Aging increases the risk for mild cognitive impairment (MCI) and Alzheimer?s disease (AD), but the underlying mechanisms are poorly understood. Next-generation sequencing studies (e.g., transcriptomics, RNA-seq) hold promise for identifying novel mediators of age-related AD. However, many such studies have focused on coding genes only. The purpose of this NIA administrative supplement is to test the hypothesis that an age-related accumulation of non-coding repetitive element (RE) transcripts, which can stimulate AD- relevant pathological processes (e.g., inflammation), may play a role in MCI/AD. In our parent R21 (responsive to NIA PA-17-089, Exploratory Analyses of Existing Cohorts, Data Sets, and Stored Biospecimens to Address Clinical Aging Research Questions), we are using RNA-seq, ATAC-seq and existing clinical (blood) samples to determine if: 1) RE transcripts accumulate with aging and are linked with age-related inflammation; and 2) chromatin changes may underlie these events. These studies are based on evidence that RE transcript accumulation may cause inflammation via activation of innate immune sensors, a process that is also implicated in the neuroinflammation observed in MCI/AD. In our current R21 work, we have observed strong links among RE transcript levels, age and inflammation. We also have evidence that RE transcripts may be involved in biological aging, which could suggest a role in age- related diseases like AD, and we have collected preliminary data showing that: a) RE transcripts accumulate with age in human peripheral tissues and brains; b) similar RE transcripts are increased in AD patient brains; and c) RE transcript accumulation is associated with increased double-stranded RNA (dsRNA, an innate immune activator) both systemically and in the brain. These findings suggest that a systemic increase in RE transcripts could play a role in MCI/AD. To investigate this, we are collaborating with investigators at the University of Colorado School of Medicine Alzheimer?s and Cognition Center who have a large set of existing samples from older controls, MCI and AD patients. These subjects have undergone comprehensive clinical evaluations and testing for circulating markers of systemic/neuro-inflammation and neurodegeneration. The associated samples/data are an excellent opportunity to expand our existing award and develop a focus on a novel mechanism of MCI/AD, which could provide insight into new therapeutic targets or biomarkers. Therefore, in this supplement, we propose to add ~120 samples (from 70 controls, 30 MCI and 20 AD patients) to our ongoing analyses and conduct: 1) high-depth, total RNA-seq to profile RE transcripts and determine if they are related to inflammation/neuro-inflammation, cognitive impairment or AD pathology; and 2) ATAC-seq on a subset of duplicate samples to determine if these changes may be linked with chromatin dysregulation.
Alzheimer?s disease (AD) is associated with systemic inflammation and neuroinflammation, but the upstream causes of these processes are unknown. The purpose of the proposed research is to use transcriptomics (sequencing of RNA) to characterize AD-associated differences in non-coding RNAs that may contribute to systemic and neuroinflammation. This may provide clues to previously unrecognized causes of inflammation in AD, as well as potential biomarkers and targets for future interventions.
