NTR: tunneling nanotube

[lubianat]

Please provide as much information as you can:

• Suggested term label: tunneling nanotube

• Definition (free text) A cytoplasmic projection that has a straight, bridge-like structure and mediates the intercellular transfer of compounds between cell pairs.

• Reference, in format PMID:#######

  • Original observation: PMID:14963329
  • The main reference for the description above: PMID:24778759

• Gene product name and ID to be annotated to this term NA

• Parent term(s) GO:0120025 - actin-based cell projection

• Children terms (if applicable) Should any existing terms that should be moved underneath this new proposed term? NA

• Synonyms (please specify, EXACT, BROAD, NARROW or RELATED)

  • EXACT --> TNT (https://pubmed.ncbi.nlm.nih.gov/37249209)

  • EXACT --> intercelular nanotubes (https://pubmed.ncbi.nlm.nih.gov/22216308)

• Cross-references NA

• For enzymes, please provide RHEA and/or EC numbers. NA

• Can also provide MetaCyc, KEGG, Wikipedia, and other links. https://en.wikipedia.org/wiki/Tunneling_nanotube

• Any other information

The Wikipedia article treats cytonemes (https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0035230) as TNT-like projections (https://en.wikipedia.org/wiki/Cytoneme).

The review cited as reference divides them and other TNT-like structures. There might be some extra modeling necessary.

It could be reasonable to model like:

• cell membrane bound cellular projection:
  • TNT-like projection
  • TNT
  • cytoneme (re-organized in the GO hierarchy)
  • streamer (new term)
  • nanopodium (new term)

For the two last terms there seems to be less supporting literature, so maybe they should not be curated at the moment.

In any case, I am not an expert in such projections. I just found the TNT structure to be missing in GO and though about sharing.

[raymond91125]

It seems to me that it is not trivial to come up with necessary and sufficient definitions for TNT and TNT-like projections. e.g. wikipedia:Cytoneme says that TNT is a type of filopodia but the review (Table 2) indicates that TNT and filopodia are distinct. PMID:14963329 states "These structures facilitate the selective transfer of membrane vesicles and organelles but seem to impede the flow of small molecules. " Has this been refuted? Are there gene products that can help to distinguish between these structures? If not, do we want to strive to model them now?

[cmungall]

@lubianat do you have a use case such as distinguishing between different cell types?

[lubianat]

No application in mind, and I don't think there are particular markers of the structure. I think this would be a low-priority ticket.

I was reading this article about mRNA transfer between cell types (https://www.jidonline.org/article/S0022-202X(19)31568-4/fulltext) trying to understand some scRNA-seq data and it popped up.

I hadn't seen a mention of the structure before, but there seem to be quite a few mentions of the terms in the literature (66 on PubMed).

The only use I see in the moment is generic (e.g. for entity grounding in text annotation).

[pgaudet]

Maybe we shouldn't create this term then, it seems like it will be difficult to annotate, without a clear, unique description.

[raymond91125]

Thanks for the comments. We can reopen this ticket when annotations are ready to be made.