I came across some recent articles that suggest that the ratio of Th17 cells to T reg cells is important indicator of inflammation and autoimmunity. Would it make sense to use the markers CD3 (pan T cell marker) and CD25 (T reg cell marker) to determine cell population and conclude based on this the propensity for inflammation progression/autoimmunity?
There's a couple dangers of doing CD3 vs CD25 to measure general inflammation.
First and most important, CD25 (the IL2 receptor alpha chain) is upregulated on activated T cells, so if there is inflammation, it becomes less reliable as a Treg marker. This will make it hard to compare Treg to other T cells on the basis of CD25 alone (FoxP3 is better, but intracellular staining might not be feasible depending on your experiment).
Second, Th17 and Treg have a very tight relationship, and require many of the same cytokines to develop. This is likely why the Th17/Treg ratio is used: in an inflammatory environment, a common precursor will become a Th17, while in a tolerogenic environment, that precursor will become a Treg. Here's a paper on the Th17 vs Treg development if you are interested: https://www.nature.com/articles/pr2009119
But the short answer is that it would probably be better to look at FoxP3+ cells instead of CD25 for Treg to compare to other T cells, and probably better still to carefully define what inflammation means in your context (IFNg-producing T cells? IL6 in the blood? CRP? Infiltration of M1-polarized macrophages?) and then stain for that directly.
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