Maggie Lewis

August 2021

When my students ask why I pursued science, I always tell them it is because science helps me make sense of the world around me. My experiences this summer in the Salama Lab at Fred Hutchinson Cancer Research Center has helped me make sense of my world in ways that I hadn’t even anticipated when I first started.

My maternal grandfather suffered terrible pain for his entire adult life from a stomach ulcer. Although he passed away when I was very young, his presence - and his ulcer - still make themselves known in my life. To this day, I don’t consider dinner to be a complete meal unless there is a side of bread served and a glass of milk. Both of those were unsuccessful home remedies that my grandfather - and his family - tried to treat his ulcer with the incorrect thinking at the time being that these foods would help soak up the acid in his stomach. These dietary restrictions were actually some of the milder treatments that my grandfather tried. The more extreme treatments included a major surgery aimed at cutting the pain receptors to his stomach. This operation ultimately ended up as unsuccessful as milk and bread with meals, although much more invasive. It wasn’t until 1982 that Dr. Barry Marshall and Dr. Robin Warren first discovered that the Helicobacter pylori bacteria was the cause of most ulcers. So, my grandfather and his doctors couldn’t have known in the 1960s and 70s that his illness was most likely caused by this tiny, helical shaped bacteria and many of his symptoms could have been treated simply with antibiotics.

My grandfather was actually one of the luckier ones. H. pylori infections are also associated with various stomach cancers and it has the distinction of being the only bacteria classified by the International Agency for Research on Cancer as a carcinogen. The bacteria is thought to be transmitted in childhood, through oral routes, and may be asymptomatic in some individuals. In looking at the ripple effect of my grandfather’s ulcer (and his likely H. pylori infection), I’ve wondered who else in the family he may or may not have transmitted his H. pylori to? And, if he did transmit to his family members, why was he the only one to suffer the symptoms?

The fact that H. pylori can successfully colonize and cause symptoms in some individuals but not in others has been a driving force in the research I participated in this summer in the Salama Lab as a participant in the Hutch Fellowship for Excellence in STEM Teaching. Typically, H. pylori is helical in shape but various mutations can result in bacteria that are straight or curved rods. Previous research done in the Salama Lab has examined H. pylori swimming speeds in cell shape mutants. Findings from these experiments have shown that the helical, wild-type bacteria are better able to move further in jelly-like media that mimics the stomach’s mucous layer. The conclusion from this and other research is that the cell shape of H. pylori can impact whether the bacteria can effectively colonize the stomach lining. If H. pylori is unable to colonize the stomach, this could be a way to prevent disorders such as ulcers or gastric cancers. Therefore, understanding the genes involved with determining the helical shape of H. pylori is of critical importance.

The research I participated in this summer zeroed in on the genetics that control a cytoskeletal protein known as CcmA. CcmA is a bactofilin, a class of proteins found in (as the name would imply) bacteria like H. pylori. One of the driving questions of my summer research is how does the ccmA gene control cell shape? An H. pylori cell mutant made in the Salama lab that was a ccmA knockout resulted in a loss of the signature curlicue corkscrew shape and instead produced rod-shaped cells that more closely resembled hot dogs. It was hoped that further research could drill down even further to determine how CcmA functions.

One way to begin to understand how a protein functions is by mutating certain amino acids and seeing how they change the function of the protein. Previously at my lab, PhD student Sophie Sichel (who served as my mentor this summer) had engineered different strains of H. pylori with single amino acid changes in CcmA. One of those strains changed an amino acid in the ccmA gene from an arginine to a histidine, which resulted in a changed cell shape. However, the switch from arginine to histidine was potentially not as dramatic as it could be since both amino acids were of a similar charge and size. One of the summer projects I worked on in partnership with Amanda Rainwater, another Teacher Fellow also working in the Salama lab, was to create a new strain of H. pylori but this time instead of making the change to histidine, it would be changed to alanine. By comparison to histidine and arginine, alanine is a neutral amino acid that could have possibly resulted in a more significant change to the cell’s phenotype.

The second project I worked on this summer also built upon questions raised from another mutant strain made in the Salama lab. In this mutant, the CcmA protein was truncated by deleting a half-dozen amino acids, which also resulted in H. pylori cells with a changed cell shape. However, questions remained: were the changes seen in the phenotype a result of the specific amino acids that were missing or was it simply because the CcmA protein was shorter than it typically would be? To answer that question, my project would create another H. pylori strain that was an alanine scan of this same short region of CcmA - this time instead of deleting these amino acids, they would be replaced by alanines. Alanine was, once again, chosen for this job because it was a small, neutral, unassuming amino acid that could serve as a placeholder or stand-in for the deleted amino acids.

One significant thing that I learned this summer was about the ongoing nature of science. Unlike the school year, which comes to a screeching halt in June, the results of one experiment typically raise questions that lead into a new experiment. Our work on the alanine scan is ongoing - it isn’t easy to swap out a half-dozen or so amino acids. It’s actually pretty technically challenging to change even just one amino acid and requires using a variety of bench techniques, including many skills that were completely new to me like SOE-PCR, site-directed mutagenesis, SDS-PAGE, and working with a microscope that magnifies samples 1000 times.

Despite challenges along the way, we were able to see the outcome of the arginine-to-alanine mutant and were able to see for ourselves how one small amino acid change can result in a big difference in phenotype. This mutant showed similarities to the histidine mutant made previously in the lab, although it was slightly longer which was a somewhat puzzling finding given that CcmA controls curvature and a completely different set of proteins control cell length. Like many aspects of science, my work this summer has generated many more new questions and avenues for further research.

My work at Fred Hutch as a part of the Hutch Fellows program this summer has left me inspired to share my experiences with my biotechnology students at Kamiak High School this upcoming school year. My plan is to incorporate my experiences working in the lab into richer, project-based experiences for high school students so that they, too, can make sense of their world in ways different from which they may have initially expected. I plan to include in my biotechnology curriculum a stomach cancer case study that follows a fictional H. pylori patient whose medical history is similar to that of my maternal grandfather. The goals of these lessons are to give students an opportunity to better understand the relationship between genes and proteins and, hopefully, understand how one small amino acid can make a big difference.

Photos by Maggie Lewis, Fred Hutchinson Cancer Research Center, 2021.