John Rawls

Overview:

We seek to understand how the intestinal microbiome contributes to vertebrate physiology and disease. To that end, we leverage complementary zebrafish and mouse models to study the integrative physiology of host-microbiome interactions. This work has identified novel and conserved mechanisms by which intestinal bacteria regulate dietary fat metabolism and systemic innate immunity. We also apply genomic approaches in these animal models to understand the transcriptional regulatory pathways utilized by the intestinal epithelium to mediate host responses to the microbiome. Using this approach, we have identified mechanisms of transcriptional and chromatin regulation that have been conserved during vertebrate evolution and also contribute to modern human diseases such as the inflammatory bowel diseases, obesity, and diabetes. To further advance our understanding of obesity pathophysiology, we developed the zebrafish as a model system for studying adipose tissues and identifying new environmental and genetic regulators of adiposity. We are also engaged in translational research in humans and animal models to define microbial and metabolic determinants of obesity and efficacy of weight loss intervention. Grounded in comparative and integrative physiology, our research program has been effective in discovering ancient mechanisms of host-microbiome interaction that are conserved across animal taxa and contribute to the etiology of modern human diseases. These insights are advancing our understanding of host-microbiome relationships in vertebrate physiology and identifying novel therapeutic targets for human diseases ranging from inflammatory bowel disease to obesity to neurological disorders.

Positions:

Professor of Molecular Genetics and Microbiology

Molecular Genetics and Microbiology
School of Medicine

Professor in Medicine

Medicine, Gastroenterology
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

B.S. 1996

Emory University

Ph.D. 2001

Washington University in St. Louis

Grants:

Cellular and Environmental Regulation of Protein Absorption and Utilization in the Early Intestine

Administered By
Cell Biology
Awarded By
National Institutes of Health
Role
Co Investigator
Start Date
End Date

Genetic and Epigenetic Regulation of Intestinal Inflammation

Administered By
Cell Biology
Awarded By
National Institutes of Health
Role
Co Investigator
Start Date
End Date

Regulation of Luminal Protein Uptake and Trafficking By Lysosome-Rich Enterocytes

Administered By
Basic Science Departments
Awarded By
National Institutes of Health
Role
Co-Sponsor
Start Date
End Date

Lightsheet Imaging System

Administered By
Biology
Awarded By
National Institutes of Health
Role
Major User
Start Date
End Date

Summer Scholars Program in Genome Sciences and Medicine

Administered By
Duke Center for Applied Genomics and Precision Medicine
Awarded By
National Institutes of Health
Role
Significant Contributor
Start Date
End Date

Publications:

Using zebrafish to understand reciprocal interactions between the nervous and immune systems and the microbial world.

Animals rely heavily on their nervous and immune systems to perceive and survive within their environment. Despite the traditional view of the brain as an immunologically privileged organ, these two systems interact with major consequences. Furthermore, microorganisms within their environment are major sources of stimuli and can establish relationships with animal hosts that range from pathogenic to mutualistic. Research from a variety of human and experimental animal systems are revealing that reciprocal interactions between microbiota and the nervous and immune systems contribute significantly to normal development, homeostasis, and disease. The zebrafish has emerged as an outstanding model within which to interrogate these interactions due to facile genetic and microbial manipulation and optical transparency facilitating in vivo imaging. This review summarizes recent studies that have used the zebrafish for analysis of bidirectional control between the immune and nervous systems, the nervous system and the microbiota, and the microbiota and immune system in zebrafish during development that promotes homeostasis between these systems. We also describe how the zebrafish have contributed to our understanding of the interconnections between these systems during infection in fish and how perturbations may result in pathology.
Authors
Levraud, J-P; Rawls, JF; Clatworthy, AE
MLA Citation
Levraud, Jean-Pierre, et al. “Using zebrafish to understand reciprocal interactions between the nervous and immune systems and the microbial world.J Neuroinflammation, vol. 19, no. 1, June 2022, p. 170. Pubmed, doi:10.1186/s12974-022-02506-x.
URI
https://scholars.duke.edu/individual/pub1525468
PMID
35765004
Source
pubmed
Published In
Journal of Neuroinflammation
Volume
19
Published Date
Start Page
170
DOI
10.1186/s12974-022-02506-x

Advanced Obesity Treatment Selection among Adolescents in a Pediatric Weight Management Program.

Background: Treatment options for adolescents with obesity are limited. Yet, therapies previously reserved for adults, such as medications and bariatric surgery, are increasingly available to adolescents in tertiary obesity treatment settings. We aimed to identify the factors associated with selecting an advanced obesity treatment (diets, medications, and surgery) beyond lifestyle therapy among adolescents presenting to a tertiary, pediatric weight management program. Methods: We conducted a secondary analysis of adolescents (N = 220) who participated in a longitudinal, observational case-control study within a pediatric weight management program. The exposures were potential individual and clinical factors, including sociodemographic characteristics and comorbidities. The outcome was treatment selection, dichotomized into lifestyle vs. advanced treatment. We modeled associations between these factors and treatment selection using logistic regression, controlling for confounding variables (age, race/ethnicity, sex, and insurance). Results: The study population included a majority of non-Hispanic Black (50.5%) and Hispanic/Latino (19.5%) adolescents, of whom 25.5% selected advanced treatment. Adolescents were more likely to choose an advanced treatment option if they had a greater BMI [odds ratio (OR) 1.09, 95% confidence interval (95% CI) 1.04-1.15], lived further from the clinic (OR 1.03, 95% CI 1.00-1.05), and had an elevated glycohemoglobin level (OR 2.46, 95% CI 1.24-4.92). Conclusions: A significant fraction of adolescents seeking obesity treatment in a specialized care setting chose new and emerging obesity treatments, particularly those at high risk of developing diabetes. These findings can inform patient-clinician obesity treatment discussions in specialty care settings. Clinical Trial Registration number: NCT03139877.
Authors
Suarez, L; Skinner, AC; Truong, T; McCann, JR; Rawls, JF; Seed, PC; Armstrong, SC
MLA Citation
Suarez, Lilianna, et al. “Advanced Obesity Treatment Selection among Adolescents in a Pediatric Weight Management Program.Child Obes, vol. 18, no. 4, June 2022, pp. 237–45. Pubmed, doi:10.1089/chi.2021.0190.
URI
https://scholars.duke.edu/individual/pub1501310
PMID
34757829
Source
pubmed
Published In
Child Obes
Volume
18
Published Date
Start Page
237
End Page
245
DOI
10.1089/chi.2021.0190

Starvation causes changes in the intestinal transcriptome and microbiome that are reversed upon refeeding.

BACKGROUND: The ability of animals and their microbiomes to adapt to starvation and then restore homeostasis after refeeding is fundamental to their continued survival and symbiosis. The intestine is the primary site of nutrient absorption and microbiome interaction, however our understanding of intestinal adaptations to starvation and refeeding remains limited. Here we used RNA sequencing and 16S rRNA gene sequencing to uncover changes in the intestinal transcriptome and microbiome of zebrafish subjected to long-term starvation and refeeding compared to continuously fed controls. RESULTS: Starvation over 21 days led to increased diversity and altered composition in the intestinal microbiome compared to fed controls, including relative increases in Vibrio and reductions in Plesiomonas bacteria. Starvation also led to significant alterations in host gene expression in the intestine, with distinct pathways affected at early and late stages of starvation. This included increases in the expression of ribosome biogenesis genes early in starvation, followed by decreased expression of genes involved in antiviral immunity and lipid transport at later stages. These effects of starvation on the host transcriptome and microbiome were almost completely restored within 3 days after refeeding. Comparison with published datasets identified host genes responsive to starvation as well as high-fat feeding or microbiome colonization, and predicted host transcription factors that may be involved in starvation response. CONCLUSIONS: Long-term starvation induces progressive changes in microbiome composition and host gene expression in the zebrafish intestine, and these changes are rapidly reversed after refeeding. Our identification of bacterial taxa, host genes and host pathways involved in this response provides a framework for future investigation of the physiological and ecological mechanisms underlying intestinal adaptations to food restriction.
Authors
Jawahar, J; McCumber, AW; Lickwar, CR; Amoroso, CR; de la Torre Canny, SG; Wong, S; Morash, M; Thierer, JH; Farber, SA; Bohannan, BJM; Guillemin, K; Rawls, JF
MLA Citation
Jawahar, Jayanth, et al. “Starvation causes changes in the intestinal transcriptome and microbiome that are reversed upon refeeding.Bmc Genomics, vol. 23, no. 1, Mar. 2022, p. 225. Pubmed, doi:10.1186/s12864-022-08447-2.
URI
https://scholars.duke.edu/individual/pub1513680
PMID
35317738
Source
pubmed
Published In
Bmc Genomics
Volume
23
Published Date
Start Page
225
DOI
10.1186/s12864-022-08447-2

A Planar Culture Model of Human Absorptive Enterocytes Reveals Metformin Increases Fatty Acid Oxidation and Export.

BACKGROUND & AIMS: Fatty acid oxidation by absorptive enterocytes has been linked to the pathophysiology of type 2 diabetes, obesity, and dyslipidemia. Caco-2 and organoids have been used to study dietary lipid-handling processes including fatty acid oxidation, but are limited in physiological relevance or preclude simultaneous apical and basal access. Here, we developed a high-throughput planar human absorptive enterocyte monolayer system for investigating lipid handling, and then evaluated the role of fatty acid oxidation in fatty acid export, using etomoxir, C75, and the antidiabetic drug metformin. METHODS: Single-cell RNA-sequencing, transcriptomics, and lineage trajectory was performed on primary human jejunum. In vivo absorptive enterocyte maturational states informed conditions used to differentiate human intestinal stem cells (ISCs) that mimic in vivo absorptive enterocyte maturation. The system was scaled for high-throughput drug screening. Fatty acid oxidation was modulated pharmacologically and BODIPY (Thermo Fisher Scientific, Waltham, MA) (B)-labeled fatty acids were used to evaluate fatty acid handling via fluorescence and thin-layer chromatography. RESULTS: Single-cell RNA-sequencing shows increasing expression of lipid-handling genes as absorptive enterocytes mature. Culture conditions promote ISC differentiation into confluent absorptive enterocyte monolayers. Fatty acid-handling gene expression mimics in vivo maturational states. The fatty acid oxidation inhibitor etomoxir decreased apical-to-basolateral export of medium-chain B-C12 and long-chain B-C16 fatty acids, whereas the CPT1 agonist C75 and the antidiabetic drug metformin increased apical-to-basolateral export. Short-chain B-C5 was unaffected by fatty acid oxidation inhibition and diffused through absorptive enterocytes. CONCLUSIONS: Primary human ISCs in culture undergo programmed maturation. Absorptive enterocyte monolayers show in vivo maturational states and lipid-handling gene expression profiles. Absorptive enterocytes create strong epithelial barriers in 96-Transwell format. Fatty acid export is proportional to fatty acid oxidation. Metformin enhances fatty acid oxidation and increases basolateral fatty acid export, supporting an intestine-specific role.
Authors
Gomez-Martinez, I; Bliton, RJ; Breau, KA; Czerwinski, MJ; Williamson, IA; Wen, J; Rawls, JF; Magness, ST
MLA Citation
Gomez-Martinez, Ismael, et al. “A Planar Culture Model of Human Absorptive Enterocytes Reveals Metformin Increases Fatty Acid Oxidation and Export.Cell Mol Gastroenterol Hepatol, vol. 14, no. 2, 2022, pp. 409–34. Pubmed, doi:10.1016/j.jcmgh.2022.04.009.
URI
https://scholars.duke.edu/individual/pub1520242
PMID
35489715
Source
pubmed
Published In
Cellular and Molecular Gastroenterology and Hepatology
Volume
14
Published Date
Start Page
409
End Page
434
DOI
10.1016/j.jcmgh.2022.04.009

Transcriptional Integration of Distinct Microbial and Nutritional Signals by the Small Intestinal Epithelium.

BACKGROUND & AIMS: The intestine constantly interprets and adapts to complex combinations of dietary and microbial stimuli. However, the transcriptional strategies by which the intestinal epithelium integrates these coincident sources of information remain unresolved. We recently found that microbiota colonization suppresses epithelial activity of hepatocyte nuclear factor 4 nuclear receptor transcription factors, but their integrative regulation was unknown. METHODS: We compared adult mice reared germ-free or conventionalized with a microbiota either fed normally or after a single high-fat meal. Preparations of unsorted jejunal intestinal epithelial cells were queried using lipidomics and genome-wide assays for RNA sequencing and ChIP sequencing for the activating histone mark H3K27ac and hepatocyte nuclear factor 4 alpha. RESULTS: Analysis of lipid classes, genes, and regulatory regions identified distinct nutritional and microbial responses but also simultaneous influence of both stimuli. H3K27ac sites preferentially increased by high-fat meal in the presence of microbes neighbor lipid anabolism and proliferation genes, were previously identified intestinal stem cell regulatory regions, and were not hepatocyte nuclear factor 4 alpha targets. In contrast, H3K27ac sites preferentially increased by high-fat meal in the absence of microbes neighbor targets of the energy homeostasis regulator peroxisome proliferator activated receptor alpha, neighbored fatty acid oxidation genes, were previously identified enterocyte regulatory regions, and were hepatocyte factor 4 alpha bound. CONCLUSIONS: Hepatocyte factor 4 alpha supports a differentiated enterocyte and fatty acid oxidation program in germ-free mice, and that suppression of hepatocyte factor 4 alpha by the combination of microbes and high-fat meal may result in preferential activation of intestinal epithelial cell proliferation programs. This identifies potential transcriptional mechanisms for intestinal adaptation to multiple signals and how microbiota may modulate intestinal lipid absorption, epithelial cell renewal, and systemic energy balance.
Authors
Lickwar, CR; Davison, JM; Kelly, C; Mercado, GP; Wen, J; Davis, BR; Tillman, MC; Semova, I; Andres, SF; Vale, G; McDonald, JG; Rawls, JF
MLA Citation
Lickwar, Colin R., et al. “Transcriptional Integration of Distinct Microbial and Nutritional Signals by the Small Intestinal Epithelium.Cell Mol Gastroenterol Hepatol, vol. 14, no. 2, 2022, pp. 465–93. Pubmed, doi:10.1016/j.jcmgh.2022.04.013.
URI
https://scholars.duke.edu/individual/pub1520243
PMID
35533983
Source
pubmed
Published In
Cellular and Molecular Gastroenterology and Hepatology
Volume
14
Published Date
Start Page
465
End Page
493
DOI
10.1016/j.jcmgh.2022.04.013

Research Areas:

Muser Mentor