Retrotransposable Element Expression in Neural Stem Cell Senescence and Aging

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Neurodegenerative conditions and dementias, including Alzheimer's disease, create a significant economic burden and are responsible for considerable human suffering. Aging is the primary risk factor for development of these conditions. The decline in neural stem cell (NSC) function that occurs with age is a major factor contributing to the development of these conditions. However, the mechanisms resulting in NSC functional decline are poorly understood. Recent work from our laboratory and others reveals that chromatin undergoes global remodeling with age, with an opening of heterochromatic regions and a relative closing of euchromatic regions. The highly heterochromatic regions contain large numbers of retrotransposable elements (RTEs). We have previously shown that RTE expression also increases with age and culminates in active transposition events. Somatic transposition can lead to insertional mutagenesis and genome rearrangements creating genome instability and triggering cellular senescence. This leads us to our hypothesis: Age-associated changes in chromatin structure lead to de-repression of RTEs, resulting in DNA damage and genome instability, ultimately triggering cellular senescence and a decline in NSC function. To test this hypothesis we will perform a set of experiments designed to determine the role of increased RTE expression with age in loss of NSC function. In Specific Aim 1 we will begin by investigating the chromatin architecture in senescent and aged NSCs, and determine the effects on the transcriptome, in particular on the expression of RTEs. To obtain reinforcing and complementary whole genome data, we will use high-throughput Illumina sequencing in conjunction with three methods to define changes in chromatin structure and function: assay for transposase accessible chromatin (ATAC-seq), chromatin immunoprecipitation using antibodies against repressive and activating chromatin histone marks (ChIP-seq), and RNA-seq to define the transcriptome, including RTE expression. Specific Aim 2 will investigate the relationship between RTE expression and DNA damage accumulation in NSC functional decline. We will determine the dynamics of DNA damage accumulation and senescence in NSCs over time. The effects of RTE deregulation on NSC function and senescence will be determined using a reporter construct designed to over express the long interspersed nuclear element L1. Finally, we will determine the role of RTE expression in NSC functional decline in vivo in Specific Aim 3. The effect of RTE de-repression on the ability of NSCs to regenerate neurons in the olfactory bulb will be investigated through olfactory discrimination tests in young and aged mice exposed to the reverse transcriptase inhibitor 3TC, which represses RTE transposition. To determine if RTE repression extends NSC healthspan, the neurogenic capabilities of NSCs will be investigated in 3TC treated mice. Taken together the results of the experiments outlined in this proposal will give us new insight into the mechanisms that result in NSC functional decline with age and may ultimately lead to therapeutic interventions that can extend human healthspan.