skeletal muscle satellite cell

[cmungall]

this is classified as a muscle precursor, but Al says this is not the case:

[Term] id: CL:0000594 name: skeletal muscle satellite cell namespace: cell def: "An elongated, spindle-shaped, quiescent myoblast that are located between the basal lamina and the plasmalemma of the muscle fibres. They are thought to play a role in muscle repair and regeneration." [GOC:tfm, MESH:A.11.635.500.700] is_a: CL:0000035 ! single fate stem cell is_a: CL:0000188 ! skeletal muscle cell is_a: CL:0000680 ! muscle precursor cell *****

Note also the text def says that this is a (quiescent) myoblast, but the relationships say that it develops_from myoblast.

Original comment by: cmungall

[cmungall]

The CL has a pretty broad definition of a muscle precursor cell (somatic, non-terminally differentiated cell that develops from mesoderm). Agreed definition for this term needs to change.

Original comment by: tfmeehan

[cmungall]

Some thoughts as I was looking at muscle satellite cell.

How to better deal with stem cells? In this case the muscle satellite cell has an alternate differentiation path where the myoblast instead of differentiating directly into a muscle cell becomes a satellite cell, with different morphology, gene expression etc, specific location, and then lays in waiting for the right moment to then become a muscle cell.

Currently, we don't do any autoclassification of developmental potential. Certainly cell types that can develop into another could be classified as a "precursor cell" (in this case muscle precursor cell). However, "steminess" is different, it is perhaps more a quality of a cell or a reflexive developmental property, whereby the cell is able to divide and reproduce the same cell type whilst spinning off potentially more differentiated types.

'skeletal muscle satellite cell' is currently multiply classified as a 'muscle precursor cell', a 'skeletal muscle cell' and a 'single fate stem cell'. 'skeletal muscle cell' is inferred as any muscle cell that is part of skeletal muscle. I don't think satellite cell qualifies...

Here is a nice review on classification of satellite cells in particular: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2967620/?tool=pubmed

Original comment by: mellybelly

[cmungall]

• assigned_to: David Osumi-Sutherland
• Group: --> GO-Cell-XP

Original comment by: cmungall

[cmungall]

Remember this one as being hard to classify as their is a debate to its role. This recent review considers them as adult stem cells

http://physrev.physiology.org/content/93/1/23.long

On 25/06/2014 00:45, Chris Mungall wrote:

• _assignedto: David Osumi-Sutherland
• Group: --> GO-Cell-XP

---

[cell-ontology-cl-requests:#204] http://sourceforge.net/p/obo/cell-ontology-cl-requests/204/ skeletal muscle satellite cell

Status: open Group: GO-Cell-XP Created: Tue Aug 07, 2012 09:16 PM UTC by Chris Mungall Last Updated: Tue Aug 07, 2012 09:16 PM UTC Owner: David Osumi-Sutherland

this is classified as a muscle precursor, but Al says this is not the case:

[Term] id: CL:0000594 name: skeletal muscle satellite cell namespace: cell def: "An elongated, spindle-shaped, quiescent myoblast that are located between the basal lamina and the plasmalemma of the muscle fibres. They are thought to play a role in muscle repair and regeneration." [GOC:tfm, MESH:A.11.635.500.700] is_a: CL:0000035 ! single fate stem cell is_a: CL:0000188 ! skeletal muscle cell is_a: CL:0000680 ! muscle precursor cell *****

Note also the text def says that this is a (quiescent) myoblast, but the relationships say that it develops_from myoblast.

---

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Terry Meehan, Ph.D. Project Co-Leader, Mouse Informatics tmeehan@ebi.ac.uk +44(0)1223 492 591 European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

Original comment by: tfmeehan

[cmungall]

When I worked on the muscle cells in CL last year, I was surprised to see skeletal muscle cell defined as any cell that is part of skeletal muscle, but decided not to question it. Under this definition it is correct to have satellite cells classified as skeletal muscle cells. Note that we have a separate term for skeletal muscle fiber (which is what you might expect skeletal muscle cell to refer to). For GO purposes, if we stick with the current CL def of skeletal muscle cell, I think it is still worth reviewing the GO terms to see whether they might more sensibly defined in terms of CL:'skeletal muscle fiber'.

A stem cell, in the strict sense, is a precursor cell that divides by budding - i.e. it retains its identity following division. However, stem cell is used more loosely to refer to precursor cells in general. I think we should have a term for stem cells in the strict sense, perhaps dealing with the looser usage via synonyms.

However, satellite cells don't fit neatly into this classification.

From the ref that Terry posted: "Close examination of satellite cell divisions on single myofibers revealed that satellite cells can undergo both asymmetric division and symmetric division (280)."

Which type of division they undergo depends on their microenvironment. So, perhaps best to have satellite cells as muscle precursor cells and make a new subclass for 'skeletal muscle satellite stem cell'. From skimming the ref, evidence for satellite cells forming other tissues in vivo (rather than in culture) looks sketchy. So I'd just ignore this issue unless/until better evidence emerges.

Original comment by: dosumis

[cmungall]

So satellite cells are thought to be "quiescent" until new muscle cells are needed, upon which time they de-differentiate and provide muscle precursor cells. Are these multipotent? what is their "steminess"? What is the role that the satellite cells have in the absence of repairing the muscle? There are subpopulations of satellite cells, and whether whether satellite cells are stem cells, committed progenitors, or dedifferentiated myoblasts seems yet to be definitively determined.

see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718740/

Also note that not all satellite cells may come from somitic mesoderm, some may also be derived from embryonic vasculature or in the adult from other tissues such as bone marrow (for example http://www.ncbi.nlm.nih.gov/pubmed/12437931)

Perhaps the question about how skeletal muscle cell is defined has to do with what people expect to return when they search on skeletal muscle as a tissue or organ. On a cellular level, it seems very odd to me to classify satellite cells as such - it would be like classifying a neural crest cell as a peripheral neuron. Agree about using 'skeletal muscle fiber' - that makes much more sense.

Other recent reviews: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0090398 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177780/

Original comment by: mellybelly

[cmungall]

Implemented: Added new subclasses of 'skeletal muscle satellite cell': 'activated skeletal muscle satellite cell' 'quiescent skeletal muscle satellite cell' 'skeletal muscle satellite stem cell'

This gives us suitable terms for defining satellite cell division/proliferation (not applicable if they are always mitotically quiescent). From the lit, it is clear that only a subset of these cells are true stem cells.

Have changed skeletal muscle cell in CL to 'cell of skeletal muscle'

Original comment by: dosumis

[amyleesterling]

What does it mean that "this is classified as a muscle precursor, but Al says this is not the case" ? Literally someone is running ML on cell classifications and it's learning how to improve ontologies?

[cmungall]

@amyleerobinson sorry only just noticed your comment now. In fact "Al" refers to a bloke called "Alistair", not an Artificial Intelligence!

We do use reasoners to classify ontologies, but these never learn (unfortunately), they just make inferences based on what you tell them and the logic of OWL.

In fact there are various approaches to automating and learning ontologies from data, text, etc. I think we are a long way from replacing human editors but if you're interested look up the work on Elyssa Chessler (ODE) and Trey Ideker (Nexo) for bioinformatics approaches, NELL for text-based and the work of Jens Lehmann's group on generalized class learning. I'm missing off a ton but that should get you started.

[paolaroncaglia]

Looks like @dosumis already edited as needed (https://github.com/obophenotype/cell-ontology/issues/384#issuecomment-112630091), so I'll close.