Increased epigenetic age and granulocyte counts in the blood of Parkinson's disease patients

Steve Horvath, Beate R Ritz, Steve Horvath, Beate R Ritz

Abstract

It has been a long standing hypothesis that blood tissue of PD Parkinson's disease (PD) patients may exhibit signs of accelerated aging. Here we use DNA methylation based biomarkers of aging ("epigenetic clock") to assess the aging rate of blood in two ethnically distinct case-control data sets. Using n=508 Caucasian and n=84 Hispanic blood samples, we assess a) the intrinsic epigenetic age acceleration of blood (IEAA), which is independent of blood cell counts, and b) the extrinsic epigenetic age acceleration rate of blood (EEAA) which is associated with age dependent changes in blood cell counts. Blood of PD subjects exhibits increased age acceleration according to both IEAA (p=0.019) and EEAA (p=6.1 x 10(-3)). We find striking differences in imputed blood cell counts between PD cases and controls. Compared to control subjects, PD subjects contains more granulocytes (p=1.0 x 10(-9) in Caucasians, p=0.00066 in Hispanics) but fewer T helper cells (p=1.4 x 10(-6) in Caucasians, p=0.0024 in Hispanics) and fewer B cells (p=1.6 x 10(-5) in Caucasians, p=4.5 x 10(-5) in Hispanics). Overall, this study shows that the epigenetic age of the immune system is significantly increased in PD patients and that granulocytes play a significant role.

Keywords: DNA methylation; Parkinson's disease; epigenetic clock; epigenetics; granulocyte; neutrophil.

Conflict of interest statement

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1. Epigenetic age analysis of PD
Figure 1. Epigenetic age analysis of PD
(A-C) DNA methylation age (y-axis) versus chronological age (x-axis) in (A) all subjects, (B) Caucasians only, and (C) Hispanics only. Dots corresponds to subjects and are colored by PD disease status (red=PD, black=control). We define three measures of epigenetic age acceleration. (D-F) presents results for the “universal” measure of epigenetic age acceleration, which is defined as residual to a regression line through the control samples, i.e. the vertical distance of a point from the line. By definition, the mean age acceleration in controls is zero. (G-I) The bar plots relate measures of intrinsic epigenetic age acceleration to PD status. This measure is independent of blood cell counts. The fourth row (panels J-L) reports findings for the measure of extrinsic epigenetic age acceleration, which does relate to changes in cell composition. Each bar plot depicts the mean value (y-axis), 1 standard error, and the group size (underneath the bar). The p-value results from a Student T-test.
Figure 2. Levodopa medication (x-axis) versus epigenetic…
Figure 2. Levodopa medication (x-axis) versus epigenetic age acceleration in PD subjects
Each scatter plot depicts the amount of levodopa medication (milligram per day) versus (A,B,C) universal epigenetic age acceleration, (D,E,F) intrinsic epigenetic age acceleration (G,H,I), extrinsic epigenetic age acceleration. The first, second, and third column correspond to all subjects, Caucasians only, and Hispanics only, respectively. Each dot (PD patient) is colored in red for the sake of consistency with Figure 1. The heading of each plot reports a robust correlation coefficient (biweight midcorrelation and a corresponding p-value).
Figure 3. Levodopa medication status versus epigenetic…
Figure 3. Levodopa medication status versus epigenetic age acceleration in PD patients
The first, second, and third column correspond to all subjects, Caucasians only, and Hispanics only, respectively. Levodopa medication status versus (A,B,C) universal epigenetic age acceleration, (D,E,F) intrinsic epigenetic age acceleration (G,H,I), extrinsic epigenetic age acceleration. Each bar plot depicts the mean value (y-axis), 1 standard error, and the group size (underneath the bar). The p-value results from a non-parametric group comparison test (Kruskal Wallis).
Figure 4. Blood cell counts versus PD…
Figure 4. Blood cell counts versus PD status
As indicated in the heading of each panel, the panels alternate between the two data sets. PD status (x-axis) versus (A,B) proportion of cytotoxic CD8+ T cells, (C,D) naïve CD8+ T cell count, (E,F) percentage of exhausted CD8+ T cells (defined as CD8+CD28-CD45RA-), (G,H) proportion of helper CD4+ T cells, (I,J) naïve CD4+ T cell count, (K,L) proportion of natural killer cells, (M,N) proportion of monocytes, (O,P) granulocytes, (Q,R) B cells, (S,T) plasma blasts (activated B cells). The abundance measures of blood cell counts were estimated based on DNA methylation levels using the epigenetic clock software. The y-axis of (E,F) reports a percentage, that of (C,D,I,J) a cell counts but it is best to interpret these measures as ordinal abundance measures. The y-axis of the other panels reports estimated proportions based on the Houseman method [45]. Each bar plot depicts the mean value (y-axis), 1 standard error, and the group size (underneath the bar). The p-value results from a non-parametric group comparison test (Kruskal Wallis).
Figure 5. Amount of medication (x-axis) versus…
Figure 5. Amount of medication (x-axis) versus epigenetic age acceleration in PD subjects
As indicated in the heading of each panel, the panels alternate between the two data sets. PD status (x-axis) versus (A,B) proportion of CD8+ T cells, (C,D) naïve CD8+ T cell count, (E,F) exhausted CD4+T cell counts (defined as CD8+CD28-CD45RA-), (G,H) proportion of CD4+ T cells, (I,J) naïve CD4 T cell count, (K,L) proportion of natural killer cells, (M,N) proportion of monocytes, (O,P) granulocytes, (Q,R) B cells, (S,T) plasma blasts (activated B cells). All cell types were estimated based on DNA methylation levels as described in Methods. The heading of each plot reports a robust correlation coefficient (biweight midcorrelation and a corresponding p-value).
Figure 6. Medication status versus blood cell…
Figure 6. Medication status versus blood cell counts in PD patients
As indicated in the heading of each panel, the panels alternate between the two data sets. Levodopa medication status (x-axis) versus (A,B) proportion of CD8+ T cells, (C,D) naïve CD8+ T cell count, (E,F) exhausted CD+T cell counts (defined as CD8+CD28-CD45RA-), (G,H) proportion of CD4+ T cells, (I,J) naïve CD4+ T cell count, (K,L) proportion of natural killer cells, (M,N) proportion of monocytes, (O,P) granulocytes, (Q,R)B cells, (S,T) plasma blasts (activated B cells). All cell types were estimated based on DNA methylation levels as described in Methods. Each bar plot depicts the mean value (y-axis), 1 standard error, and the group size (underneath the bar). The p-value results from a non-parametric group comparison test (Kruskal Wallis).

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