Date of Award
8-14-2024
Degree Name
Doctor of Philosophy (PhD)
Degree Type
Dissertation
Abstract
Genome-wide association studies (GWAS) have identified more than 70 genetic loci that are linked to Alzheimer disease (AD) risk. Many of these risk genes are involved in microglial function, including MS4A4A, TREM2, and PLD3, suggesting a relationship between microglial phagocytosis, metabolism, inflammation, and AD pathogenesis. However, the mechanisms by which AD risk genes alter microglia function and contribute to disease remains inadequately explored. In this dissertation, I leveraged functional genomics methods to understand the impact of MS4A4A, TREM2, and PLD3 on microglia function in stem cell and mouse models as well as human brain tissue. MS4A4A is a microglial gene that encodes a membrane protein known to regulate alternative activation in macrophages. The protective variant rs1582763 and the risk variant rs6591561 at the MS4A4A loci are associated with the CSF sTREM2 levels. To better understand how MS4A4A modifies microglial behavior and contributes to AD pathology, we leveraged single-cell sequencing datasets from human brains. By comparing the microglial transcriptomic profiles between variant carriers, we found that rs1582763 promotes the generation of MS4A4A-positive microglia, shifting these cells from a chemokine state to an interferon state, enhancing lipid metabolism, and reducing inflammatory cytokines. In contrast, rs6591561 diminishes lipid metabolism and promotes pro-inflammatory cytokines. Furthermore, by mimicking the effect of rs1582763 on this microglial state, we identified an HDAC inhibitor that increases Aβ and myelin phagocytosis, highlighting its potential as a therapeutic approach for AD. TREM2 encodes a microglial receptor that detects pathological proteins such as Aβ and tau, thereby activating microglia to enhance phagocytosis and metabolism. Variants in TREM2 are associated with risk for AD, frontotemporal dementia and Nasu-Hakola disease (NHD). The rare TREM2 Q33X mutation is a null mutation that causes NHD, a disease characterized by bone cysts and dementia. To better understand how TREM2 deficiency impacts microglial function, we reprogrammed fibroblasts from two NHD patients and a healthy sibling control into induced microglia-like cells (iMGL). We found that NHD iMGL lacked surface TREM2 expression and sTREM2 secretion. Bulk RNA sequencing and flow cytometry revealed reduced cell activation and antigen presentation in NHD microglia and macrophages. The NHD mutation also impaired phagocytic and lysosomal functions, as shown by phagocytosis assays and immunostaining. Electron microscopy showed decreased lipid droplets in NHD microglia. In summary, TREM2 deficiency significantly impairs microglial survival, activation, phagocytosis, and metabolism, emphasizing the necessity of TREM2 in neurodegenerative diseases and providing a roadmap for treating TREM2 abnormalities in AD. PLD3 encodes an enzyme that catalyzes the hydrolysis of membrane phospholipids. Variants in PLD3 have been implicated in late-onset AD, and PLD3 expression is drastically reduced in AD brains. The synonymous variant PLD3 A442A disrupts splicing mechanisms, resulting in reduced expression of Exon 11, which is sufficient to increase Aβ plaque deposition. By comparing PLD3 A442A iPSC-derived neurons to CRISPR/Cas9-corrected isogenic controls, we confirmed that the PLD3 A442A mutation significantly increases Aβ precipitation in neurites. Silencing Pld3 expression via AAV in mice brains reduces the Aβ turnover rate, and knocking down Pld3 in transgenic mice leads to less compact Aβ plaques in the brain, indicating PLD3's role in containing plaque aggregation and toxicity. Additionally, we observed reduced recruitment of microglia to amyloid plaques in the absence of Pld3. These findings suggest that PLD3 may impact amyloid accumulation and AD risk through disrupted microglial function, as PLD3 is enriched in disease-associated microglia (DAM) in human brains. In conclusion, my work highlights the role of genetic architecture in AD pathophysiology and begins to point to potential disease mechanisms. By identifying key variants in genes such as MS4A4A, TREM2 and PLD3, we have demonstrated how these genetic variants can disrupt cellular function, influence Aβ metabolism, and ultimately contribute to neurodegeneration. Our findings highlight the importance of understanding the genetic basis of AD for developing targeted therapeutic strategies. Future research should focus on exploring these genetic interactions in greater detail and investigating potential interventions that can mitigate the effects of these pathogenic variants. By doing so, we can pave the way for more effective treatments and ultimately improve outcomes for individuals affected by Alzheimer disease.
Language
English (en)
Chair and Committee
Celeste Karch
Committee Members
Carlos Cruchaga; David Holtzman; Naresha Saligrama; Oscar Harari
Recommended Citation
You, Shih-Feng, "Functional genomics approaches to understanding the impact of common and rare risk variants on microglia function in neurodegenerative diseases" (2024). Arts & Sciences Electronic Theses and Dissertations. 3327.
https://openscholarship.wustl.edu/art_sci_etds/3327