The Genetics of Starvation
An interview with PhD Student Jingxian Chen on tumor suppressors and her work.
Continuing with the theme of genetics and genomics, I had the privilege of interviewing Jingxian Chen, an extremely talented PHD student at the Baugh lab
Background
Before graduate school, Jingxian had an internship at Cal Tech’s worm lab. At this lab, Jingxian solidified her interest in worm studies and made the decision that she wants to do warm studies in whatever graduate school that she attends.
This is what led her to choose to work at Dr. Baugh’s lab at Duke University. The Baugh lab uses worms to understand how animals adapt to starvation using primary genetic and genomic approaches. The lab specifically tackles three questions:
How does nutrient availability affect growth and development?
How do animals survive starvation?
What are the long-term consequences of starvation? How might it lead to health issues in adulthood and even affect future generations?
One of the projects at the lab focuses on the relationship between tumor suppressor networks and starvation resistance. This project was very appealing to Jingxian because she was interested in the connection between these two distantly related topics.
Project
Jingxian’s project focused on two tumor suppressor genes called PTEN and RB. A tumor suppressor gene is gene that regulates a cell during cell division and replication. This is important because if the cell grows and divides uncontrollably, it will result in cancer. This is why when you look at a lot of tumor patients, their tumor suppressor genes are usually mutated because that suppressing is lost and the cells are allowed to grow uncontrollably.
PTEN is one of the most frequently mutated tumor suppressor gene in humans and mice. While both of these genes have extensive functions in a variety of system, there is no established connection between the two. The first objective of Jingxian’s project was trying to link these two genes. Although this project is currently in its early stages, Jingxian actually already found that PTEN can regulate RB in worms.
Jingxian’s study employed worms at the first larval stage (L1) for a specific reason. These L1 worms exhibit a unique characteristic: they remain static in terms of growth and development in the absence of food. As soon as they emerge from the embryo, their development enters a consistent phase. This exceptional trait enables scientists to thoroughly investigate specific properties within these worms, ensuring a stable and controlled experimental environment for their research.
Using both of these tumors suppressor genes and L1 worms, Jingxian project studies starvation resistance in worms. In fact, the lab already found that the presence RB increases the worms’ sensitivity to starvation. This is an important finding because as mentioned before, they already found that PTEN can regulate RB, meaning that if you lose PTEN, you also lose RB. Thus, the team only needs to pinpoint and inhibit the factor that causes the loss of PTEN so that they can both prevent the loss of RB, and fortify the worms’s ability to respond effectively to nutrient scarcity.
Methods
The key techniques that allowed Jingxian to uncover these results were as follows:
Jingxian found the connection between PTEN and RB based on their protein levels. Western blot was the specific technique that allowed Jingxian to detect these protein levels.
In traditional bulk RNA sequencing, you have a huge amount of RNAs; however, since our current sequencing technologies can not handle that long of a molecule, we chop those RNAs up and sequence each segment. Afterwards, you piece the information together into a long strand of RNA and you get your results. While this may work for RNAs, this does not work for proteins because their compositions consist of four different levels.
While mass spectrometry is too complex of a tool for me to accurately explain, here are two excellent sources that can explain it far better than I can: explanation from the Broad Institute, and explanation from Microbe Notes.
PCR (Polymerase Chain Reaction)
This is a molecular biology technique that is widely used to amplify or make copies of a specific DNA segment. The process starts with denaturation, where they heat the DNA sample to a high temperature (around 94-98°C). This step causes the DNA double-strands to separate into single strands. This is important because the single-stranded DNA will serve as templates for DNA synthesis. The next step is annealing. The temperature is now lowered to around 50-65°C and short DNA segments called primers are added to the reaction mixture. These primers are designed to bind to the target DNA segments. These primers provide a starting point for DNA synthesis. The final step is extension. The temperature is then raised to around 72°C. In this step, a DNA polymerase enzyme starts making new DNA strands that match the single strands of DNA. The DNA polymerase adds nucleotides to the primers in a sequence following the pattern in the original DNA. As a result, we now have two new DNA strands, one for each single strand we had at the beginning.
Challenges
The only main challenge in Jingxian’s experiment was regarding PTEN. PTEN itself is actually an enzyme, meaning that it catalyzed and acts on different proteins, which is why its called a tumor suppressor network. It is not necessarily a direct connection between PTEN and RB, but it could be that PTEN actually affects something that in turn affects RB. At this point, Jingxian is trying to dins one connection between in the large tumor suppressor network. Fortunately, there is some information from literature on mammalian systems that implied what might be the linker between PTEN and RB. However, this link has yet to be validated in worms. Jingxian is currently seeing if this factor is really the linker between PTEN and RB in worms.
Conclusion
In the final segment of our interview, Jingxian and I discussed an interesting technique called 3D sequencing and her advice on how to read scientific papers. As we know, some non-coding DNA (DNA that do not participate in the transcription and translation process) can actually play an important role in dictating our traits by affecting the DNA that do code for RNA. The problem lies in pinpointing those DNA. Since our DNA and thus our entire genome is in a coiled shape, we can use 3D sequencing to uncover the shape of our genome. A DNA that would normally be really far away in a linear model of a genome can actually be right next to another DNA in this coiled shape, possibly revealing connections that we would have never guessed before. The only reason that this technology is not always used is because it is expensive and some experiments just do not need structural information.
Finally, for people who are interested in learning more about topics in the scientific space, research papers are a perfect way to gain insight into a variety of fields and learn about different techniques. The problem lies in understanding their complex and intimidating jargon. For Jingxian, the key was to just constantly keep reading them no matter how little you understand at first. Eventually, as you look up and begin to understand all the terms and language, these papers will eventually become easier and you will understand more. At the start, read through the entire paper top to bottom. As you get more advanced, Jingxian is just simply able to look at the figures and get a general idea of the paper’s premise.
I think that this idea of constant practice can apply to all aspects in life. Whatever skill you are trying to perfect or even get into, practice is the only way that you will find success in it. If you think that you are interested in a certain scientific field, the only way to know if you truly love it is to practice and try some things out. I leave you with a quote that I like from Stephen King: “Talent is cheaper than table salt. What separates the talented individual from the successful one is a lot of hard work.”