Imaging with Mass Spectrometry: Spatial Metabolomics to Study Intestinal Inflammation

Boone M. Prentice
Department of Chemistry, University of Florida, Gainesville, FL

Boone Prentice, BS, PhD (Presenter) University of Florida

Presenter Bio: Boone Prentice is an Associate Professor and holds the Scott Family Professorship in the Department of Chemistry at the University of Florida. He received his B.S. in Chemistry from Longwood University (Farmville, VA), and completed his Ph.D. in Chemistry at Purdue University (West Lafayette, IN) under the mentorship of Prof. Scott McLuckey studying gas-phase ion/ion reactions and ion trap instrumentation. He then completed his postdoctoral work in the Department of Biochemistry at Vanderbilt University (Nashville, TN) as an NIH NRSA fellow under the guidance of Prof. Richard Caprioli before joining the faculty at UF in 2018. He was awarded an NIH Focused Technology Research and Development R01 grant in 2020, a JDRF Innovation Award in 2023, an NSF CAREER award in 2024, and an Alfred P. Sloan Research Fellowship in Chemistry in 2025 to support his research developing gas-phase reactions and imaging mass spectrometry technologies to study the molecular pathology of diabetes, infectious disease, neurodegeneration, and neuropharmacology. He was also awarded the 2022 Young Investigator Award from Eli Lilly and Company, which is an unsolicited award given annually by Eli Lilly’s Analytical Chemistry Academic Contacts Committee to recognize a “rising star” in analytical chemistry. He was highlighted as a 2023 Emerging Investigator by the Journal of the American Society for Mass Spectrometry, a 2023 Young Investigator in (Bio-)Analytical Chemistry by Analytical and Bioanalytical Chemistry, a 2024 Early Career special selection by the Journal of Mass Spectrometry, and a 2024 Young Scientist Feature by the International Journal of Mass Spectrometry. Boone was also the recipient of the 2023-2024 CLAS Faculty Advising/Mentor Award and the 2024-2025 UF Doctoral Dissertation Advisor/Mentoring Award, and was promoted to Associate Professor with tenure in 2025.

Relevant Financial Disclosures (within past 24 months, reported on Apr 23, 2026) No relevant financial relationship(s) to disclose.

Clostridioides difficile infection (CDI) is the most common nosocomial infection and has been classified as an urgent health threat by the CDC. The incidence, severity, and costs associated with CDI in the United States have all increased dramatically in recent years. One major comorbidity associated with CDI is inflammatory bowel disease (IBD), which is characterized by chronic inflammation of the gastrointestinal tract and dysbiosis of the gut microbiome. IBD patients are at an increased susceptibility to CDI and recurrent infections, and are at higher risk of poor CDI outcomes. There is some data suggesting that this increased susceptibility to disease in linked to microbial dysbiosis and altered gut metabolism in IBD patients. However, the mechanistic drivers of increased CDI severity in IBD patients are currently unknown.

Molecular studies in targeted diagnostics and therapeutics have historically been limited to systems with some a priori knowledge of the specific molecules or biological pathways to be studied. New technologies have allowed for more comprehensive analyses of biological and clinical samples in recent years, which are in turn enabling greater insights into basic cellular biology and providing new opportunities for curative therapies. Imaging mass spectrometry is one such technology that allows for the untargeted spatial mapping of a wide array of biomolecules in tissue specimens. Our lab develops novel imaging MS technologies and leverages these advances, working alongside Prof. Joseph Zackular and his team at the Children’s Hospital of Philadelphia and the University of Pennsylvania, to understand the molecular metabolism associated with microbial systems and infectious disease.

Our early matrix-assisted laser desorption/ionization (MALDI) imaging MS experiments revealed metabolic remodeling in mouse gut during Enterococcus and C. difficile coinfection and helped to spatially define localization patterns associated with specific microbes, pathogens, and host immune cells during gastrointestinal coinfection. For example, we discovered that Enterococcus and C. difficile participate in a parallel process of amino acid nutrient restriction and cross-feeding that reprograms C. difficile metabolism, resulting in increased virulence. We have now extended these spatial metabolomics methods to study CDI and IBD metabolism. Our initial experiments have revealed altered expression of nutrient uptake transporters. Some amino acids are C. difficile-toxin dependent (i.e., they may be liberated from the host) and others are C. difficile-toxin depleting (i.e., they are likely used by C. difficile). Finally, a novel metabolite, isocaproyltaurine, may allow for discrimination between IBD and IBD+CDI groups. Distinction between these highly similar phenotypes is important, as treatment and health outcomes are divergent. Overall, spatial metabolomics offers a powerful and promising method to study intestinal inflammation.