cell proliferation

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e-mail from Pascale:

This all looks good to me.

One other thing is about the definition of cell proliferation, which currently is "The multiplication or reproduction of cells, resulting in the rapid expansion of a cell population." Can we remove "rapid"? and have "The multiplication or reproduction of cells, resulting in the expansion of a cell population." ??

(this may be relevant for people not on the development list)

Pascale

I can't see anything wrong with this suggestion. I'll implement in a week if nobody objects.

Thanks,

Jen

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/2575":https://sourceforge.net/p/geneontology/ontology-requests/2575

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As noted on the development list, please review the relevant email in the archive first!

m

Original comment by: mah11

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I have written to the go and development lists for comment on 13/6/5. Proposal to be implemented on 20/6/5.

Jen

Original comment by: jenclark

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Looks fine. One suggestion, instead of using "expansion of a cell population", I prefer using "increase in number of cells of same or group of different types of cells.""

Original comment by: jaiswalp

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I'm happy that that part of the definition is clear and non-circular, but I will change it if others prefer. Pankaj, can you take another look at that suggestion you've made? It's not clear what you mean.

Thanks,

Jen

Original comment by: jenclark

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Sorry for not being clear.

Def: The multiplication or reproduction of cells, resulting in the INCREASE of a cell NUMBER OF A GIVEN TYPE OR A GROUP OF CELLS OF DIFFERENT TYPES.

CAPS section is from this suggestion.

-Pankaj

Original comment by: jaiswalp

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I meant that your suggestion didn't quite make sense. Did you mean something like this?

def: The multiplication or reproduction of cells. This results in an increase in the number of cells of a given type, or an increase in number of cells in a group of cells of different types.

Jen

Original comment by: jenclark

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its fine. -pankaj

Original comment by: jaiswalp

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Splendid :-)

Jen

Original comment by: jenclark

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Wait! Don't implement this yet! I'm not sure that this is such a good idea. Shouldn't there be a distinction between cell division and cell proliferation? There was a big ol' discussion about this waaaay back (it's in the email archives somewhere) and I think it also came up during the cell cycle discussion. It may be worth consulting some dictionaries because I'm sure that 'proliferate' is associated with speed and quantity. It certainly is in my mental dictionary, anyway!

Original comment by: girlwithglasses

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I agree with Amelia that this should not be implemented until we hear some more comments.

The problem is that there is nothing in GO that captures 'growth rates' other than cell proliferation. The 'rapid cell proliferation' is reminescent of cancer growth and therefore SHOULD NOT be in the GO (as such).

I am not sure how other people use 'cell proliferation'.

Pascale

Original comment by: pgaudet

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PMID: 15939553 PMID: 15208345 PMID: 15155880

Here are a few plant examples. In plants the cell proliferation is often asociated to plant hormone regulation response.

Some more sources of definitions requested by Amelia are http://www.google.com/search?hl=en&lr=&q=define%3Aproliferation&btnG=Search

Original comment by: jaiswalp

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I personally don't care if the word "rapid" is removed from the definition, but I would point out that the expansion of lymphocyte populations upon encounter with antigen, for instance, certainly qualifies as a rapid expansion of cell population, and certainly the rates of cell division associated with developmental processes in both plants and animals are clearly rapid as well. In the right setting, bacteria too are capable of phenomenal rates of cell division. Thus, rapid expansion of cell population for me is not at all associated with cancer (some cancers in fact grow very slowly); what characterizes cancer is disregulation of cell division and apoptosis.

Removing the word "rapid" allows the definition to cover all rates of cell division without bias towards what different people feel rapid means in terms of their organism.

-- Alex

Original comment by: addiehl

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It sounds to me as if the 'rapid' should stay. Pascale, would you be happy to leave it in after what you've heard?

Jen

Original comment by: jenclark

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Further suggestions from the development mailing list:

Hi Jen,

The structure at the bottom looks good to me. I can't really think of how to deal with the multiple part-of relationships, but I think they are true. As for cell proliferation, I don't think it really matters if the word rapid is in the definition or not, since everyone can have a different view of rapid. I think the distinction between cell proliferation and cell division is a difference between an individual cell and a generic representation of cells. In that way, cell division could be a part of cell proliferation.

David

reply:

Hi David,

Yes I see what you mean.

Currently we have

[i]cellular physiological process ---[i]cell division ---[i]cell proliferation

cell division def: The processes resulting in the physical partitioning and separation of a cell into daughter cells.

cell proliferation def: The multiplication or reproduction of cells, resulting in the rapid expansion of a cell population.

This could become:

[i]cellular physiological process ---[i]cell proliferation ------[p]cell division

cell proliferation def: The multiplication or reproduction of cells, occuring as a consequence of multiple cell division events, resulting in the expansion of a cell population.

That way we lose the word 'rapid', but keep the distinction between cell division and cell proliferation.

Would that seem like a plan? I'll post it in the sourceforge item.

Thanks,

Jen

Original comment by: jenclark

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reply sent to list re suggestion:

> [i]cellular physiological process > ---[i]cell proliferation > ------[p]cell division

I think not -- it's better if the current structure does not change. Many cell division events take place in contexts that would not be considered proliferation (some have been mentioned in the old 'proliferation' exchanges).

Original comment by: mah11

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I agree completely with Midori. Cell division and cell proliferation were carefully separated during the cell cycle work and I would rather those changes weren't undone for a little while at least!

You could always make a cross product of cell division and cell proliferation if you want to have the connection between the two concepts - eg cell proliferation [p]cell division during cell proliferation ... cell division [i]cell division during cell proliferation

Original comment by: girlwithglasses

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Maybe it would help if I described what we are trying to capture when we use the "cell proliferation" term. There are many papers that have statements like " Cells overexpressing protein X exhibit a reduced growth rate in suspension culture " (PMID: 12074548).

So perhaps we need a new term, for example "cell multiplication", to decribe that process? And cell proliferation could be a child of that, when the multiplication occurs at an accelerated rate (compared to some basic multiplication rate for that cell type).

Another possibility is to remove 'rapid' from the cell proliferation term, and add a term "rapid cell proliferation".

To me, cell proliferation or cell multiplication include cell division.

Pascale

Original comment by: pgaudet

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I've done some digging in the mailing list archive and found that this def is discussed in a thread with subject line 'RE: high-level term definitions' around 19/7/01. I thought I'd mention in case anybody else wasn't there and wants to know what's gone before.

Jen

Original comment by: jenclark

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Bonjour Pascale -

Am I right in thinking that you're wanting a term to describe the growth of a cell population, but where the cells in question aren't part of an organism and hence can't be covered by the generic 'growth' term (def: The increase in size or mass of an entire organism, a part of an organism or a cell.)? From that line you quoted from the paper, it looks like you're wanting a term to describe negative regulation of cell population growth rate - is that right? In that case, aren't you really just talking about many examples of the division of individual cells being slowed down, ie. negative regulation of cell division?

Of course, it may be that the whole "life cycle" of the cell is being slowed down, so there's actually negative regulation of cell growth as well as of cell division.

Before I make things even more confusing, am I on the right track in thinking that you're wanting terms to describe up- or downregulation of cell population growth?

Amelia.

Original comment by: girlwithglasses

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For cell proliferation fans I have found another thread with subject line 'Re: cell growth and maintenance' on the go list of 30/6/03-ish that's worth a look.

Jen

Original comment by: jenclark

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Amelia,

you are definetly on the right track. The thing about cell division though is that the definition is "The processes resulting in the physical partitioning and separation of a cell into daughter cells." (which may just be wrong; this sounds like --- so it's too specific. And it's not necessarily "cell cycle "-type terms either. I would be looking for a parent terms of all these.

Does that make sense? Or are you thinking I should be using another term to capture this information?

Pascale

Original comment by: pgaudet

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Maybe we should be using 'cell cycle'?

I am looking for a term that would encompass cell growth and cell division. Maybe this is not universal enough?? Don't most cells grow and divide?

Thanks again,

Pascale

Original comment by: pgaudet

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Yes, I think I know what you mean - the cell division term is too specific as it's referring to the physical event, whereas the phenomenon you're trying to capture is that the whole life cycle of each cell in the population has been slowed down, and hence the growth rate of the population is lower. I know that the paper says that it's not involved in the cell cycle, but in a unicellular organism, isn't the cell cycle equivalent to the life cycle? Hmmmm.

Original comment by: girlwithglasses

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Ah, your comment appeared whilst I was submitting mine. Perhaps we should add something like 'life cycle of unicellular organism' as a related string (I don't dare say synonym...) for the term 'cell cycle'?

Original comment by: girlwithglasses

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The problem with 'cell cycle' is that people use cell cycle is articles (at least in Dicty papers) more like what we (at GO) think of as 'regulation of cell cycle'. That is, I am not sure anyone looking for changes in growth rates would search on 'cell cycle'. Mostly they would search on growth (but that is clearly a dicty biais). I thought proliferation was the next best thing.

I cannot beleive that this whole thing only applied to unicellular organisms. Surely other cells grow and divide???

Pascale

Original comment by: pgaudet

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> 'life cycle of unicellular organism' as a related string > for the term 'cell cycle'

would this adequately cover things like bacterial spore formation, or the nifty morphological changes that Caulobacter crescentus undergoes, or mating of unicellular fungi (considered part of the life cycle in budding yeast at least)?

In other words, the answer to the earlier question ... > in a unicellular organism, isn't the cell cycle > equivalent to the life cycle?

... might well be 'no'.

m (troublemaker me)

Original comment by: mah11

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Midori,

I agree that 'life cycle' is something else. Dicty can form a multicellular fruiting body, which generates spores that become ameobae after hatching, and that whole process is the dicty 'life cycle' --- not the cellular divisions that occur during vegetative growth.

Pascale

Original comment by: pgaudet

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For cell proliferation fans I have found another thread with subject line 'Re: cell growth and maintenance' on the go list of 30/6/03-ish that's worth a look.

Jen

Original comment by: jenclark

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Obviously cell cycle doesn't equate with life cycle for all unicellular organisms, and there must be unicellular organisms where the life cycle stages resemble those of the cell cycle, but biologists in the field wouldn't ever use the term 'cell cycle' in connection with the organism. It was just a thought as it might help curators faced with phenomena like retarded or accelerated population growth to work out what process is actually occurring.

Going back to Pascale's comments: > The problem with 'cell cycle' is that people use cell cycle > is articles (at least in Dicty papers) more like what we (at > GO) think of as 'regulation of cell cycle'. That is, I am > not sure anyone looking for changes in growth rates would > search on 'cell cycle'. Mostly they would search on growth > (but that is clearly a dicty biais). I thought proliferation > was the next best thing.

I think part of the trouble is that your papers are dealing with the dynamics of populations of individuals, and so the tendency is to think of things in terms of the population, rather than what's happening in each individual organism. Perhaps we need something like 'regulation of cell division during vegetative growth'? Or a broader term like 'regulation of cell growth and division cycle during vegetative growth' [1], plus a general term 'cell growth and division cycle'? It's a bit hand-wavey and vague, but could be useful for organisms which undergo cell cycle-like processes for some or all of their life cycle. The appropriate secondary strings (=GO synonyms) could be added to aid searching.

[1] comparable to existing term 'cellular morphogenesis during vegetative growth ; GO:0000903'

Original comment by: girlwithglasses

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Original comment by: jenclark

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The cell proliferation def has been adjusted in other work, so this is pretty much dealt with.

Original comment by: mah11

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Original comment by: mah11

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Original comment by: cooperl09

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The multiplication of cells, resulting in the expansion of a cell population.

' or reproduction ' is probably a non essential phrase.

Original comment by: jaiswalp