About

Craig W Vander Kooi, Ph.D., is a Professor in the Department of Biochemistry and Molecular Biology at the University of Florida College of Medicine, where he also serves as Co-Director of the Center for Spatial Biomolecule Research (CASBR) and Assoc. Director of the BMS/BMB PhD Program. His research focuses on determining the mechanisms of physical interactions underlying fundamental biological processes and human disease. His laboratory utilizes structural and mass-spectrometry based tools combined with biochemical, cellular, and animal model systems to gain deep biological insights. Vander Kooi's training includes experience with NMR and biochemical tools for structural biology during his graduate studies with Dr. Walter Chazin, and expertise in X-ray crystallography and biophysical tools for receptor function studies during his postdoctoral fellowship with Dr. Daniel Leahy. His ongoing work involves using structural biology to describe the mechanisms of glucan kinases and phosphatases, understanding the molecular basis of hearing loss associated with GIPC3 mutations, and developing novel technologies for biological and pathological process analysis through spatial imaging. He has held academic positions at the University of Kentucky before joining the University of Florida in 2022.

Research topics

• Biology
• Biochemistry
• Chemistry
• Immunology
• Computational biology

Selected publications

• GAA-based therapeutic strategies for neurological glycogen storage diseases

  Molecular Genetics and Metabolism · 2026-02-01

  articleOpen access
  PublisherDOI

• Metabolic Coherence of the Mouse Brain

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-09

  articleOpen access

  The brain's metabolic demands are well established, but how metabolism is coordinated across anatomically distinct regions remains poorly understood. Here, using matrix-assisted laser desorption/ionization (MALDI) imaging integrated with the Allen Brain Atlas and optimal transport-based computational analysis, we map the spatial metabolome across twelve major mouse brain divisions. We define an optimal-transport-derived inter-regional metabolite similarity metric and refer to it as metabolic coherence. This structure is largely preserved in an amyloid mouse model of Alzheimer's disease despite widespread changes in individual metabolite and lipid levels. Individual metabolites and lipids shift in a coordinated manner across regions, sustaining inter-regional relationships even as absolute levels change in patterns indicative of mitochondrial dysfunction. To test whether the coherence metric is responsive to local intervention, we targeted the left hippocampus of mice from this model via lentiviral shHIF1α knockdown or neuronal AAV-mediated AOX expression. Both interventions were associated with metabolite normalization at the injection site. More importantly, normalization extended across distal regions sharing high metabolic similarity with the hippocampus and was accompanied by improved social memory in a single behavioral assay. Gene modulation and amyloid plaque reduction localized to the injection site.

  PublisherOA PDFDOI

• Mass Spectrometry-Based Spatial Imaging of the Cochlea

  Journal of the American Society for Mass Spectrometry · 2026-04-03

  articleOpen accessSenior authorCorresponding

  Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) is transforming spatial molecular studies. However, applying MALDI-MSI to small, anatomically complex tissues remains challenging. One such structure is the cochlea, the auditory part of the inner ear that is critical for hearing. To address these challenges, we developed and implemented a streamlined workflow for sample preparation and processing to obtain MALDI-MSI data on mouse cochlea. Sample acquisition was optimized to minimize time and processing steps, allowing use of flash-frozen neonatal mouse heads. This workflow enabled high spatial resolution metabolomic and lipidomic imaging of the sagittally cryosectioned mouse cochlea using N-(1-naphthyl) ethylenediamine dihydrochloride (NEDC) matrix via sublimation. Optimized NEDC sublimation allowed high signal-to-noise, reduced delocalization, and salt tolerance, allowing acquisition of 5 μm-resolution imaging data on a MALDI-MSI instrument. Sublimation was found to be superior to spraying as a method for matrix application due to its higher signal-to-noise, particularly for lipids and fatty acids, and improved spatial resolution. Diverse metabolites and lipids were measured throughout the cochlear region, revealing distinct spatial distributions. Clustering identified reproducible physiological regions, including the otic capsule and spiral ducts. High spatial resolution imaging revealed distinct tissues, cell types, and molecular signatures within the cochlea. These findings establish the utility of high spatial resolution MALDI-MSI for auditory research, enabling molecular mapping of cochlear function and dysfunction.

  PublisherDOI

• Mapping glycogen accumulation and treatment effect in Pompe disease with saturation transfer MRI

  Translational research · 2026-02-19

  articleOpen access

  Pompe disease is a glycogen storage disease caused by the impaired breakdown of glycogen in lysosomes, leading to abnormal glycogen accumulation in tissue. Here we use glycogen nuclear Overhauser effect (glycoNOE) MRI to detect glycogen levels in skeletal muscle in a mouse model of Pompe disease. Moreover, we evaluated if glycoNOE MRI could detect changes in glycogen load after enzyme replacement therapy. The results show that glycoNOE MRI can distinguish between Pompe mice and wildtype controls. Furthermore, the technique detected treatment-dependent changes in muscle glycoNOE signals, which were validated with ex vivo biochemical assays. To demonstrate potential human translation, glycoNOE MRI was applied to two Pompe patients and revealed elevated glycogen levels in patients compared to healthy controls.

  PublisherDOI

• Shaping Human Health and Nutrition Through Innovations in Spatial Metabolism

  Annual Review of Nutrition · 2026-05-19

  article1st authorCorresponding

  Spatial metabolomics has emerged as a transformative approach for understanding how metabolism is organized within tissues and how nutritional factors influence health and disease. By preserving the spatial context of metabolites within intact tissue architecture, techniques such as MALDI and DESI imaging mass spectrometry reveal metabolic heterogeneity that bulk analyses cannot capture. This review examines how spatial metabolomics advances nutrition research across multiple domains: from mapping nutrient distributions in foods to understanding how diet reshapes tissue metabolism in disease states. We highlight recent innovations, including single-cell-resolution imaging, 3D metabolome reconstruction, stable isotope tracing, and multiomics integration. Key applications demonstrate how dietary patterns drive glycogen accumulation in cancer, alter lipid zonation in fatty liver disease, and modulate brain metabolism through the gut-brain axis. These spatially resolved insights establish direct mechanistic links between nutrition, tissue metabolism, and disease pathogenesis.

  PublisherDOI

• Protocol for high-power, brain-focused microwave fixation to define rodent metabolism

  STAR Protocols · 2025-04-25 · 1 citations

  articleOpen access

  Analysis of metabolites provides key insights into brain physiology and function. Due to post-mortem metabolism, both the euthanasia method and dissection time can make a critical difference. Here, we describe a protocol to euthanize rodents by microwave irradiation. This workflow details steps for animal placement, tissue fixation, and post-fixation processing. This protocol enables the rapid halting of metabolic activity for the accurate assessment of the metabolome in situ for analyses such as mass spectrometry and nuclear magnetic resonance. For complete details on the use and execution of this protocol, please refer to Juras et al. 1 • Instructions for securing rodents in appropriate holder • Procedures for safely operating and optimizing microwave apparatus • Guidance on post-fixation processing Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Analysis of metabolites provides key insights into brain physiology and function. Due to post-mortem metabolism, both the euthanasia method and dissection time can make a critical difference. Here, we describe a protocol to euthanize rodents by microwave irradiation. This workflow details steps for animal placement, tissue fixation, and post-fixation processing. This protocol enables the rapid halting of metabolic activity for the accurate assessment of the metabolome in situ for analyses such as mass spectrometry and nuclear magnetic resonance.

  PublisherDOI

• Spatial Molecular Imaging of the Glycome Using Mass Spectrometry

  Journal of Visualized Experiments · 2025-11-28 · 1 citations

  articleOpen accessSenior author

  The spatial organization of the glycome within tissues is key to the molecular basis for physiological function. The diverse and dynamic glycome is critical for fundamental cellular processes, including metabolism, signaling, and adhesion. Innovations in spatial biology have ushered in new avenues for spatial molecular imaging of diverse glycome classes. Here, we describe an optimized protocol for spatial biomolecular imaging of the glycome in fresh-frozen mouse liver. The workflow comprises (1) rapid harvesting and freezing, (2) cryostat sectioning at optimal thickness and position, (3) tissue preparation and on-tissue enzyme digestion using carbohydrate-active enzymes, (4) matrix application and data acquisition by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), and (5) data processing and visualization to place the findings in biological context. Use of this approach allows acquisition of detailed spatial maps of N-linked glycans and glycogen, revealing key physiological and cellular features. These data allow the definition of key spatial glycomic heterogeneity associated with liver function and dysfunction. This workflow enables highly reproducible and sensitive spatial glycomics of the mouse liver. Additionally, it is readily adaptable to other tissues or species, facilitating novel spatial insights into glycome biology in health and disease.

  PublisherOA PDFDOI

• Hyper-Glycosylation as a Central Metabolic Driver of Alzheimer’s Disease

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-05 · 1 citations

  preprintOpen access

  Abstract Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by devastating degenerative decline. Metabolic disruptions are widely observed, yet their involvement in the molecular etiology of AD remains underexplored. Utilizing spatial metabolomics, lipidomics, and glycomics in both mouse models and human post-mortem samples, we identified a hyper-glycosylation phenotype as a hallmark of AD. To investigate the underlying mechanisms and whether the observed effect was a driver of the observed decline, we developed an advanced spatial isotopic tracing pulse-chase method to study the dynamics of N-linked glycans. Our analysis revealed enhanced glycan biosynthesis in AD mouse models. Based on these findings, we performed genetic and dietary interventions to modulate glycan biosynthesis. Genetic knockdown of glycan biosynthetic enzymes ameliorated the hyper-glycosylation and improved cognitive and behavioral outcomes in AD mice. In contrast, oral glucosamine supplementation drove hyper-glycosylation and exacerbated cognitive and behavioral deficits. To assess the clinical relevance of these findings, we conducted a retrospective analysis of a large population of patients with mild cognitive impairment (MCI), AD, and Alzheimer’s Disease Related Dementias ( ADRD) stratified by glucosamine use, leveraging electronic health records. Consistently, glucosamine supplementation was associated with increased mortality in AD and ADRD patient cohorts, and significantly elevated progression from MCI to AD compared to age-matched controls. Collectively, our findings establish hyper-glycosylation as a pathological driver of AD and highlight glycan metabolism as an actional target in the fight against AD.

  PublisherOA PDFDOI

• Spatial mapping of the brain metabolome lipidome and glycome

  Nature Communications · 2025-05-12 · 23 citations

  articleOpen access

  Metabolites, lipids, and glycans are fundamental but interconnected classes of biomolecules that form the basis of the metabolic network. These molecules are dynamically channeled through multiple pathways that govern cellular physiology and pathology. Here, we present a framework for the simultaneous spatial analysis of the metabolome, lipidome, and glycome from a single tissue section using mass spectrometry imaging. This workflow integrates a computational platform, the Spatial Augmented Multiomics Interface (Sami), which enables multiomics integration, high-dimensional clustering, spatial anatomical mapping of matched molecular features, and metabolic pathway enrichment. To demonstrate the utility of this approach, we applied Sami to evaluate metabolic diversity across distinct brain regions and to compare wild-type and Ps19 Alzheimer’s disease (AD) mouse models. Our findings reveal region-specific metabolic demands in the normal brain and highlight metabolic dysregulation in the Ps19 model, providing insights into the biochemical alterations associated with neurodegeneration. Clarke et al. presents a framework for spatial analysis of the metabolome, lipidome, and glycome from a single tissue section using mass spectrometry imaging. Applying this approach, they revealed region-specific metabolic diversity and dysregulation in both normal and diseased mouse brains.

  PublisherOA PDFDOI

• Abstract 4164: Targeting glycogen metabolism as a potential therapy for Ewing sarcoma

  Cancer Research · 2025-04-21

  article

  Abstract Ewing sarcoma (EWS) is a malignant bone tumor or soft-tissue tumor that mainly affects children, adolescents, and young adults. We recently demonstrated that the PAS+ accumulations in EWS indicate extensive deposits of glycogen, a macro-metabolite that provides an immediate source of glucose to support cellular energy needs. In this study, we sought to elucidate the role of glycogen and its related enzymes in EWS tumorigenesis and metastasis. Though complex carbohydrates like glycogen are traditionally difficult to study due to their biochemical and biophysical properties, the Gentry and Sun laboratories recently developed a robust workflow of matrix-assisted laser desorption/ionization (MALDI)-imaging of complex carbohydrates (MICC), a spatial technique to visualize glycogen in situ. Leveraging this technique, we profiled glycogen accumulation in a cohort of EWS patient tumors. This analysis revealed glycogen levels were dramatically higher in the intra-tumoral regions across all EWS samples. Additionally, through our comprehensive pan-cancer study encompassing 12 different cancer classes, we revealed that glycogen accumulation varies among tumor origins, signifying its unique role in EWS. Lysosomal glycogen degradation is catalyzed by acid α-glucosidase (GAA). Preliminary data from our laboratory demonstrates that glycogen colocalizes with GAA in EWS patient tumors and that small-molecule inhibition of GAA significantly impairs EWS cell proliferation and migration. Transcriptomic analyses revealed a strong correlation between GAA expression and known EWS metastasis regulators, including TGF-β and Wnt/β-catenin signaling pathways. Further experiments revealed that while glycogen synthase 1 inhibitor reduced glycogen levels and impaired EWS cell viability, a small molecule promoting lysosomal glycogen degradation reduced glycogen but paradoxically enhanced cell viability. These findings highlight the critical role of lysosomal glycogen utilization in EWS cell viability, suggesting a potential link between GAA-regulated glycogen degradation, energy homeostasis, and apoptotic pathways in EWS. Moving forward, we are defining the efficacy and mechanism of GAAi in the treatment of EWS preclinical models both as a single agent and in additive therapy with other chemotherapies. To assess the efficacy of GAAi in metastatic EWS, spontaneous lung metastatic mice models will be established by subcutaneous implantation of EWS patient-derived tumor in NSG mice. Our state-of-the art integrated spatial analysis of metabolome, lipidome, and glycome followed by high dimensionality reduction and spatial clustering, annotation, pathway enrichment analysis will provide in-depth spatial insights into tumor and stromal metabolism profile of EWS. Future potential of GAAi study is to conduct clinical trial to identify when and how to add GAAi to current standard care EWS therapy and improve survival outcomes. Citation Format: Yueying Liu, Pankaj K. Singh, Lyndsay E. Young, Harrison A. Clarke, Tara R. Hawkinson, Meagan L. McCall, Elias Sayour, Craig W. Vander Kooi, Li Chen, Ramon C. Sun, Matthew S. Gentry. Targeting glycogen metabolism as a potential therapy for Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4164.

  PublisherDOI

Recent grants

• NIH Grant R01GM094155

  NIH · $1.3M · 2016

• Structural Basis for Glucan Phosphatase Function in Photosynthetic Organisms

  NSF · $450k · 2018–2022

• NIH Grant P20RR020171

  NIH · $17.4M · 2014

Frequent coauthors

• Matthew S. Gentry

  55 shared

• Hong Lü

  University of Kentucky

  24 shared

• Alan Daugherty

  University of Kentucky

  24 shared

• Congqing Wu

  University of Kentucky

  23 shared

• Deborah A. Howatt

  Cardiovascular Research Center

  22 shared

• Jessica J. Moorleghen

  University of Kentucky

  22 shared

• Lisa A. Cassis

  University of Kentucky

  21 shared

• Anju Balakrishnan

  Shri Dharmasthala Manjunatheswara College of Ayurveda and Hospital

  20 shared

Education

• Ph.D., Biochemistry and Molecular Biology

  University of Florida

  2000

• M.S., Biochemistry and Molecular Biology

  University of Florida

  1996

• B.S., Biochemistry and Molecular Biology

  University of Florida

  1994