Yizhen Jia

Program: Neurosciences

Current advisor: Jin-Moo Lee, MD, PhD

Undergraduate university: Purdue University, 2021

Enrollment year: 2022

Research summary
I use a click-labeled APP reporter to pinpoint where amyloid-β is generated inside neurons. By tracking labeled Aβ through early endosomes, late endosomes, and lysosomes, I aim to identify the compartment driving Alzheimer’s pathology.

Amyloid-β (Aβ), the peptide that accumulates into plaques in Alzheimer’s disease, is produced inside neurons by sequential cleavage of the amyloid precursor protein (APP). Although it has long been clear that this happens somewhere along the endosomal–lysosomal pathway, the specific compartment where the final, Aβ-releasing cut occurs is still unresolved. The question matters therapeutically: γ-secretase inhibitors failed in clinical trials largely because they block the enzyme everywhere it acts, producing unacceptable off-target effects. Knowing which compartment generates Aβ would make compartment-selective intervention possible.

The obstacle has been technical. Aβ is small, and conventional fluorescent tags inserted into its sequence disrupt normal processing, so Aβ itself has never been directly visualized as it is made. Our laboratory solved this by engineering an APP reporter that incorporates an unnatural amino acid within the Aβ region, providing a chemical handle for click labeling. I attach a cell-impermeant red dye that can only reach APP at the cell surface, while a green fluorescent protein on the APP C-terminus marks the fragment that stays membrane-bound. Because the dye labels only surface APP, this creates a synchronized cohort of molecules that I can follow inward through the cell over time.

My current work maps that itinerary. I label surface APP, chase for intervals from minutes to six hours, fix the cells, and immunostain for markers of individual compartments — EEA1 for early endosomes, Rab7a for late endosomes, and LAMP1 for lysosomes. Using 3D image segmentation, I identify vesicles containing both APP and a given marker, then measure the red and green signals within them. So far, APP-containing vesicles leave early endosomes and accumulate in late endosomes and lysosomes in the expected sequence, and the red-to-green ratio climbs in every compartment, reaching its highest values in lysosomes. These findings are consistent with biochemical work placing γ-secretase activity in the lysosomal membrane. To test whether the signal depends on the enzyme itself, I run parallel experiments with the γ-secretase inhibitor compound E, which reproducibly reduces the number of APP-positive late endosomes.

I am now extending this in two directions. First, I am refining the measurement to quantify red and green within individual vesicles rather than averaging across them, which will let me detect the spatial separation of the two labels that directly signals cleavage. Second, I am perturbing the pathway — knocking down the Alzheimer’s risk gene SorLA and other retromer components — to test whether redirecting APP away from the lysosomal route reduces Aβ generation. Together, these experiments should establish both where Aβ is made and whether that site can be manipulated therapeutically.

Graduate publications
Liu Z, Hildebrand DGC, Morgan JL, Jia Y, Slimmon N, Bagnall MW. 2022 Organization of the gravity-sensing system in zebrafish. Nat Commun, 13(1):5060. PMCID: PMC9420129

Jia Y, Bagnall MW. 2022 Monosynaptic targets of utricular afferents in the larval zebrafish. Front Neurol, 13():937054. PMCID: PMC9355653