The PCA they show is probably capturing those differences instead of real differences given by disease status and, by the way, I question the usefulness of this PCA.
The only real statistical inference they show is on the pathway analysis yet no mention is made on the abstract. I suggest bringing this result up to the surface and making it more relevant even from the abstract. You can refer to it as methodological alternative, in the introduction, for the limited number of cases and lack of control group; issues that must be tackle in a larger study.