Investigating retrotransposon activation and retrotransposon-associated genetic variants associated with human tauopathy

Objective: To gain insights into retrotransposon activation in specific cell types, our first objective is to analyze differential transposable element expression in bulk sequenced microglia from Alzheimer’s disease patient brain tissue versus controls (NG00105).
Study design: Reads will be aligned to the GRCh38 human reference genome with STAR using parameters optimized for aligning transposon derived multi-aligning reads. Read counts for transposon and gene loci will be obtained using TEtranscripts. Differential expression of genes and transposons will then be calculated using Deseq2.
Analysis plan: Unsupervised machine learning techniques will be applied to cluster transcription counts by variance to make associations between specific retrotransposons and microglial/immune response associated genes.

Objective: We have identified multiple candidate non-reference mobile element insertion variants using nanopore long read sequencing of DNA extracted from frontal cortex of patients at Braak 0, III, and V/VI. Our second objective is to utilize the ADSP umbrella whole genome sequencing dataset (NG00067) to determine if our findings are conserved in a larger cohort of patients with Alzheimer’s disease.
Study Design: CRAM alignment files aligned to the GRCh38 reference genome from the ADSP discovery (snd10000) and PSP-UCLA (snd10017) WGS data sets will be analyzed with xTea (Chu et al. 2021) to identify the presence of mobile element insertions previously identified via nanopore. Only genomic regions containing insertions of interest will be analyzed.
Analysis Plan: Non-reference mobile insertions identified via nanopore will be compared in control, Alzheimer’s disease, and PSP NIAGADS datasets. Insertions meeting the designated criteria will be considered for a replication analysis using cohorts from the ADSP umbrella dataset. We will determine whether these variants can predict the longitudinal clinical rate of disease progression and correlate with other features such as tau PET positivity, CSF tau, and cognitive testing. We will also consider sex, age, and high-risk genotypes.

Objective 1:
Almost half of the human genome is composed of transposable elements, or “jumping genes.” Retrotransposons are activated in human Alzheimer’s disease and related “tauopathies,” as well as in Drosophila and mouse models of tauopathy. In the current study, we will analyze retrotransposon activation specifically in microglia, the immune cells of the brain, in the context of tauopathy. In addition, we will determine if retrotransposons activation correlates with expression of neighboring immune response genes.
Objective 2:
We have previously identified tau-induced retrotranpsoson activation as driver of neurodegeneration.
In a preliminary analysis of Alzheimer’s disease patient samples and controls, we have used long-read whole genome DNA sequencing technology to discover non-reference retrotransposon insertions that are unique to Alzheimer’s disease patients. In the current study, we expand these analyses to determine if our findings are conserved in a larger patient cohort, and how these novel insertions relate to disease
progression.