FAQ  •  Register  •  Login

separating type (lineage) and state (functional) markers

Forum rules
Please be as geeky as possible. Reference, reference, reference.
Also, please note that this is a mixed bag of math-gurus and mathematically challenged, so choose your words wisely :-)
<<

markrobinsonca

Participant

Posts: 11

Joined: Wed Apr 19, 2017 7:35 pm

Post Mon Nov 26, 2018 8:02 pm

separating type (lineage) and state (functional) markers

Hi all,

First, I wanted to say that Lukas' diffcyt framework has been updated ..

Preprint: https://goo.gl/mED5pa
Software: http://bioconductor.org/packages/releas ... ffcyt.html
Vignette: http://bioconductor.org/packages/releas ... kflow.html

Second, I wanted to solicit some feedback in relation to some feedback we received from reviews on the diffcyt paper. I posted this recently on Twitter (https://twitter.com/markrobinsonca/stat ... 5390495744), but I thought that this mailing list might be a more relevant place to ask my question. Below is more-or-less a cut-and-paste of it:

An interesting thread came through pretty strong from the reviewers .. and (ourselves) have gone back-and-forth on this discussion many times, so I thought I would spell it out a bit here ..

So, basically what we do in our cytometry "differential discovery" analyses (think: 1000s of cells for each sample, 20-50 markers measured, multiple samples across experimental conditions) is split the markers into "type" (those that we cluster on) and ..

"state" (not clustered on, but we are interested in type-specific changes therein). So, we frame the statistical problem as i) differences in abundance of cell types/clusters .. or ii) given a cell "type", changes in "state". The reviewers rightly challenged this ..

saying "I like the way that the authors propose to model [type] and [state] markers differently, although it’s not clear that this should always be done" and "there is no consensus in the field regarding the difference between ‘cell-type’ and ‘cell-state’" .. we totally agree!

But, we still think that a method should offer the capability to separate type/state (many don't). There are cases when it's clear. Re: sensitivity, the method should detect interesting differences no matter how the dichotomy is set and we think it helps interpretation.

Any opinions about this?

Thanks in advance and best regards, Mark
<<

mleipold

Guru

Posts: 5792

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Mon Nov 26, 2018 8:46 pm

Re: separating type (lineage) and state (functional) markers

Hi Mark,

Interesting question.

A few thoughts:
1. My initial thought is "type" = "surface phenotype" while "state" = "functional" (phosphorylation state, cytokine production, etc).
Granted, these aren't something that are *completely* separated: for example, cells that make a lot of cytokines often decrease expression of CD4 or CD3 as well, and express more CD69. But the order of operations of that (chicken vs egg) may not be straightforward without kinetic studies. Not to mention, short stimulations like for phosphoflow wouldn't change the surface phenotype of a cell....the length of stimulation before fixation to halt the stim is too short for protein turnover.

2. Using the above examples, it's also a bit different between phospho and cytokine/ICS, in that you are more likely to have a fairly uniform response in phospho than in ICS. By this I mean that if a particular stim makes one CD4+ starts phosphorylating FactorX, all or most CD4+ will also start phosphorylating FactorX.....the entire population shifts. In contrast, I don't think even PMA+I makes *every* CD4+ start making a particular cytokine.....certainly not every protein or peptide would stimulate every CD4+.

3. In terms of making your algorithm, does this "type" vs "state" really make a difference, or is this just a terminology question? I do think there's benefit to having both "the number of CD4+ cells increased after treatment" *as well as* "the number of CD4+ making IL-10 increased after treatment".....is that what you're asking?



Mike
<<

JamesW

Contributor

Posts: 37

Joined: Tue Nov 21, 2017 6:59 am

Post Tue Nov 27, 2018 5:09 am

Re: separating type (lineage) and state (functional) markers

Hi Mark,
Certainly, I agree that it is very useful to be capable of examining differential abundance of clusters and also identify differential expression of non-clustering markers within clusters. I think the only minor quibble is the terminology, in that “Type” and “State” are very movable terms. Depending on the question I am trying to answer I may well want to define the type as either a main lineage like CD4 or a sub-population such as Th1. Whether or not Th1 is a “type” or a “state” rather depends on your perspective so it might be better to use more neutral terminology.
By the way, nice paper! I’m still trawling through the vignettes but the combination of this with CATALYST seems quite handy.
Best,
James

Return to CyTOF data analysis

Who is online

Users browsing this forum: No registered users and 6 guests

cron