[ENQ] Need help mapping cell types to CL

[brittneydwick]

Hi there,

I am working on a dataset from "Cross-tissue immune cell analysis reveals tissue-specific features in humans" Domínguez Conde et al. Science. 2022.

I am feeling uncertain about which CL terms to map the following cell types to or if we may need to add a new term for these:

cycling cell erythophagocytic macrophage intestinal macrophage

Below are terms that I've mapped to CL terms, but I'm not sure if they are correct. I would appreciate any feedback.

original annotation => CL term Tgd_CRTAM+ => gamma-delta T cell CRTAM+ Tnaive/CM_CD4 => naive T cell, central memory CD4+, alpha-beta T cellcentral memory T cell Tnaive/CM_CD4_activated => naive T cell, central memory T cell Trm_gut_CD8 => effector memory CD8+, alpha-beta T cell

If it helps, this paper identified cells using CellTypist.

[paolaroncaglia]

Hi @brittneydwick ,

Thank you for your ticket. My contract for HCA ontology work was completed as of May 31st, so I'll remove my assignment, and I'll tag and assign @bvarner-ebi. I'll leave Zoë co-assigned for now, but I know that she's on annual leave this week. One of them will be able to assist you. Thank you and take care,

Paola

[ghost]

Hi @brittneydwick,

Thank you for the inquiry. To address the first part of your question...

I have not found existing cell types in CL that represent cycling cell or erythophagocytic macrophage. There are specific cell types that are erythrophagocytic macrophages, but I don't see a grouping class for them. Feel free to submit new term request tickets for those.

For intestinal macrophage, would gut-associated lymphoid tissue macrophage or any of the subclasses be appropriate for your needs?

[brittneydwick]

Hi @bvarner-ebi,

Thank you for looking into this for me! Sounds great, I will submit new term requests for cycling cell and erythophagocytic macrophage.

For intestinal macrophage, I was hoping to find a more general term than the one you suggested. Would it be possible to submit a term request for that cell type as well?

Would you also be able to provide feedback on the following cell types I mapped here: "_original annotation => CL term Tgd_CRTAM+ => gamma-delta T cell CRTAM+ Tnaive/CM_CD4 => naive T cell, central memory CD4+, alpha-beta T cellcentral memory T cell Tnaive/CM_CD4_activated => naive T cell, central memory T cell Trm_gutCD8 => effector memory CD8+, alpha-beta T cell"

Thanks! :)

[ghost]

@brittneydwick, as always feel free to create "New Term Request" tickets in the CL repo. If any are urgent, kindly add a "high priority" label since we are working through a backlog.

I asked in the 'cl-editors' channel for someone who may have more knowledge about immunology to provide feedback on your mappings. If no one volunteers, I'll will do some research and give feedback.

[addiehl]

I will look into these cell types. --Alex

[brittneydwick]

@addiehl Thank you so much, Alex!

[brittneydwick]

Hi @addiehl,

Just checking in to see if you had the chance to look at this! Thanks.

[addiehl]

Today, I promise

[brittneydwick]

Hi @addiehl,

Just checking in on this.

[ghost]

@addiehl, if you don't have bandwidth for this, can you recommend someone else who can take a look?

[addiehl]

1) I don't believe 'cycling cell' belongs in the Cell Ontology at all, as it is too general and very much a phenotypic description that is not tied to a specific cell type.

2) 'erythrophagocytic macrophage' refers to any macrophage that is capable of phagocytosis of erythrocytes, which is really a functional characterization of a macrophage. The authors of Domínguez Conde et al. as well as earlier papers say that macrophages in multiple locations in the body, including the liver 'Kupffer cell' and the 'splenic red pulp macrophage' are capable of this process.

We can define 'erythrophagocytic macrophage' as "A macrophage capable of phagocytosis of erythrocytes." with the following equivalence axiom: macrophage and 'capable of' some 'erythrocyte clearance'

('erythrocyte clearance' GO:0034102 defined as "The selective elimination of erythrocytes from the body by autoregulatory mechanisms." Source: PMID:12905029, PMID:14754397, GOC:add)

When we run the reasoner, we will magically see that 'Kupffer cell' and 'splenic macrophage' are now subtypes of 'erythrophagocytic macrophage' because someone (GOC:add, probably, and probably a decade or more ago) had already thoughtfully given them the logically axiom 'capable of' some 'erythrocyte clearance'.

3) 'intestinal macrophage' is very general. The DL query macrophage and 'part of' some intestine returns 6 cell types: 'Peyer's patch macrophage' 'anorectum macrophage' 'appendix macrophage' 'colon macrophage' 'gastrointestinal tract (lamina propria) macrophage of large intestine' 'gastrointestinal tract (lamina propria) macrophage of small intestine'

We could create a general 'intestinal macrophage' with the logical axiom macrophage and 'part of' some intestine for use in data annotation for this paper, although we sort of, kind of, decided at some point to try to avoid general cell types like brain cell, kidney cell, etc., and arguably the intestines are not even one organ, but several. But since Uberon groups all the varied bits of the gut together under 'intestine', let's just go ahead and make this cell type.

I'll try to deal with the T cell part tomorrow.

[ghost]

Hi @addiehl, checking to see if you have additional feedback on this ticket. @brittneydwick, do you require any additional feedback?

[addiehl]

I recommend annotating Tgd_CRTAM+ to 'gamma-delta intraepithelial T cell' or just 'mature gamma-delta T cell'. I can't find a lot of literature about the expression of CRTAM on gamma-delta T cells, although some sources say it is expressed on subsets of gamma-delta T cells in passing. Without better experimental evidence, I can't support creating a new cell type for CDTAM+ gamma delta T cells. If someone can provide a strong reference, that would be good.

Tnaive/CM_CD4 seem to correspond to TMNP cell type identified in PMID:27270402(in Nature). We can probably create a new subclass of memory T cell (not naive) based on that reference.

Tnaive/CM_CD4_activated would be a subclass of the TMNP cell type, like 'TMNP, activated'. We could create this based on analogy with other activated T cell classes we already have, although this is more a cell state than a cell type.

Trm_gut_CD8: We don't have any tissue resident memory T cell classes. These are probably needed, rather than mapping to effector memory T cells. PMID:25526304 would be a starting point for working on these classes, though certainly other references exist.