Discover Internships: Cancer Genetics Research

What do computers, the small intestine, and thousands of acronyms have in common? Check out Floyd L. Evans, Jr.’s narrative on his time with the Dabro lab to find out!

What do computers, the small intestine, and thousands of acronyms have in common? The answer: they are all crucial elements of my Experiential Learning Experience for Spring 2022. To understand how these elements can be used in a research project, one must understand what happens inside the body of every single person.

The human body is an elaborate machine. Undoubtedly, the many organs in the body, including the brain, heart, kidneys, small intestine, spleen, and lungs, work together so the body can stay alive and healthy. Every one of these organs, in addition to the many others, are all made of one special kind of miniature building block of life: cells. Not only are organs made of cells, but the cells also carry out many functions to keep these organs functioning properly. Cells must keep replicating at a steady rate to keep the organ alive, which helps keep the body alive. The cells will eventually die, but because they replicate at a moderate rate, the new cells replace the old ones, keeping the organ healthy. Cells maintain this steady rate because their genes, which are the instruction manuals for how cells must function, give them instructions on how often to reproduce. Unfortunately, some cells have mutations (mistakes) in their genes located in their DNA; this is especially a problem when those genes tell the cells to reproduce more often than they should. Because cells are obedient to their genes, they reproduce so much that the organ cannot function properly because the cells may overcrowd the organ. They hog resources from the rest of the organ and the rest of the body. They can even spread to other organs in the body and cause similar problems. If the organ(s) does not function properly for a long enough time, a patient may lose their life. Such is the unfortunate situation when these rogue cells, called cancer cells, appear. This is a terrible outcome for many patients. However, scientists have learned how to use a multitude of tools to battle specific kinds of cancer. This is where my research experience enters the story.

SQL queries to select genes present in two lists: a 30-gene table that we had found from our exome sequencing and another table from a graduate student. This would help use narrow down our list of possible candidates to explore.

Dr. Ben Darbro is a cancer genetics researcher at the University of Iowa. The kind of tumor he attempts to learn about is called a small intestinal carcinoid. As one would guess, small intestinal carcinoids are located in the small intestine. They arise from neuroendocrine cells, which are cells that have a neurological function and a hormonal function. The neuroendocrine cells in the small intestine are called Enterochromaffin cells. These enterochromaffin cells secrete serotonin. When the enterochromaffin cells become carcinoid tumors, they secrete an overabundance of serotonin, leading to a serotonin shock that induces symptoms such as anxiety, agitation, nausea, and even death. Although carcinoids are relatively tiny and well-defined tumors, a few cells from these carcinoids can break off and find other organs in the body to attach to and grow on. This is called metastasis. Unfortunately, as with many other cancers, small intestine neuroendocrine tumors often lead to death.

Fortunately, the Darbro lab has a strategy for helping more people survive these carcinoids. The Darbro lab takes cells from carcinoids, breaks the cells open, and extracts the DNA (instruction manual of the cell) from these cells. Machines and molecules can be used to perform exome sequencing. Exome sequencing is like genome sequencing, but it shows what every protein in the body should look like. If the Darbro lab can find out what mutation (mistake) occurred in the exome, they can find out what protein is functioning improperly. This understanding can help other scientists perform experiments and find ways to stop these proteins from wreaking havoc on the body.

My lab had found the exons from thousands upon thousands of genes from a particular family. Dr. Darbro used bioinformatics/computational tools that would compare and contrast the genetic sequence of these exons with what they were in healthy individuals. The computer’s tools were also able to identify specific kinds of mutations that we may have been searching for.

Pedigree identifying members of the family we studied who had a history of neuroendocrine tumors. This helped us make hypotheses about the kinds of genes that may be involved in the process.

This is when my slightly-less-than-one-school-year-long role became a part of the process. Since this was a computational genetics research experience, I usually spent my time in research in my home. Sometimes, I even did it in the car! Usually, during weekly Zoom meetings, I would learn about cancer or genetics from Dr. Darbro. I would also gain insights into how the various genetic tools worked and how their algorithms enhanced our ability to identify probable cancer-causing candidates. On my own, I would use a list of mutated genes that Dr. Darbro presented to me and learn about them in databases such as PubMed, Google Scholar, GeneCards, STRINGDB, and more. Using the information I learned about various genes, I presented my findings to Dr. Darbro. We used those to see whether our hypotheses about which kinds of genes may cause carcinoid formation were well-supported.

This experience truly fostered my self-discovery and personal growth in multiple ways. This provided me an opportunity to grow in knowledge. Though this was not a “hands-on” lab experience, it was extremely beneficial because much of the scientific process involves thinking about science, proposing hypotheses, and searching through literature. This was something I realized I grew in significantly through the past semester. I also enjoyed writing computer code to select desired gene names from thousands of gene candidates. As a double major in Microbiology and Computer Science, I was able to envision myself in such a career!

In conclusion, computers and biology are more related than recognized in previous generations. With a deep understanding of how cells work to help the human body, one can use the weapons of computer algorithms to stop cancer by cracking the genetic code deep within the cell!

Author Bio: Floyd L. Evans, Jr. is a just graduated at the University of Iowa with double majors in Microbiology (B.S.) and Computer Science (B.A.). He is from Tiffin Iowa. When Floyd is not writing computer programs, reading about microbes, or studying for exams, he enjoys his free time by spending time with his family, running, making and listening to music, or reading a great book.

Edited by: Abbey Jordahl, Honors Student Admin


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