Subdivide astrocytes by brain region

[dosumis]

Based on whole mouse brain scRNAseq + MERFISH - there are transcriptomically distinct types of astyrocytes in different brain regions:

Telencephalon Cerabellum Olfactory areas Sub-telencephalic

Add these subtypes with definition text making clear that they are transcriptomically distinct.

[AvolaAmg]

https://www.nature.com/articles/s41467-019-14198-8 https://www.nature.com/articles/s41593-021-00905-6 https://pmc.ncbi.nlm.nih.gov/articles/PMC7139801/

[dosumis]

Is there a positive term we can use in place of non-telencephalic - excluding olfactory cortex (OLF) and cerebellum as well as telencephalon?

[RiveraAndrea83]

I need to visualise the atlas but if we are exclusing all telencephalon maybe diencephalic or gross anatomical terms might suffice to distinctually represent the data.

[RiveraAndrea83]

the term "subcortical" would be precisely vague enough to exclude telencephalon, OLF and cerebellum.

[dosumis]

For Astro-CB - we already have

CL:0002603 ; astrocyte of the cerebellum

maybe rename to 'cerebellar astrocyte' for brevity.

[dosumis]

Issue:

Autoclassification => nesting among siblings

OTOH - spatial segregation looks v. strong. We just lack the names for the areas.

Looks less clean in CCF at division level...

[dosumis]

Some suggested manual defs from spatial transcriptomics:

Astro-NT - A transcriptomically defined type of astrocyte that occurs throughout the telencephalon (and in deep regions of the cerbellum Check ?). In most regions of the telencephalon it is the only type of astrocyte present, although in some region (e.g. the olfactory areas) it is mixed with other types.

Astro-CB - A transcriptomically defined type of astrocyte found only in the cerebellum, in layers deeper than the Purkinje cell layer where the Bergman glia are. subClassOf: part_of some cerebellum

Atro-OLF - A transcriptomically defined type of astrocyte located exclusively in the olfactory areas. subclassOf

Atro-NT - A transcriptomically defined type of astrocyte located almost exclusively in subcortical regions where it is the only astrocyte type. The ?? has both telencephalic and non-telencephalic types of astrocyte.

Question: Should we make these general or just mouse for now?

[RiveraAndrea83]

I'd make them only for mouse. There are quite a few differences between astrocytes in human vs mouse (even vs rat) however, I am not sure if the differences are captured transcriptomically. To be safe I would confine them to mouse first and then see how the data fit humans.

[dosumis]

Looking more closely at NT - it seems they are broader then telencephalon

e.g. major subtype in Striatum

Astro-TE NN_3 Crym astrocyte (Mmus) on ABC atlas

Maybe more accurate to say (largely) restricted to cerebrum?

[dosumis]

@RiveraAndrea83. I think good for you to review manual text defs on WMB Astrocytes against ABC atlas & finalise this week. I'm inclined to add this down to the cluster level as lots of really striking localization patterns. These make me more hopeful that robust types are represented.

[dosumis]

@RiveraAndrea83 - I think this was fixed but not closed? Please confirm.

[RiveraAndrea83]

I should probably do more work. I can see one term done but maybe expand on all of them. it is quite timeconsuming to check them manually though.