Qualifying Exam prep

or how I learned to attack problems

My qualifying exam (QE) is in three short days and it’s been quite interesting going through the process. For those lucky enough to not have heard of it, the QE determines if you are suitable to one day (far, far away) defend your PhD dissertation. Passing the QE means you’ve risen from the ranks of a lowly, marginally useful graduate student with no marketable skills to the level of a lowly, marginally useful dissertating graduate student with not marketable skills. At our institution, students must write an NIH style grant on a subject of their choosing and defend this proposal in front of three faculty members deemed experts on the topic. It’s kind of like that Shark Tank show without any of the niceties of Robert Herjavec softening the ego-shattering tongue lashings from Kevin O’Leary.

In reality, preparing for the QE has been a great way to learn how to evaluate my ideas in an extremely rigorous manner. Below I outline some of the approaches I have learned during the QE process and how it’s helped me think about problems (scientific and not) through a structured framework.

Define the problem

This turned out to be very difficult. I didn’t want to be too general in defining the problem, but at the same time I didn’t want to limit my self to a yes or no answer. So I went through a few iterations of the question I wanted to study starting with the broad: “What are common metabolic pathways that are essential to all cancers”. Glycolysis? Glutamine usage? TCA Cycle? Pentose-Phosphate-Pathway? Oh so nebulous …too many pathways to juggle in one proposal! After pairing it down a little more, I came up with a question I was fairly content with: “What oncogenic drivers determine the fate of glutamine usage in pancreatic cancer (PDAC)”. Much better. The problem becomes more focused on one metabolite in one specific cancer that has a lot of background literature on its oncogenic drivers.

What are the assumptions?

Once I had a grasp on what I wanted to study, I next considered what I assumed to be true of the question at hand. The field of cancer biology has assumed that all cancers use glutamine to fuel anaplerotic reactions through the TCA cycle, just at a higher rate than normal cells. However, this hasn’t been rigorously proven in the context of PDAC and it’s possible that glutamine usage is very different given the unique anatomy and microenvironment of the tumor. Boom. That was my angle built off of non-challenged assumptions.

Break it down

Next, I needed to break down my question into testable hypotheses. To start, I needed a rationale to show that PDAC use glutamine differently than other cancers. The answer to this question came from an old Nature paper that showed that PDAC cell lines can be rescued from glutamine deprivation by the addition of cell permeable glutathione, an essential antioxidant. I thought that was very weird because glutathione isn’t part of intermediary pathways through the TCA cycle. Aha! A hypothesis is born: I hypothesize that PDAC utilize non-canonical glutamine metabolism to maintain the redox balance in tumor cells.

Oh so testable! Determine potential pathways that can synthesize glutathione via glutamine or maintain reduced glutathione through NADPH production via glutamine. There are only a handful of known enzymes that can do this.

Awesome. But there was still the overarching question, what oncogenes are driving this yet-to-be defined pathway? Given that >95% of PDAC are KRAS mutated and that mutated KRAS is important to reprogram glycolytic metabolism, it seems feasible to believe that KRAS might be important in this metabolic rewiring. Boom second testable hypothesis.

Consider all outcomes — good and bad

Next I designed experiments to test each hypothesis. While I thought my experiment designs were the most brilliant thing since WhatsApp, my committee chair had a different idea. When I presented him the experimental design he seemed un-impressed. Maybe I didn’t sell it right or let the suspense build when I was describing it to him? Nope. He challenged me to consider all possible results from the experiments I proposed, not just the good ones. This was very uncomfortable for me as it meant my “brilliantly” designed experiments could fail. Not something I wanted to think about. But as uncomfortable as it was, it was the only way to truly master a topic — expect points of failure. But don’t stop there, figure out what that failure means and use it to guide your next experiments. In other words, dispassionately plan for failure as if it’s a certainty (but hope for the best!).

KISS — simple is ample

After a few iterations and meetings with my chair, I finally had a written proposal I could submit. Now began the hard part: the presentation. At first, I thought the process would be quite easy, just copy and paste the bullet points from the proposal. Ha! When I did that I had a 52-slide powepoint behemoth that even DropBox didn’t want. So, I presented it to my wife and realized my story had very little flow; it was the Soulja Boy of scientific story telling. Finding the weak point was very easy: I tried to make the story seem non-obvious, to the point where it was disjointed. I took out about 30 slides to get the point across as simply as possible. I wanted viewers to feel like they were part of the thought process as a linear series of events. That’s where I’m at right now and it’s bound to change a few more times before Tuesday, but I’m happy with the process and progress!

Now, passing the actual exam is a whole other question …