Defining the role of rare genetic variants that drive risk and pathogenesis of Alzheimer’s disease
Date of Award
Doctor of Philosophy (PhD)
Alzheimer’s disease (AD) is the leading cause of dementia and is pathologically defined by the aggregation of extracellular amyloid plaques and intracellular neurofibrillary tangles. Rare heritable mutations within the genes for amyloid precursor protein (APP) and presenilin 1 (PSEN1), and presenilin 2 (PSEN2) cause early onset AD and account for approximately 1% of AD cases. While the majority of AD cases are late-onset (LOAD), which is defined by a markedly more complex genetic architecture that is comprised of many genetic risk factors that influence AD through multiple cellular pathways. The advent of deep sequencing analyses have allowed for the identification of novel risk factors and genetic variants. By identifying these genetic risk factors, characterizing their cellular and molecular function, and then identifying the roles they play influencing AD risk, this knowledge may be leveraged for the development of more effective therapeutics. In this dissertation, I look more deeply into three risk factors: LMNA, RAB10, and PLD3. Through a combination of computational analysis and functional/biochemical assays, I attain a deeper understanding of the roles of these genes as they affect AD pathogenesis.The first of these genes, LMNA, encodes a nuclear lamin protein that is associated with the accelerated aging condition Hutchinson-Guilford Progeria Syndrome (HGPS). In this condition, a mutation in LMNA leads to the production of progerin, which is unable to be processed by ZMPSTE24 and constitutively incorporates into the nuclear membrane, causing nucleoskeletal dysfunction. In AD, some of these same nucleoskeletal deficiencies have also been observed. Through mRNA expression analysis of laser-captured microdissected neurons, we observe a significant elevation of LMNA expression coupled with a reduction of ZMPSTE24 expression in diseased brains, resulting in more immature, unprocessed prelamin A. When we induced progerin expression in iPSC-derived cortical neurons, we observed disruption in pathways associated with the oxidative stress response as well as the lysosome, which has been associated with AD pathology in the literature. Further genomic analyses in increasingly larger datasets has led to the identification of genetic variants that protect against AD. One study by our group identified a rare SNP in the 3’-untranslated region (3’-UTR) of RAB10 (rs142787485). As a Rab GTPase, RAB10¬ plays a role in the endo-lysosomal network (ELN), a central pathway to the processing of APP and the production of Aβ. In AD brains, we observe increased levels of RAB10 mRNA and RAB10 protein expression. Overexpressing RAB10 in N2A695 cells increases the ratio of extracellular Aβ42/40, which is associated with increased pathogenicity. Furthermore, when investigating the rs142787485 SNP, the location of this SNP is predicted to interfere with the binding of multiple miRNAs. However, these predictions still need to be validated through functional and biochemical assays. In our efforts to better understand AD genetics, there remain challenges posed by genes that remain uncharacterized in terms of their function. One such gene is PLD3, a member of the phospholipase D family, but lacks any confirmed phospholipase activity or substrate. Whole exome sequencing of families densely affected by LOAD uncovered the rare variant in PLD3 p.V232M. Further deep sequencing uncovered additional variants associated with increased disease risk. In our work we find that one particular synonymous variant, p.A442A, activates a cryptic splice site, resulting in the reduced expression of exon 11. Furthermore, studies of AD patients show that PLD3 is reduced in the neurons of AD brains. When we look at loss of Pld3 in amyloid model mice, we observe significantly decreased Aβ turnover and altered plaque pathology which we further attribute to reduced microglial plaques, mirroring what has been observed in Trem2-deficient amyloid mice. Together, these studies illustrate the critical role of nuclear and ELN function in AD risk and resilience.
Chair and Committee
Celeste M. Karch
Rosene, Matthew James, "Defining the role of rare genetic variants that drive risk and pathogenesis of Alzheimer’s disease" (2022). Arts & Sciences Electronic Theses and Dissertations. 2657.
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