We have isolated exosomes from human CSF and profiled protein and RNA. Now we wish to find out whether the CSF-derived exosomes are shed from specific brain cell types and specific brain regions. What is the best way to go about this? Are there protein or gene databases for specific brain cell types and specific brain regions? Are there marker proteins and marker genes specific for brain cell types and brain regions?
Hi @turck. I’m going to leave your first question, as well as questions of protein databases for others to address. You can find genes specific to cell types and brain regions using Allen Brain Map tools. To find genes selectively expressed in one adult human brain as compared to all others, you can use the “Differential Search” option at the Allen Human Brain Atlas–here is an example looking at markers for Amygdala. We have several available tools for finding and viewing cell type-specific genes in the Cell Types Database: RNAseq data. Probably the easiest to use is for human MTG. To find markers for a specific cell type, click on “Set 1 Selection”, choose your cell type of interest, and then click on “Find Marker Genes”. All of the atlases also of options for viewing gene expression of a specific gene (or genes) in the context of brain regions or cell types, so if you have a gene list from your experiment, you can visualize the results that way. Best of luck!
Hi Jeremy, thanks much for getting back to me! Admittedly, I am struggling a bit with the different options. What I have is a protein list generated by mass spectrometry and a gene list generated by RNAseq. They both come from exosomes collected form one big CSF pool (1 liter worth, collected and pooled from a great number of patients). What I what to find out is what cell types and brain regions this pool of exosomes is coming from. In other words, this is a profiling exercise for future studies where we will compare individual patient CSF exosome profiles. At this point I merely want to find out what one can expect to find in terms of exosome markers representing cell types and brain regions. Chris
Hi Chris, if it were me, I’d probably start by taking the top 500-1000 genes from your list and putting them in ToppFun tool of the ToppGene suite, which is “a one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network”. In addition to gene ontology terms (which will likely pull out “exosome”-related categories), you can calculate enrichment for various coexpression modules, lists from papers, drug targets, etc… If you are willing to do some computation, we also published a list of genes differentially expressed between each pair of brain structures in the platform paper for the Allen Human Brain Atlas, and you could compare your gene list against these (see supplementary table 5). Finally, you could take the top RNAseq genes and view them in the cell type and brain region atlases, as I mentioned above. I’m not sure what to do with the protein lists–I’d expect moderate but not tremendous overlap with your RNAseq, so maybe this could be used to filter the RNA-seq gene lists, or maybe you could compare these against other protein databases.