Loss of Y chromosome in Alzheimer's patients co-occurs with somatic mutations beyond CHIP drivers

Abstract

Loss of Y chromosome (LOY) and clonal hematopoiesis of indeterminate potential (CHIP) are common age-related events with implications for aging and Alzheimer disease (AD). LOY is linked to increased AD risk, whereas CHIP may be protective, and their co-occurrence remains unclear. We conducted whole-exome sequencing of CD4⁺ T cells, NK cells, and myeloid cells from AD patients and controls exhibiting LOY or retention of Y chromosome. We identified 39 variants in known myeloid and lymphoid driver genes, with up to 35% co-occurring with LOY in the same clone. In addition, we detected 192 unknown drivers of clonal hematopoiesis, enriched in AD-LOY individuals (odds ratio 4.8, P = 0.041). In myeloid cells, total driver burden correlated with LOY (ρ = 0.52, P = 0.00041). These results indicate that LOY is a primary driver of clonal hematopoiesis in AD, seeding myeloid clones that accumulate unknown driver variants, whereas most canonical CHIP mutations arise independently. Our study reveals distinct, partially overlapping clonal architectures for LOY and CHIP and highlights LOY-driven myeloid expansion as a contributor to AD pathogenesis.

Figure 1.. Landscape of clonal hematopoiesis (CH) in 118 analyzed subjects.

Each type of CH variants is stratified by the disease status (AD patients versus controls) and chromosome Y status (LOY versus ROY). Each column represents one subject. Each gray rectangle in the first row represents the LOY subject. Each following row represents one type of CH variants, and the presence of variants in subject is indicated by a specific color: blue—known myeloid driver gene (MD-CH), green—known lymphoid driver gene (LD-CH), and red—unknown driver gene (UD-CH). AD: n = 66 (32 LOY, 34 ROY); CTRL: n = 52 (23 LOY, 29 ROY); AD, Alzheimer disease; LOY, loss of Y chromosome; ROY, retention of Y chromosome; CTRL, control.

Figure 2.. Association between loss of Y chromosome (LOY) and CH types.

(A, B, C, D) LOY and MD-CH; (B) LOY and LD-CH; (C) LOY and UD-CH; (D) LOY and all CH combined (Any-CH). Proportions of subjects with each CH type were compared between LOY and ROY groups within AD patients (AD) and controls (CTRL) using logistic regression adjusted for age and age². Odds ratios (ORs) with 95% confidence intervals (CI) are shown. P-values were Benjamini-Hochberg adjusted for eight comparisons (P.adj), with significant adjusted P < 0.05 marked by an asterisk. Arrows indicate CIs extending beyond axis limits.

Figure 3.. VAFs of different types of CH variants versus loss of Y chromosome (LOY).

The boxplots present the distribution of VAFs of variants detected in LOY and ROY subjects. (A, B) VAFs of MD-CH, LD-CH and UD-CH variants in the cohort stratified according to the subject’s chromosome Y status only (AD patients and controls combined); (B) VAFs of UD-CH variants in AD patients and controls. In case if more than one variant of the same CH type was detected in a subject, only the variant with the highest VAF was included in the analysis. The differences between distributions of VAFs in LOY and ROY subjects were tested using the Mann-Whitney U test. The P-values were adjusted for multiple testing using Benjamini-Hochberg method assuming five tests. Statistically significant adjusted P-value was marked with an asterisk. The line inside the boxplot represents the median; the cross inside the box represents the mean; the upper border of the box represents Q3; the lower border of the box represents Q1; whiskers extend from minimum to maximum. VAF, variant allele frequency; AD, Alzheimer disease; LOY, loss of Y chromosome; ROY, retention of Y chromosome; CH, clonal hematopoiesis; MD, myeloid driver; LD, lymphoid driver; UD, unknown driver; Q3, third quartile; Q1, first quartile.

Figure 4.. CH versus loss of Y chromosome (LOY) across analyzed cell types.

Scatterplots display the percentage of cells carrying each CH variant type (x-axis) versus the corresponding percentage of cells with LOY (y-axis). (A, B, C) MD-CH versus LOY in CD4⁺ T cells, NK cells and myeloid cells; (B) LD-CH versus LOY in the same cell types; (C) UD-CH versus LOY in the same cell types. Each point represents one variant detected in one subject. All variants detected in a given subject were shown. Gray background encodes Y chromosome status on the subject level (LOY ≥ 15% in any cell fraction); point shape denotes cell type. Gene symbols are annotated for MD-CH and LD-CH variants.

Figure 5.. Total CH burden versus loss of Y chromosome across cell types.

For CD4⁺ T-cells, NK-cells, and myeloid cells in respective facets, these scatterplots illustrate the strength and direction of the monotonic association between total CH burden (defined as sum of VAFs of all post-zygotic variants detected in a sample; x-axis) and loss of Y chromosome level (y-axis). Axes are equal-scaled, variables are converted to ranks within their respective cell-type, and bottom and left rugs indicate marginal rank distributions. Each subject is shown as a pie glyph depicting the proportional contribution of MD-CH (blue), LD-CH (green) and UD-CH (red) variants. Samples lacking detectable CH are rendered as solid grey pies. Dashed black lines are least-squares fits to the ranked data, visually representing Spearman’s correlation coefficient ⍴ and its BH adjusted P-values.