Loinc 13336-3: "CD4+CD45RA+ cells/100 cells in Blood"

[nicolevasilevsky]

Suggest creating a new term for Loinc: 13336-3 [CD4+CD45RA+ cells/100 cells in Blood]
New term label: Abn CD4+CD45RA+ T cell count
New term comment (if any): and need increased class (need to look up if the downregulated term is needed too)
Your biocurator ID for loinc2hpo (if desired): HPO:nvasilevsky

[pnrobinson]

Human mature CD4+ T cells are functionally heterogeneous and can be divided into naive and memory/effector populations based on the expression of cell surface markers. Although the most significant differences between these two populations are functional, the leukocyte common Ag (CD45) was promoted as a potential marker of memory T cells. CD45 Ag may be found in various isoforms depending on alternative splicing of three extracellularly expressed exons. The expression of the highest molecular weight isoform, referred to as CD45RA, defines the population of CD4+ unprimed lymphocytes. Activation of naive lymphocytes through TCR engagement is followed by loss of CD45RA Ag and transition to the expression of the smallest molecular weight isoform CD45RO. These primed cells express high levels of activation Ags, acquire effector functions, and need less costimuli requirements for further activation. [PMID:12133935]

[nicolevasilevsky]

I think this should be annotated as:
'Abnormal proportion of naive T cells'
'Elevated proportion of naive T cells'
'Reduced proportion of naive T cells'

Does that seem correct @pnrobinson?

[pnrobinson]

Yes!

[nicolevasilevsky]

closing this ticket - this term is not needed, and I'll add this annotation in LOINC2HPO.

[pnrobinson]

but we do want the three terms noted above right? I think we can craft a definition from the citation above.

[nicolevasilevsky]

These terms already exist:
HP_0031396 'Abnormal proportion of naive T cells'
HP_0031398 'Elevated proportion of naive T cells'
HP_0031397 'Reduced proportion of naive T cells'

There is a comment on the abnormal term that describes the phenotype:
Following the development of T cells in the thymus, they enter the blood stream and recirculate between the blood and peripheral lymphatic tissues. Mature recirculating T cells that have not yet encountered their specific antigen are known as naive T cells. Mature T cell not yet exposed to antigen with the phenotype CCR7-positive, CD45RA-positive, and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low.

[pnrobinson]

Ok, we'll let's add Abn proportion of CD4+CD45RA+ cells as a synonym etc., I will also revise the comment to add some of the detail -- I will reopen for now,

[nicolevasilevsky]

Ok! Related to #4289

[pnrobinson]

done!

[nicolevasilevsky]

@pnrobinson - naive T cells could be CD4+ or CD8+. The synonym 'Abnormal proportion of CD4+CD45RA+ cells' should be a related synonym, not exact.

[pnrobinson]

changed to related synonym. Thanks for picking this up!