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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Revise cell label and definition for cortical VIP neurons in CL. #2344

Closed AvolaAmg closed 1 month ago

AvolaAmg commented 5 months ago

In the light of having a complete taxonomy for cell types of the CNS, we are reviewing terms present in the Jorstad paper (see citation below). This ticket aims to discuss a definition for VIP GABAergic interneuron and their subclasses that includes also their transcriptomic signature.

The concept is to add a CxG link to the cell definition of VIP GABAergic interneurons and indication where these cells can be found.

Another point is to add the supercluster: CGE-derived interneurons and to group cells underneath accordingly.

Nikolas L. Jorstad et al. ,Transcriptomic cytoarchitecture reveals principles of human neocortex organization.Science382,eadf6812(2023).DOI:10.1126/science.adf6812

AvolaAmg commented 5 months ago

In this ticket the following points are discussed:

Points related to this ticket, will be discussed in other tickets.

vip GABAergic cortical interneuron

New Definition: A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_cluster', cluster Vip.

database_cross_reference: https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/

has related synonym: VIP-Expressing GABAergic Neuron database_cross_reference PMID:35221922

has related synonym: VIP type database_cross_reference PMID:37824655

has related synonym: VIP interneuron database_cross_reference PMID:33108272

has related synonym: VIP neuron database_cross_reference PMID:33108272

has related synonym: cortical VIP neuron database_cross_reference PMID:36384143

has related synonym: Vip GABAergic neuron database_cross_reference ILX:0770151

has related synonym: Vip database_cross_reference ILX:0770151

Parent term: CGE-derived interneuron (term to be generated)

Location: Neocortex

Symbol: VIP neuron

Points of discussion

1) Adding subtypes downstream to vip GABAergic cortical interneuron based on the information from this paper or just include these subtypes in the comment section. This paper addresses the morphoelectric properties of cortical GABAergic interneurons in human. Some molecular markers are shown with Patch-seq. In the context of VIP neurons, 4 different subtypes are found: VIP LBH, VIP SYT6, VIP CCD184, VIP ADAMTSL1. Their soma location, morphology, electrophysiology informations is available; however, there is no CxG reference dataset. image

Should these cells be mentioned in the comments of vip GABAergic cortical interneuron

i.e. Comments: VIP neurons show heterogeneity in morphology, layer positioning and electrophysiological properties. In the Homo Sapiens cortex, 4 different subtypes of VIP neurons are identified; these neurons show different morphologies, soma location and electrophysiological properties (Lee et al., 2023). Specifically, the 4 VIP types are defined according to their transcriptomic markers: LBH-VIP (bipolar neuron, soma location L2), SY16-VIP (soma location L3), CCD184-VIP (bipolar neuron, soma location L3), ADAMTSL1-VIP (soma location L3).

Or should I just add these as 4 different new CL terms downstream to the vip GABAergic cortical interneuron?

I am a bit torn whether adding them or not as separate CL terms. I think there is no harm adding them as 4 new CL terms, for practical reasons as they would be easier to track. However, I had a look at CxG and the VIP neurons and only the LBH-VIP, and ADAMTSL1-VIP coincide with specific VIP clusters, so their markers do not fully coincide with the scRNA-seq data from Jorstad. Personally, I would prefer to adding them as CL terms. However I am not opposed to the idea of mentioning them just in the comments section (or completely ignore them)

2) The second point of discussion is related to the grouping of some VIP neurons found in CL:

AvolaAmg commented 5 months ago

@dosumis please review. @aleixpuigb @Caroline-99 @JABelfiore please review (except the text definition).

dosumis commented 5 months ago

For lineage (CGE) -

AvolaAmg commented 2 months ago

Regarding the points of discussion: After a call with the authors of the paper I have decided to add the 4 VIP cell types as new CL IDs.

The main point of the ticket is to re-draft the text definition of VIP interneurons as t-type. @dosumis please review the ticket, so that I can turn it into a PR.

dosumis commented 2 months ago

Please go ahead and make PR(s) with the new defs and terms.