Stanford researchers constructed an atlas of the proteins found in the lysosome across different brain cell types, a recently published paper reported. 

Lysosomes are cell organelles that play essential roles in recycling “garbage” in a cell, and their breakdown can lead to neurodegenerative diseases like Alzheimer’s and Parkinson’s. The atlas provided scientists with insights into lysosomes’ function and breakdown — processes that were still widely under-researched. 

“The question is, which one of these cell [types] is the most affected in these different types of [neurodegenerative] diseases?” said Monther Abu-Remaileh, senior author on the paper and assistant professor of chemical engineering and genetics at Stanford. He also leads the Abu-Remaileh Lab. “You can look at this by starting off by defining where these proteins that are affected in neurological diseases mostly exist, in lysosomes of which cell types.”

In the past, research investigating cell organelles like lysosomes was very time-consuming and challenging to conduct. Prior work conducted by Abu-Remaileh created a new protocol, called LysoIP, that uses magnetic protein tags to isolate and preserve lysosomes from the cell rapidly and effectively. This new method set the foundation to be able to analyze the protein contents of lysosomes. 

The team was “able to look directly in lysosomes from different cell types, by simply fishing them out from the cells,” Abu-Remaileh said. “Now you can look at the full spectrum of molecules that exist inside them, and define which proteins related to disease are actually in lysosomes of neurons, astrocytes, oligodendrocytes and microglia.”

Constructing the atlas yielded an array of insights about lysosomes and neurodegenerative diseases. They found that lysosomes share core proteins across different cell types, but many of their specialized cell-specific proteins are associated with neurodegenerative and neurological diseases. 

The atlas also identified important proteins that weren’t previously recognized to be found in the lysosome.

“We discovered a new lysosomal protein… SLC45A1: a transporter that is only expressed in neurons and enriched in lysosomes, the challenge was to find a function for that,” said Ali Ghoochani, co-first author on the paper and research scientist in the Abu-Remaileh Lab. “It’s like you are in the ocean, and you don’t know which direction you have to swim. We needed to set up a lot of experiments to understand the function of SLC45A1.”

SLC45A1 was previously thought to be associated with neuron membranes, not lysosomes. “This data will put it in a completely different category, different fields will be interested in it,” Abu-Remaileh said. “Most importantly, it will get us even closer to a real therapy instead of focusing for many years on things that will end up failing because you are not defining the disease in the right way at the molecular level.”

The team hopes this atlas will serve as a practical tool and launching pad for other scientists. “[If] you are interested in a protein because it’s linked to a disease that you are studying, or is coming out of one of your screens, now you can go into our database and see immediately if it might have something to do with the lysosome,” said Alessandro Ori, associated research group leader at the Leibniz Institute on Aging of the Fritz Lipmann Institute, which collaborated with the Stanford team on the paper.

“Our paper demonstrated these kinds of things are possible, and now people can just build on it,” Ori said. “We provide all the methods… for people to take over and do more experiments.”

Looking ahead, the team hopes to investigate the many connections that have appeared between lysosomal protein composition and neurological disease. 

“We see very, very specific characteristic alteration of the composition of the lysosomes [across different cell types],” Ori said. “This is telling us something fundamental about disease pathobiology, which is something that we are pushing quite substantially now.”