[NTR] intestine resident memory T cell

[dosumis]

Please check that the term does not already exist by using the ontology search tool OLS:
https://www.ebi.ac.uk/ols4/ontologies/cl

Preferred term label

intestine resident memory T cell

Synonyms (add reference(s), please)

Definition (free text, with reference(s), please. PubMed ID format is PMID:XXXXXX)

A memory T cell that is resident in the intestine

Parent cell type term (check the hierarchy here https://www.ebi.ac.uk/ols4/ontologies/cl)

memory T cell

Anatomical structure where the cell type is found (check Uberon for anatomical structures: https://www.ebi.ac.uk/ols4/ontologies/uberon)

Your ORCID

Additional notes or concerns

These come in CD4 and CD8 flavours - should these be grouped?

From Perplexity:

Structure
Markers: Gut TRM cells are characterized by the expression of markers such as CD69 and CD103. CD69 is involved in tissue retention by inhibiting the sphingosine-1-phosphate receptor 1 (S1PR1), preventing cell egress. CD103 (αE integrin) binds to E-cadherin on epithelial cells, anchoring TRM cells to the gut epithelium125.
Subsets: TRM cells in the gut include both CD8+ and CD4+ populations. CD8+ TRM cells predominate and exhibit cytotoxic functions, while CD4+ TRM cells contribute to cytokine production and immune regulation25.
Transcriptional Regulation: Gut TRM differentiation is influenced by local signals such as TGF-β, which upregulates CD103 expression. Transcription factors like Blimp-1 and Id3 further regulate their effector and memory potential15.

Location
Gut TRM cells are found primarily in two key compartments:
Intraepithelial Layer: CD8+ TRM cells are abundant here, closely interacting with epithelial cells to monitor for infections.
Lamina Propria: Both CD4+ and CD8+ TRM cells reside here, contributing to broader immune regulation and cytokine production19.

[dosumis]

@addiehl - please comment. I think we need your input before Jasmine can work on this.

[addiehl]

I disagree with creating a 'intestine resident memory T cell' grouping class, which is too broad, as these are conventional alpha-beta T cells.

The paper "Human intestinal tissue-resident memory T cells comprise transcriptionally and functionally distinct subsets" (references 125 and 25 in the Perplexity derived text above), clearly identifies four subtypes of intestine resident memory T cells, which could be named in CL as follows:
CD103-positive, CD8-positive, alpha-beta intestine tissue resident memory T cell
CD103-negative, CD8-positive, alpha-beta intestine tissue resident memory T cell
CD103-positive, CD4-positive, alpha-beta intestine tissue resident memory T cell
CD103-negative, CD4-positive, alpha-beta intestine tissue resident memory T cell

Probably we should handle these similarly to the set of T cells that have TEMRA as a synonym. Thus an appropriate grouping hierarchy might be
alpha-beta tissue resident memory T cell (new)
-----alpha-beta-positive intestine tissue resident memory T cell (new)
----------CD103-positive, CD8-positive, alpha-beta intestine tissue resident memory T cell (new)
----------CD103-negative, CD8-positive, alpha-beta intestine tissue resident memory T cell
----------CD103-positive, CD4-positive, alpha-beta intestine tissue resident memory T cell (new)
----------CD103-negative, CD4-positive, alpha-beta intestine tissue resident memory T cell (new)
-----lung resident memory alpha-beta T cell (new)
-----------lung resident memory CD4-positive, alpha-beta T cell (CL:4033038)
-----------lung resident memory CD8-positive, alpha-beta T cell (CL:4033039)

We need to add the broad synonym TRM all these cell classes as well.

As shown above, I am proposing the 'alpha-beta tissue resident memory T cell' as an important grouping class for the incoming tissue resident T cell classes. This class could have TRM as an exact synonym.

We use the axiom 'output of' some 'memory T cell differentiation' to identify memory T cells. This is a bit of a hack, but the markers broke down with the TEMRA cells as a reliable means to identify memory T cells (CD45RO vs CD45RA). In fact, we should add this axiom to CL:4030002 in order to get it put under 'memory T cell' by the reasoner.

There is a lot of complexity here and I am too tired to explain it all.
--Alex