Fine-mapping of the TMEM106B locus reveals four haplotypes that are differentially associated with risk for neurodegeneration
Henne Holstege (Amsterdam UMC, Katholieke Universiteit Leuven)
Alex N. Salazar (Amsterdam UMC)
Lydian Knoop (Amsterdam UMC)
Yolande A.L. Pijnenburg (Amsterdam UMC)
Sven J. van der Lee (Amsterdam UMC)
Sanduni Wijesekera (Amsterdam UMC)
Jana Krizova (Amsterdam UMC)
Mikko Hiltunen (University of Eastern Finland - Kuopio Campus)
Marcel JT Reinders (TU Delft - Pattern Recognition and Bioinformatics)
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Abstract
Background
Genome-wide association studies (GWAS) linked TMEM106B variants to susceptibility for neurodegenerative diseases, but the causal genetic elements remain unclear.
Method
We used genotyping data from 5,792 Alzheimer disease cases and controls, and applied COJO to identify haplotypes in the TMEM106B locus that independently associated with AD. Then, we used long-read sequencing data from 513 individuals to annotate these haplotypes with structural variations that map into them.
Results
Analysis of the genotyping data revealed that the TMEM106B locus consists of four major haplotypes: HA/Ha (covering the coding region), and HB/Hb (covering the upstream regulatory region). These combine into four combinations with varying population-frequencies: HAB (57%), HaB (34%), Hab (9%), and HAb (<1%). Long-read sequencing of 513 individuals showed that HA haplotypes (marked by 185-Threonine) carry unique methylated CpG sites and an AluYb8-retrotransposon in the 3' UTR, while the Ha haplotypes are marked by the 185-Serine allele. Hb haplotypes carry several structural variants (SVs) in nearby distal enhancers, including a 19 Kbp rearrangement, absent in all other haplotypes. Joint association models revealed that the HAB combination (AluYb8+185-Threonine) is risk-increasing, while Hab (SVs+185-Serine) confers the protective effect. HaB (185-Serine only) is neutral, while HAb was too rare to assess. Relative to middle-aged non-demented controls, cognitively healthy centenarians were more enriched with Hab (OR=1.49, padj=2.18×10-2) than with HaB (OR=1.23, padj=5.06×10-2). Proteomic analysis of temporal cortex tissues (n = 182) indicated that relative to the neutral HaB combination, the protective Hab is associated with 1.1-fold lower TMEM106B C-terminal peptide abundance, while the risk-increasing HAB is associated with 1.16-fold higher abundance.
Conclusion
Our data indicates that the genetic structure underlying the association of the TMEM106B locus with neurodegenerative diseases is driven by the effect of multiple haplotypes.
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