Non-coding and Loss-of-Function Coding Variants in TET2 are Associated with Multiple Neurodegenerative Diseases

Abstract

We conducted genome sequencing to search for rare variation contributing to early-onset Alzheimer's disease (EOAD) and frontotemporal dementia (FTD). Discovery analysis was conducted on 435 cases and 671 controls of European ancestry. Burden testing for rare variation associated with disease was conducted using filters based on variant rarity (less than one in 10,000 or private), computational prediction of deleteriousness (CADD) (10 or 15 thresholds), and molecular function (protein loss-of-function [LoF] only, coding alteration only, or coding plus non-coding variants in experimentally predicted regulatory regions). Replication analysis was conducted on 16,434 independent cases and 15,587 independent controls. Rare variants in TET2 were enriched in the discovery combined EOAD and FTD cohort (p = 4.6 × 10^-8, genome-wide corrected p = 0.0026). Most of these variants were canonical LoF or non-coding in predicted regulatory regions. This enrichment replicated across several cohorts of Alzheimer's disease (AD) and FTD (replication only p = 0.0029). The combined analysis odds ratio was 2.3 (95% confidence interval [CI] 1.6-3.4) for AD and FTD. The odds ratio for qualifying non-coding variants considered independently from coding variants was 3.7 (95% CI 1.7-9.4). For LoF variants, the combined odds ratio (for AD, FTD, and amyotrophic lateral sclerosis, which shares clinicopathological overlap with FTD) was 3.1 (95% CI 1.9-5.2). TET2 catalyzes DNA demethylation. Given well-defined changes in DNA methylation that occur during aging, rare variation in TET2 may confer risk for neurodegeneration by altering the homeostasis of key aging-related processes. Additionally, our study emphasizes the relevance of non-coding variation in genetic studies of complex disease.

Keywords: AD; ALS; Alzheimer; FTD; TET2; aging; amyotrophic lateral sclerosis; frontotemporal dementia; genome sequencing; non-coding.

Figure 1

QQ plot of p Values from the Discovery Burden Analysis of Early-Onset Alzheimer’s Disease (EOAD) and Fronto-temporal Dementia (FTD) Cases versus Controls and Private, CADD > 10 Variants TET2 is the top and only hit reaching statistical significance (corrected p < 0.05). No genomic inflation was observed (λ = 0.95). The uniform distribution and theoretical 95% confidence interval based on a beta distribution is shown. Note that, in addition to passing the correction threshold, TET2 also falls well outside of theoretical random p value distributions.

Figure 2

Qualifying Non-coding Variation in TET2 Is Enriched at a Similar Level as Coding Variation and Occurs in Key Predicted Functional Regulatory Regions (A) Odds ratios are shown for combined analyses (cohorts described in Table 2). Breaking out coding and non-coding variation reveals similar effect sizes and p values. ^∗ indicates p < 0.01, ^∗∗ indicates p < 0.001, and ^∗∗∗ indicates p < 0.0001 by Fisher’s exact test. (B) Non-coding variants near the TET2 transcription start site (hg19 chr4:106,066,000–106,070,000) serve as an example of variant enrichment in key regions predicted to have regulatory function. GSP indicates GenoSkyline-Plus regions.

Figure 3

Longitudinal CDRSB Changes in ADNI Participants with MCI and Qualifying TET2 Rare Variants TET2 rare variant carriers with mild cognitive impairment (MCI) from the Disease Neuroimaging Initiative (ADNI) show greater Clinical Dementia Scale Sum of Boxes Score (CDRSB) changes over time compared to non-carriers after controlling for age, sex, and education, APOE ε4, and baseline CDRSB score (β ± SE = 0.64 ± 0.12; ^∗p = 6.2x10⁻⁸, Bonferroni corrected p value for total number of longitudinal assessments: ^∗p = 3.1 × 10⁻⁶). The lines depicted illustrate CDRSB change with 95% confidence intervals in shading.