Pseudotime Analysis Identifies Receptor Tyrosine Kinase Ligands involved in the Temporal Development of Alzheimer's Disease Associated Microglia
Year: 2025
Type: article
Abstract: BACKGROUND: In Alzheimer's Disease (AD) microglia transition their phenotype from homeostatic to a potentially destructive disease associated phenotype (DAM). Prior research identified the ERK1/2 protein as being hyperactivated in microglia isolated from an AD mouse model. ERK1/2 is activated by the binding of upstream receptor tyrosine receptors (RTK) with their corresponding ligand(s). Further, DAM development is a progressive process, where cells transition from a homeostatic to DAM phenotype over time. METHOD: A single nucleus RNA sequencing dataset from a 5xFAD mouse model was obtained from the Gene Expression Omnibus database (GSE140511). 3 wildtype (WT) and 3 5xFAD mice samples were used for this work. The transcriptomes from these samples were processed with Seurat (v.5.0.3). The microglial population of cells was identified and loaded into NicheNetR (v2.1.0) to identify ligands suspected of driving the differential gene expression in the 5xFAD microglia. Next, a single nuclear trajectory was established using Monocle3 (v1.3.7), where the homeostatic microglia were labeled as the pseudotime origin. RESULT: Several RTK ligands were identified by NicheNet as having high likelihood of driving the DAM phenotype gene expression (Figure 1A). They include Csf1, Tgfb1, and Gas6, which are largely expressed by microglia. Notably, each of these ligands have been established as altering microglia behavior outside of AD. The Monocle3 trajectory of DAM development was then used to identify the stage in DAM development that the ligand may regulate. Csf1 and Tgfb1 changed as a function of pseudotime, shown in Figure 1B. Csf1 signaling began early in DAM development and plateaued later. Alternatively, Tgfb1 expression declined early in DAM development and further declined in the later stage. These trends align with what is known about each ligand in microglia, where Csf1 is proinflammatory and Tgfb1 is anti-inflammatory. Gas6 was generally expressed at the same level over time. This ligand is still suspected of regulating DAM, just not at a specific point of development. CONCLUSION: This analysis has identified three ligands for RTKs that are potential drivers of DAM and change expression temporally. Given their apparent role in DAM development, these ligands have therapeutic potential in AD through DAM modulation.
Source: Alzheimer s & Dementia
Authors: Brendan R Tobin, Sara Bitarafan, Levi B Wood
Institution: Georgia Institute of Technology
Language: English
Subfield: Neurology
Field: Neuroscience
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $4,200
OpenAlex ID: W7117236148
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