Jennifer Morrison

A Summer of Learning:

From Classroom to Cancer Research and Back Again

Inside the Markey Lab

This summer I worked in Dr. Kate Markey's laboratory, where I explored the fascinating intersection of the gut microbiome, hematopoietic stem cells, and cancer research. Dr. Kate Markey is a physician-scientist at Fred Hutch Cancer Center who bridges the worlds of medicine and research. As a blood and bone marrow transplant physician, she cares for patients with blood cancers undergoing stem cell transplantation and sees firsthand the challenges they face during recovery. She is an Assistant Professor in the Translational Science and Therapeutics Division and, in 2026, was named the holder of the Innovators Network Endowed Chair at Fred Hutch in recognition of her innovative research. As a scientist, she leads a research team investigating how the gut microbiome influences the immune system and complications such as graft-versus-host disease (GvHD), with the goal of improving transplant success for future patients. 

For me, in the lab, every day looked different. Some days involved analyzing data and writing curriculum. Other days involved complex laboratory experiments that required careful planning and collaboration. I quickly learned that research rarely follows a nine-to-five schedule and that successful science depends on teamwork, flexibility, and persistence. 

I also learned to work with a mouse model, gaining experience with techniques such as harvesting and flushing bone marrow to isolate hematopoietic stem cells for downstream experiments. One of the most challenging aspects of my training was learning flow cytometry, a powerful but highly technical tool used to identify and characterize specific cell populations based on the proteins they express. I’m still incredibly novice with this technique, but I learned that mastery is going to take patience, attention to detail, and guidance from experienced researchers. For me, this reinforces that scientific expertise is developed through continual practice and collaboration. 

I am especially grateful to Dr. Alex Wolfe and Saranya Chakka for their outstanding mentorship throughout my time in the Markey Lab. They were always generous with their time, patiently answering my questions, providing thoughtful guidance on experimental design and data analysis, and making sure I felt supported every step of the way. Their willingness to share their expertise, welcome me as a part of the lab team, and encourage my growth made this experience both rewarding and inspiring. They are truly amazing humans!

Research with Purpose

The Markey Lab investigates how the gut microbiome and the molecules it produces influence the effectiveness of cancer treatments, with a particular emphasis on hematopoietic stem cell transplantation and immunotherapies. Their research bridges observations from clinical studies of patients' intestinal microbiomes with experimental investigations in mouse models to uncover the biological mechanisms involved. By integrating clinical observations with advanced immunological approaches in preclinical mouse models, the laboratory seeks to clarify these biological processes, address existing gaps in knowledge, and generate evidence that can guide the development of microbiome-based strategies to improve future cancer therapies. To learn more about their work, check out these recent publications https://research.fredhutch.org/markey/en.html.  

My own project this summer investigated how short chain fatty acids affect hematopoietic stem cells (HSCs). 

Research Question
How does sodium butyrate affect the growth, colony-forming ability, and phenotype of murine bone marrow hematopoietic stem cells (HSCs)?

The goal of this project was to investigate whether sodium butyrate, a short-chain fatty acid naturally produced by beneficial gut bacteria, influences the behavior of hematopoietic stem cells (HSCs) found in mouse bone marrow. Previous studies have suggested that the gut microbiome may play an important role in blood cell regeneration and immune recovery following cancer treatments such as bone marrow transplantation, but the cellular mechanisms remain incompletely understood. This experiment was designed to determine whether exposing HSCs to different concentrations of sodium butyrate alters their ability to survive, proliferate, and form distinct blood cell colonies in culture. 

To address this question, bone marrow was collected from three mice to provide biological replicates, and the marrow cells were processed into single-cell suspensions while maintaining cell viability under sterile conditions. Hematopoietic stem and progenitor cells were then enriched using an EasySep magnetic separation system, which removes mature blood cells and enriches them for primitive stem cell populations. Hematopoietic stem cells have the ability to both self-renew and generate all blood cell types, whereas progenitor cells are early descendants of stem cells that have begun to commit to specific blood cell lineages and can produce a more limited range of mature blood cells. Cell counts were performed throughout the workflow using an automated Horiba cell counter to ensure accurate cell concentrations for downstream experiments. 

Flow cytometry was also used to evaluate the effectiveness of the magnetic enrichment process by comparing stem cell purity before and after isolation. This was accomplished by staining the enriched cell population with fluorescent antibodies against Lineage markers , Sca-1, and c-Kit (which mark mature cells) to identify the Lineage-negative, Sca-1-positive, c-Kit-positive (LSK) population, a well-established marker profile for murine (mouse) hematopoietic stem cells. Appropriate unstained, single-color compensation, and experimental controls were included to ensure accurate identification of stem cells.

Purified HSCs were then cultured in MethoCult methylcellulose medium using the STEMvision colony-forming assay, a semisold culture system that supports the growth of individual hematopoietic stem and progenitor cells into distinct colonies. After incubation, the STEMvision imaging system automatically identifies, classifies, and quantifies the different colony types, allowing researchers to evaluate the proliferation and differentiation potential of HSCs and progenitor cells under different experimental conditions. Five treatment conditions were established containing final sodium butyrate concentrations of 0, 0.1, 0.5, 1, and 5 mM, with each condition performed in biological triplicate. Cells were incubated under controlled conditions for 10 days, allowing individual stem cells to proliferate and differentiate into colonies representing different hematopoietic progenitor lineages. The methylcellulose matrix prevented cells from migrating, ensuring that each colony originated from a single stem or progenitor cell. 

Finally, colony growth was evaluated using the STEMvision imaging system. Colonies were counted and examined microscopically to compare colony number and morphology. These measurements provided insight into how sodium butyrate affects hematopoietic stem cell function, including their capacity for self-renewal, proliferation, and differentiation. By combining magnetic cell enrichment, flow cytometric characterization, and automated colony-forming analysis, this study provides a comprehensive approach for examining how a microbiome-derived metabolite may regulate blood-forming stem cells and could ultimately contribute to improved recovery following bone marrow transplantation and other cancer therapies.

The results showed relatively similar effects across the 0.1, 0.5, and 1.0 mM sodium butyrate conditions, with a marked decrease at 5 mM, suggesting that the highest concentration was toxic rather than part of a gradual concentration-dependent response (Figure 1A; images shown in Figure 1B).   Flow cytometry demonstrated a marked reduction in live cells and a corresponding loss of hematopoietic stem and progenitor cell populations at higher concentrations (Figure 2 and 3). In contrast, lower concentrations (0.1–1.0 mM) generally maintained cell viability and colony-forming capacity, although variability between biological replicates made it difficult to identify consistent changes in individual stem and progenitor populations. Together, these findings suggest that high concentrations of sodium butyrate are cytotoxic to hematopoietic stem cells, and lower concentrations were not different to control conditions in the settings we tested. 

Figure 1: High-dose sodium butyrate suppresses colony formation by murine hematopoietic stem cells. 

Mouse HSCs were cultured in MethoCult containing the indicated concentrations of sodium butyrate (0, 0.1, 0.5, 1.0, or 5.0 mM) for 10 days, after which total colony numbers were quantified.

I then conducted a second experiment using three technical replicates at each sodium butyrate concentration, with additional flow cytometry controls to improve confidence in identifying hematopoietic stem and progenitor cell populations.

My results reinforced the findings of the first experiment, that sodium butyrate has a concentration-dependent effect on hematopoietic stem and progenitor cell growth and differentiation. STEMVision analysis showed that colony formation was maintained at 0.1 and 0.5 mM, declined at 1.0 mM, and was completely absent at 5.0 mM (Figure 4). Visual phenotyping of the colonies as CFU-GM, BFU-E, and CFU-GEMM provided additional evidence that lower concentrations permitted continued progenitor growth and differentiation, while higher concentrations reduced overall colony-forming capacity (Figure 5). Flow cytometry showed a similar pattern, with stem and progenitor populations remaining detectable at lower concentrations, with essentially no recovery at 5.0 mM (Figure 6). Together, the STEMVision and flow cytometry results supported a strong inhibitory–and at 5.0 mM, likely cytotoxic–effect of high-dose sodium butyrate on hematopoietic stem and progenitor cells.  Across both the flow cytometry and CFU assays, the highest concentration tested, 5.0 mM, produced the clearest effect: colony formation was completely absent, and flow cytometry showed essentially no recovery of LSK cells (Figure 4 and 6). At intermediate concentrations, particularly 0.5–1.0 mM, recovery of LSK populations declined substantially. CFU phenotyping showed a similar overall pattern, with fewer colonies at 1.0 mM and no colonies at 5.0 mM. Together, these results suggest that higher concentrations of butyrate strongly suppress hematopoietic progenitor survival, proliferation, and/or colony-forming capacity.

Interestingly, the response was not simply a steady decline as butyrate concentration increased. At 0.1 mM, total live-cell and LSK recovery were maintained or increased relative to the untreated control, suggesting that low-dose butyrate may have different effects on hematopoietic cells than higher doses (Figure 6 and 7). However, several populations, including MPP lineage subsets showed substantial variability among technical replicates, so apparent increases should be interpreted cautiously (Figure 8).

Overall, the agreement between the flow cytometry and colony-forming assays supports the conclusion that butyrate can alter both the abundance of hematopoietic progenitors, with high concentrations being strongly inhibitory and lower concentrations producing more complex, population-specific responses. These findings build upon the initial biological-replicate experiment and provide a foundation for further investigating how butyrate influences hematopoietic differentiation and whether these effects are connected to its known role as an epigenetic regulator.

A logical next step would be to repeat these assays and explore the lower dose ranges to identify the optimal concentration for expansion, and confirm our current data. We also propose to expand the flow cytometry analysis to better distinguish specific hematopoietic lineages and determine whether butyrate primarily affects cell survival and proliferation or also alters differentiation.

Bringing Research Back to the Classroom

Perhaps the most rewarding part of the fellowship was translating my laboratory experience into curriculum materials for my senior biomedical science students. Writing curriculum takes time and that is sometimes difficult to do when that garden needs tending and the sun is begging you to be outside. So, it was very valuable to have the opportunity to do so because of the structure of the HTF program. 

This summer I drew directly from what I learned in the Markey Lab and developed a phenomenon-driven cancer unit in which students investigate the case of a 15-year-old leukemia patient whose cancer no longer responds to treatment. During the unit, students assume the roles of physicians, immunologists, transplant specialists, and biomedical researchers. Rather than learning concepts in isolation, students uncover the science as they work through the patient's medical journey from understanding how healthy bone marrow produces blood cells, to diagnosing leukemia, exploring why tumors evade the immune system, selecting the best stem cell donor, monitoring transplant recovery, and ultimately investigating why some patients develop graft-versus-host disease (GvHD). Along the way, students build an understanding of core concepts including hematopoiesis, cancer biology, immune function, immunotherapy, stem cell transplantation, genetics, the gut microbiome, and the role of microbial metabolites such as butyrate in regulating immune recovery after transplantation.

The curriculum emphasizes authentic scientific practices through a series of laboratory investigations and clinical simulations that mirror the work of modern biomedical researchers and healthcare professionals. Students perform wet labs such as blood cell identification using stained blood smears, simulated stem cell transplant compatibility testing, microbiome competition experiments using microorganisms, and a simulated fecal microbiota transplantation investigation. Throughout the curriculum, students analyze patient charts, interpret transplant data, use the Anatomage Table to investigate human anatomy and pathology, and evaluate experimental evidence using claim-evidence-reasoning. 

My experience working in the Markey Lab made this authenticity possible by immersing me in the day-to-day practice of biomedical research. Through hands-on training in techniques such as bone marrow isolation, HSC enrichment, flow cytometry, and colony-forming assays, I gained both the technical knowledge and scientific understanding needed to translate cutting-edge research into meaningful classroom experiences. Collaborating with researchers and investigating how the gut microbiome influences stem cell transplantation inspired the development of laboratory activities and clinical storylines that would not have been possible without this HTF experience. By bringing these experiences back to my classroom, I hope to give students a genuine glimpse into how scientific discoveries are made and how research can ultimately improve patient care.

Learning Beyond the Bench

One aspect of the fellowship I especially appreciated was our weekly professional learning community (PLC). We explored topics ranging from scientific literacy and cancer careers to the educational concept of productive uncertainty. Rather than giving students immediate solutions, productive uncertainty encourages them to wrestle with challenging problems, test ideas, and gradually construct understanding with appropriate support. Experiencing this approach as a learner reinforced its power and inspired me to incorporate it more intentionally into my own teaching and curriculum writing. If you want to learn more about productive uncertainty, check it out here: https://www.fredhutch.org/en/education-training/teachers/science-education-partnership/sep-curriculum/productive-uncertainty.html

Looking Ahead

Looking back on the summer, I realized that the greatest lesson I learned was not simply about hematopoietic stem cells, the gut microbiome, or flow cytometry. It was about what it means to continually grow as both a scientist and an educator. Stepping back into the role of learner reminded me how rewarding it is to embrace uncertainty, ask questions, and persist through challenges. Those experiences will shape not only the curriculum I bring back to my classroom but also the way I support my students as they navigate their own learning journeys. In the end, I hope they leave my classroom with not only a deeper understanding of the science behind cancer, but also that discovery is driven by curiosity, perseverance, collaboration, and a lifelong commitment to learning.

References

1. Markey Lab. (n.d.). Research. Fred Hutch Cancer Center. https://research.fredhutch.org/markey/en/research.html