[Synonym] Tconv --> alpha-beta T cell

[twhetzel]

CL term alpha-beta T cell, CL:0000789

Synonym to be added (include synonym scope broad/exact/narrow/related and reference(s)) conventional T cell, Tconv

needed for INCLUDE cc @lopierra

[addiehl]

What is INCLUDE?

[dosumis]

Hi Trish, Would you be able to provide a reference to support the new synonyms? Thanks.

[twhetzel]

Hi David and Alex,

This excerpt[1] contains some information. On the first page is says:

T lymphocytes that express an αβ T cell receptor (TCR), as well as a co-receptor CD4 or CD8, are present in the peripheral blood, lymph nodes, and tissues (such as the skin), and are considered conventional T cells.

However, after a bit more research I see (also in this reference) it says: Another subset of unconventional T cells is that of the invariant natural killer T (NKT) cell... and mature NK T cell is a alpha-beta T cell so perhaps the label "conventional T cell" should be modeled to include "CD4-positive, alpha-beta T cell", http://purl.obolibrary.org/obo/CL_0000624 and "CD8-positive, alpha-beta T cell", CL:0000625 and not applied as far up the hierarchy as I have originally suggested.

INCLUDE is a project I am working on as a member of the TISLab.

[1] https://link.springer.com/chapter/10.1007/978-1-84800-165-7_6

[addiehl]

Hi Trish, Although I don't have online access to the chapter you cite, I do know a little about immunology. What the authors are trying to capture when they talk about conventional vs non-conventional T cells goes beyond marker expression, particularly in regards to alpha-beta T cells bearing CD4 or CD8. Conventional T cells generally have a full range of variable gene segments represented in their T cell receptors, are generally directed towards MHC Class I or MHC Class II bearing peptide antigens, and can be found in the blood, lymph nodes and other lymphoid tissues, and in other tissues throughout the body during an immune response.

Unconventional T cells typically bear an alpha-beta or gamma-delta TCR that relies upon a limited range of V gene segments and are often specific for a limited repertoire of antigens, including non-peptide antigens such as lipids, which are often presented via a non-classical MHC Class Ib molecule. These T cells are often tissue resident in the gut or elsewhere and in many cases do not go through T cell education in the thymus.

I don't fully see the value in trying to apply conventional versus non-conventional to any higher level T cell class in CL, as the distinction goes beyond simple marker expression. We could pick out particular more specialized hierarchies of T cells and label them in some way, as conventional or unconventional, although using synonyms is probably not the best way to do this.

Conventional T cells include 'CD4-positive helper T cell' and subclasses

Unconventional T cells include 'mature NK T cell' and subclasses 'intraepithelial lymphocyte' including subclasses 'alpha-beta intraepithelial T cell' and subclasses 'gamma-delta intraepithelial T cell' and subclasses 'dendritic epidermal T cell' 'mucosal invariant T cell'

The problem is that we have many T cell classes that do not neatly fit in the conventional/unconventional paradigm: 'CD4-positive, alpha-beta cytotoxic T cell': This includes conventional CD4 T cells that have cytotoxic function (many do actually), as well as certain 'mature NK T cell' subclasses that are considered unconventional.

'CD8-positive, alpha-beta T cell': Most of the existing classes in CL under this class are probably considered conventional, but CL is missing some unconventional subclasses here as well, such as "NK-Like CD8(+) T Cells" (PMID:28396661). Actually this paper has a nice opening sentence: "Unconventional T cells are defined by their capacity to respond to signals other than the well-known complex of peptides and major histocompatibility complex proteins."

My recommendation is that we choose not to impose conventional vs. unconventional as synonyms, but if it is important to you to include this distinction, we might try to capture this in some other way, as specialized comment or subset.

Thanks, Alex

[twhetzel]

Hi Alex,

Thanks for the detailed response. I agree with you that using a synonym (as I learn more about these cells) is not a relevant way to include this information. When I first wrote, I thought all children could be considered conventional T cells however that is not the case. Note, in the reference I posted initially it does say that CD8+ cytotoxic (TC) (or “killer”) lymphocytes are Tconv. Adding a subgroup annotation seems like that would be a useful way to include information about conventional and unconventional T cells.

[ghost]

@twhetzel, thank you for this issue. Are there any pending action items for this issue or can it be closed?

[twhetzel]

If you have an existing pattern, e.g. subgroup, etc., that makes sense to use to add an annotation for conventional and unconventional T cells I see that could be useful when searching. However, it is not critical for me currently. Thanks for the helpful discussion!

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