Fine-Mapping of the TMEM106B Locus Reveals Four Haplotypes That are Differentially Associated With Risk for Neurodegeneration
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Genome-wide association studies (GWAS) linked TMEM106B variants to susceptibility for neurodegenerative diseases, but the causal genetic elements remain unclear.
Genotyping of 5,792 Alzheimer disease cases and controls 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. Indeed, relative to middle-aged non-demented controls, cognitively healthy centenarians were more enriched with Hab (OR=1.49, p adj =2.18×10 -2 ) than with HaB (OR=1.23, p adj =5.06×10 -2 ). Finally, proteomic analysis of temporal cortex tissues (n=182) indicated that relative to the neutral HaB combination, the protective Hab is associated with 0.91-fold lower TMEM106B C-terminal peptide abundance (CI=[0.81-1.02]), while the risk-increasing HAB is associated with 1.07-fold higher abundance (CI=[0.99-1.15]).
Together, this presents a complex genetic structure underlying the association of the TMEM106B locus with neurodegenerative diseases.
ONE SENTENCE SUMMARY
GWAS and long-read sequencing suggests that the neurodegenerative genetic etiology associated with TMEM106B is conferred by multiple independent haplotypes.
