Looking back, my summer research project was a great experience and has taught me many valuable skills as well as problem solving and the value of collaboration. I was able to put the skills I learned from my bioinformatics internship last summer into practice to compare amino acid transporter expression levels in human and mouse liver cancer. Working together, Dr. Bode, Dr. Yin and I were able to find, sort, analyze and interpret large datasets of the expression levels of solute carriers in both mouse and human liver cancer.
One of the surprises for me was the sheer volume of data that we had to cull through in order to extract the relevant solute carrier data. Each dataset that we downloaded contained the expression information for about 10,000 genes across a sample size of about 200 patients. Each sample was also replicated which meant even more data to sort. This meant that we had to extract only the information regarding the expression levels of the amino acid transporters and combine the replicate data. Thankfully, the amino acid transporters we were interested in studying were only coded for by around 64 genes, a much more manageable amount of data!
Although we are in the preliminary stages of our research, our findings suggest that there are significant quantitative differences between mouse and human solute carrier gene expression, but two of the solute carriers we were particularly interested in, ASCT2 and LAT1, appear to be enhanced in both human and mouse HCC. Moving forward with the project, one of the questions we will be seeking to solve is whether we can confirm our bioinformatics’ findings with living cells. Another question is – if so, what are the implications on mouse models because of the differences between mouse and human solute carrier expression?
Deeper analysis is needed to determine the most cogent mouse models for liver cancer research and to determine if the results from our bioinformatics’ data is confirmed in actual cells. We will move forward this fall by continuing to analyze our bioinformatics results to determine the quantitative differences for each solute carrier gene between mice and humans, and generate testable hypotheses which we will seek to confirm with more traditional methods such as RT-qPCR and Western blots to screen for RNA and protein expression levels respectively.
Thanks to the head start that my research this summer has given me, I will be able to accomplish the in-depth analysis that is necessary to find the most cogent mouse model for studying liver cancer therapies during my Senior capstone project. It is my hope that by finding the most analogous mouse model for human liver cancer, we will be able to better understand the functioning of potential drugs to treat liver cancer. It is also our goal to submit our novel findings to a scientific journal for publication later this year. It is my sincere hope that other researchers will benefit from our findings and use our discoveries as a foundation to build upon for many other scientific discoveries.