changes in H3K9ac levels and nuclear lamina association (c), and mean tau-related changes in mRNA levels (d). Each dot represents a segment (n=138, sex chromosomes were excluded). Weighted linear regression line (blue line), 95% confidence interval of the mean change (shaded region), and weighted Pearson correlation are depicted in the plots. Segments were weighted by the number of H3K9ac domains. e, Columns of the heatmap represent segments sorted by lamina association first and then by chromatin accessibility to break ties since multiple segments were completely free of LADs. Chromatin accessibility was calculated using DLPFC specific annotation from the Roadmap Epigenomics Project (see Methods). Column widths reflect segment sizes. In rows one to six, color indicates the mean tau effect size observed in H3K9ac (n=669 subjects), RNA transcription (n=500 subjects), DNA methylation (n=729 subjects) at active TSSs, weakly transcribed regions, enhancers and quiescent regions. In the last two rows, color indicates the mean difference between AD and control samples observed in published transcription data from temporal cortex tissue (row seven, n=292 subjects) and dissected neurons (row eight, n=34 subjects). Weighted Pearson correlations between the mean tau effect in the segments and histone accessibility (left column) and nuclear lamina association (right column) are shown on the right side. Segments were weighted by the number of H3K9ac domains in the segments.

Figure 3:. H3K9ac alterations in AD mouse models reflect spatial pattern observed in the human cortex.

a, Bar plot shows the number of domains with significant different H3K9ac levels observed in the tau mouse model (blue bars) and the CK-p25 mouse model (green bars) compared to respective control mice for different time points. CK-p25 mice were 3 months old when p25 was induced. b,c, Boxplots depict differences in H3K9ac levels between tau mice (b) or CK-p25 mice (c) and respective control mice separately for H3K9ac domains distant to and close to LADs. The center line shows the median, the outer hinges correspond to the lower and upper quartiles, and the whiskers extend to the most extreme observed value within 1.5×IQR from the hinges. The median observed log fold changes at lamina-free and lamina-associated H3K9ac domains differed by 0.20 (p ≤ 10⁻¹⁶, Mann-Whitney-Wilcoxon test) at 11 months (0.01 at 6 months) for the tau model, and by 0.13 (p ≤ 10⁻¹⁶, Mann-Whitney-Wilcoxon test) at 4.5 months (0.04 at 3.5 months) for the CK-p25 model.

Figure 4:. Tau induces chromatin alterations in iPSC-derived neurons.

a, Horizontal bars depict the relative frequency of each chromatin state within the ATAC domains (31 Mbp) and the whole genome (3.1 Gbp). Chromatin states were obtained from H9 derived cultured neurons (E010) included in the Roadmap Epigenomics Project. For better clarity, the respective upper bars depict the relative frequencies without the quiescent state. b, Bars depict proportion of ATAC domains in neurons that were overlapped by an H3K9ac domain in the DLPFC. c, Bars depict proportion of H3K9ac domains in the DLPFC that were overlapped by an ATAC domain in neurons. d, Bars depict the number of ATAC domains stratified by TSS, TSS flanking, enhancer and other domains. Dark shading indicates the number of domains whose chromatin accessibility differed significantly between MAPT overexpressing neurons and controls at an FDR of 0.05. e, Manhattan plot depicts the log-transformed unadjusted p-values for differences between MAPT overexpressing neurons and controls of all ATAC domains along chromosome 1 (two-sided t-tests, n=18 experiments). Transformed p-values were plotted with the sign of the test statistic to distinguish between increased and decreased chromatin accessibility. Red dashed lines indicate FDR threshold of 0.05 when adjusting for all 40,637 domains. Broad genomic segments covering ATAC domains showing similar changes in chromatin accessibility are depicted as purple line segments. The gray polygon represents the chromsome’s centromere. Two ribbons at the bottom show chromatin structure related annotation. The first ribbon indicates A and B compartments. The second ribbon indicates lamina-associated domains. f, Boxplot shows different mean tau-related changes in chromatin accessibility in A compartments (n=306) and B compartments (n=283) (p=4×10⁻⁷, Mann-Whitney-Wilcoxon test). The center line of the boxplot shows the median, the outer hinges correspond to the lower and upper quartiles, and the whiskers extend to the most extreme observed value within 1.5×IQR from the hinges. Compartments with no or a very few ATAC domains (< 5) were discarded. g, Scatter plot shows association between segments’ nuclear lamina association and mean change in chromatin accessibility. Each dot represents a segment (n=89, sex chromosomes were excluded). Weighted linear regression line (blue line), 95% confidence interval (shaded region), and weighted Pearson correlation are depicted in the plot. Segments were weighted by the number of ATAC domains. h, Each dot represents either an A (n=284) or B (n=221) compartment derived from fetal human brain Hi-C data. For each compartment, the mean tau-related change in H3K9ac levels in the human DLPFC on the x-axis is plotted versus the mean change in chromatin accessibility between MAPT overexpressing neurons and controls on the y-axis (Pearson correlation ρ=−0.51). Compartments with less than 5 H3K9ac domains or less than 5 ATAC domains were discarded. i, Columns of the heat map represent the 138 genomic segments (sex chromosomes were excluded) derived from the DLPFC H3K9ac data and were first sorted by lamina association and then by chromatin accessibility. The color in the first row indicates the mean tau effect size observed in the DLPFC H3K9ac data (n=669 subjects) as shown in Fig. 2e. The second and third rows depict the differences in H3K9ac (n=3 experiments) and chromatin accessibility (n=18 experiments) observed between MAPT overexpressing neurons and control neurons. Weighted Pearson correlations between the mean tau effect in the segments and histone accessibility (left column) and nuclear lamina association (right column) is shown on the right side. Segments were weighted by the number of DLPFC H3K9ac domains in the segments. j, Bars depict the variance of differences between MAPT overexpressing and respective control iNs that can be explained by segments (see Supplementary Table 13). Blue bars indicate that the MAPT overexpressing iNs were treated with 17-DMAG.