I don't think a case-control study is what you are looking for. A case-control study is by definition retrospective: you do it when you want to know what factors increase or decrease the likelihood being a "case" vs. a control. Here, your study appears to be prospective. That said, I don't think it made sense to administer treatment to healthy subjects (your control group) without knowing much more about what the treatment was supposed to do. If, as you say, $X$ is higher in tumour patients, then why have the need for comparisons with healthy patients? Is the treatment supposed to affect $X$ across the board regardless of whether one is a tumour patient? What is the hypothesized relationship between the treatment and $X$ in healthy patients, and again: why the need to study how $X$ changes in healthy patients? Is there a level of $X$ below which the person's health would be at risk?
If this study was aimed at evaluating the effect of a novel treatment on $X$--and I think this is what you are trying to do--then the ideal design would be to have tumour patients randomised into treatment or control (placebo), then taking baseline and endline measures for all study subjects. The control group should have been other tumour patients, not healthy patients.
Since you do not have a control group, one way you can still evaluate how the treatment affects $X$ is by fitting a fixed effects model just on the "cases" group (since we don't have post-data on the "control" group, it would have been hard to do the standard comparison, e.g. difference-in-differences, anyway).
Note that with fixed effects models, anything that doesn't change between time1 and time2 are differenced out of the model (excluded from the model), so be mindful of that when you build your model.