Loss of age-associated increase in m6A-modified RNA contributes to GABAergic dysregulation in Alzheimer's disease

Dysregulated RNA metabolism is a significant feature of Alzheimer's disease (AD), yet how post-transcriptional RNA modifications like N6-methyladenosine (m6A) are altered in AD is unknown. Here, we performed deamination adjacent to RNA modification targets (DART-seq) on human dorsolateral prefrontal cortices to assess changes in m6A with nucleotide resolution. In non-AD brains, m6A sites increased with age, predominantly within the 3'UTR of transcripts encoding tripartite synapse proteins. In contrast, AD brains lost the age-associated m6A site increase and exhibited global hypomethylation of transcripts, including MAPT and APP. Hypomethylated genes involved with GABAergic signaling, glutamate transport, and ubiquitin-mediated proteolysis exhibited reduced expression, connecting m6A to synaptic excitotoxicity and disrupted proteostasis in AD. Site-specific m6A levels were linked with GABRA1 expression and protein levels, but this relationship was abolished in AD. Our findings provide insight into post-transcriptional mechanisms of dysregulated RNA metabolism in AD that are related to aging and GABAergic regulation. Overall design: Human post-mortem dorsolateral prefrontal cortex tissue (Brodmann area 9) was collected from two groups: individuals with pathologically confirmed Alzheimer's disease (AD; n=19) and age- and sex-matched neurologically normal controls (n=19). DART-seq were performed on all n=38 samples. All n=38 samples were treated with DART-WT enzyme and n=11 from each group were treated with DART-Mut enzyme (see below).