1
|
Thierer JH, Foresti O, Yadav PK, Wilson MH, Moll TOC, Shen MC, Busch-Nentwich EM, Morash M, Mohlke KL, Rawls JF, Malhotra V, Hussain MM, Farber SA. Publisher Correction: Pla2g12b drives expansion of triglyceride-rich lipoproteins. Nat Commun 2024; 15:2572. [PMID: 38519494 PMCID: PMC10959976 DOI: 10.1038/s41467-024-46847-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024] Open
Affiliation(s)
- James H Thierer
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Johns Hopkins University in Baltimore, Maryland Department of biology, Baltimore, MD, 21218, USA
| | - Ombretta Foresti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, 08003, ES, Spain
| | - Pradeep Kumar Yadav
- Department of Foundations of Medicine, NYU Long Island School of Medicine, Mineola, NY, 11501, USA
- Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, India
| | - Meredith H Wilson
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Johns Hopkins University in Baltimore, Maryland Department of biology, Baltimore, MD, 21218, USA
| | - Tabea O C Moll
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Johns Hopkins University in Baltimore, Maryland Department of biology, Baltimore, MD, 21218, USA
| | - Meng-Chieh Shen
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
| | | | - Margaret Morash
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27708, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27708, USA
| | - Vivek Malhotra
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, 08003, ES, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - M Mahmood Hussain
- Department of Foundations of Medicine, NYU Long Island School of Medicine, Mineola, NY, 11501, USA
| | - Steven A Farber
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA.
- Johns Hopkins University in Baltimore, Maryland Department of biology, Baltimore, MD, 21218, USA.
| |
Collapse
|
2
|
Thierer JH, Foresti O, Yadav PK, Wilson MH, Moll TOC, Shen MC, Busch-Nentwich EM, Morash M, Mohlke KL, Rawls JF, Malhotra V, Hussain MM, Farber SA. Pla2g12b drives expansion of triglyceride-rich lipoproteins. Nat Commun 2024; 15:2095. [PMID: 38453914 PMCID: PMC10920679 DOI: 10.1038/s41467-024-46102-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024] Open
Abstract
Vertebrates transport hydrophobic triglycerides through the circulatory system by packaging them within amphipathic particles called Triglyceride-Rich Lipoproteins. Yet, it remains largely unknown how triglycerides are loaded onto these particles. Mutations in Phospholipase A2 group 12B (PLA2G12B) are known to disrupt lipoprotein homeostasis, but its mechanistic role in this process remains unclear. Here we report that PLA2G12B channels lipids within the lumen of the endoplasmic reticulum into nascent lipoproteins. This activity promotes efficient lipid secretion while preventing excess accumulation of intracellular lipids. We characterize the functional domains, subcellular localization, and interacting partners of PLA2G12B, demonstrating that PLA2G12B is calcium-dependent and tightly associated with the membrane of the endoplasmic reticulum. We also detect profound resistance to atherosclerosis in PLA2G12B mutant mice, suggesting an evolutionary tradeoff between triglyceride transport and cardiovascular disease risk. Here we identify PLA2G12B as a key driver of triglyceride incorporation into vertebrate lipoproteins.
Collapse
Affiliation(s)
- James H Thierer
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Johns Hopkins University in Baltimore, Maryland Department of biology, Baltimore, MD, 21218, USA
| | - Ombretta Foresti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, 08003, ES, Spain
| | - Pradeep Kumar Yadav
- Department of Foundations of Medicine, NYU Long Island School of Medicine, Mineola, NY, 11501, USA
- Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, India
| | - Meredith H Wilson
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Johns Hopkins University in Baltimore, Maryland Department of biology, Baltimore, MD, 21218, USA
| | - Tabea O C Moll
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Johns Hopkins University in Baltimore, Maryland Department of biology, Baltimore, MD, 21218, USA
| | - Meng-Chieh Shen
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
| | | | - Margaret Morash
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27708, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27708, USA
| | - Vivek Malhotra
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, 08003, ES, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - M Mahmood Hussain
- Department of Foundations of Medicine, NYU Long Island School of Medicine, Mineola, NY, 11501, USA
| | - Steven A Farber
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA.
- Johns Hopkins University in Baltimore, Maryland Department of biology, Baltimore, MD, 21218, USA.
| |
Collapse
|
3
|
Jin Y, Kozan D, Anderson JL, Hensley M, Shen MC, Wen J, Moll T, Kozan H, Rawls JF, Farber SA. A high-cholesterol zebrafish diet promotes hypercholesterolemia and fasting-associated liver triglycerides accumulation. bioRxiv 2023:2023.11.01.565134. [PMID: 37961364 PMCID: PMC10635069 DOI: 10.1101/2023.11.01.565134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid-associated disorders. In this study, we provide an improved protocol to assay the impact of a high-cholesterol diet (HCD) on zebrafish lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB-containing lipoproteins (ApoB-LP) and increased plasma levels of cholesterol and cholesterol esters. Feeding of the HCD to larvae (8 days followed by a 1 day fast) and adult female fish (2 weeks, followed by 3 days of fasting) was also associated with a fatty liver phenotype that presented as severe hepatic steatosis. The HCD feeding paradigm doubled the levels of liver triacylglycerol (TG), which was striking because our HCD was only supplemented with cholesterol. The accumulated liver TG was unlikely due to increased de novo lipogenesis or inhibited β-oxidation since no differentially expressed genes in these pathways were found between the livers of fish fed the HCD versus control diets. However, fasted HCD fish had significantly increased lipogenesis gene fasn in adipose tissue and higher free fatty acids (FFA) in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes, which supplied more FFA during fasting, promoting hepatic steatosis. In conclusion, our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.
Collapse
Affiliation(s)
- Yang Jin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Darby Kozan
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Jennifer L Anderson
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States
| | - Monica Hensley
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States
| | - Meng-Chieh Shen
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States
| | - Jia Wen
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, United States
| | - Tabea Moll
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Hannah Kozan
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, United States
| | - Steven A. Farber
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, United States
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| |
Collapse
|
4
|
Abstract
Amino acids are indispensable substrates for protein synthesis in all organisms and incorporated into diverse aspects of metabolic physiology and signaling. However, animals lack the ability to synthesize several of them and must acquire these essential amino acids from their diet or perhaps their associated microbial communities. The essential amino acids therefore occupy a unique position in the health of animals and their relationships with microbes. Here we review recent work connecting microbial production and metabolism of essential amino acids to host biology, and the reciprocal impacts of host metabolism of essential amino acids on their associated microbes. We focus on the roles of the branched-chain amino acids (valine, leucine, and isoleucine) and tryptophan on host-microbe communication in the intestine of humans and other vertebrates. We then conclude by highlighting research questions surrounding the less-understood aspects of microbial essential amino acid synthesis in animal hosts.
Collapse
Affiliation(s)
- Jessica R McCann
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA; ,
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA; ,
| |
Collapse
|
5
|
Kelly C, Jawahar J, Davey L, Everitt JI, Galanko JA, Anderson C, Avendano JE, McCann JR, Sartor RB, Valdivia RH, Rawls JF. Spontaneous episodic inflammation in the intestines of mice lacking HNF4A is driven by microbiota and associated with early life microbiota alterations. mBio 2023; 14:e0150423. [PMID: 37526424 PMCID: PMC10470520 DOI: 10.1128/mbio.01504-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 08/02/2023] Open
Abstract
The inflammatory bowel diseases (IBD) occur in genetically susceptible individuals who mount inappropriate immune responses to their microbiota leading to chronic intestinal inflammation. Whereas IBD clinical presentation is well described, how interactions between microbiota and host genotype impact early subclinical stages of the disease remains unclear. The transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) has been associated with human IBD, and deletion of Hnf4a in intestinal epithelial cells (IECs) in mice (Hnf4aΔIEC) leads to spontaneous colonic inflammation by 6-12 mo of age. Here, we tested if pathology in Hnf4aΔIEC mice begins earlier in life and if microbiota contribute to that process. Longitudinal analysis revealed that Hnf4aΔIEC mice reared in specific pathogen-free (SPF) conditions develop episodic elevated fecal lipocalin 2 (Lcn2) and loose stools beginning by 4-5 wk of age. Lifetime cumulative Lcn2 levels correlated with histopathological features of colitis at 12 mo. Antibiotic and gnotobiotic tests showed that these phenotypes in Hnf4aΔIEC mice were dependent on microbiota. Fecal 16S rRNA gene sequencing in SPF Hnf4aΔIEC and control mice disclosed that genotype significantly contributed to differences in microbiota composition by 12 mo, and longitudinal analysis of the Hnf4aΔIEC mice with the highest lifetime cumulative Lcn2 revealed that microbial community differences emerged early in life when elevated fecal Lcn2 was first detected. These microbiota differences included enrichment of a novel phylogroup of Akkermansia muciniphila in Hnf4aΔIEC mice. We conclude that HNF4A functions in IEC to shape composition of the gut microbiota and protect against episodic inflammation induced by microbiota throughout the lifespan. IMPORTANCE The inflammatory bowel diseases (IBD), characterized by chronic inflammation of the intestine, affect millions of people around the world. Although significant advances have been made in the clinical management of IBD, the early subclinical stages of IBD are not well defined and are difficult to study in humans. This work explores the subclinical stages of disease in mice lacking the IBD-associated transcription factor HNF4A in the intestinal epithelium. Whereas these mice do not develop overt disease until late in adulthood, we find that they display episodic intestinal inflammation, loose stools, and microbiota changes beginning in very early life stages. Using germ-free and antibiotic-treatment experiments, we reveal that intestinal inflammation in these mice was dependent on the presence of microbiota. These results suggest that interactions between host genotype and microbiota can drive early subclinical pathologies that precede the overt onset of IBD and describe a mouse model to explore those important processes.
Collapse
Affiliation(s)
- Cecelia Kelly
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jayanth Jawahar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jeffrey I. Everitt
- Department of Pathology, Research Animal Pathology Core, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joseph A. Galanko
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Chelsea Anderson
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan E. Avendano
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - R. Balfour Sartor
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| |
Collapse
|
6
|
Petrone BL, Aqeel A, Jiang S, Durand HK, Dallow EP, McCann JR, Dressman HK, Hu Z, Tenekjian CB, Yancy WS, Lin PH, Scialla JJ, Seed PC, Rawls JF, Armstrong SC, Stevens J, David LA. Diversity of plant DNA in stool is linked to dietary quality, age, and household income. Proc Natl Acad Sci U S A 2023; 120:e2304441120. [PMID: 37368926 PMCID: PMC10319039 DOI: 10.1073/pnas.2304441120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/10/2023] [Indexed: 06/29/2023] Open
Abstract
Eating a varied diet is a central tenet of good nutrition. Here, we develop a molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL-P6 marker to 1,029 fecal samples from 324 participants across two interventional feeding studies and three observational cohorts. The number of plant taxa per sample (plant metabarcoding richness or pMR) correlated with recorded intakes in interventional diets and with indices calculated from a food frequency questionnaire in typical diets (ρ = 0.40 to 0.63). In adolescents unable to collect validated dietary survey data, trnL metabarcoding detected 111 plant taxa, with 86 consumed by more than one individual and four (wheat, chocolate, corn, and potato family) consumed by >70% of individuals. Adolescent pMR was associated with age and household income, replicating prior epidemiologic findings. Overall, trnL metabarcoding promises an objective and accurate measure of the number and types of plants consumed that is applicable to diverse human populations.
Collapse
Affiliation(s)
- Brianna L. Petrone
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
- Medical Scientist Training Program, Duke University School of Medicine, Durham, NC27710
| | - Ammara Aqeel
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Heather K. Durand
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Eric P. Dallow
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Holly K. Dressman
- Duke Microbiome Core Facility, Center for Genomic and Computational Biology, Duke University, Durham, NC27710
| | - Zhengzheng Hu
- Duke Microbiome Core Facility, Center for Genomic and Computational Biology, Duke University, Durham, NC27710
| | | | - William S. Yancy
- Duke Lifestyle and Weight Management Center, Durham, NC27710
- Department of Medicine, Duke University School of Medicine, Durham, NC27710
| | - Pao-Hwa Lin
- Department of Medicine, Nephrology Division, Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC27705
| | - Julia J. Scialla
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA22903
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA22903
| | - Patrick C. Seed
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL60611
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
- Duke Microbiome Center, Duke University School of Medicine, Durham, NC27710
| | - Sarah C. Armstrong
- Department of Pediatrics, Duke University School of Medicine, Durham, NC27710
| | - June Stevens
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Lawrence A. David
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
- Duke Microbiome Center, Duke University School of Medicine, Durham, NC27710
| |
Collapse
|
7
|
Heppert JK, Lickwar CR, Tillman MC, Davis BR, Davison JM, Lu HY, Chen W, Busch-Nentwich EM, Corcoran DL, Rawls JF. Conserved roles for Hnf4 family transcription factors in zebrafish development and intestinal function. Genetics 2022; 222:iyac133. [PMID: 36218393 PMCID: PMC9713462 DOI: 10.1093/genetics/iyac133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 12/13/2022] Open
Abstract
Transcription factors play important roles in the development of the intestinal epithelium and its ability to respond to endocrine, nutritional, and microbial signals. Hepatocyte nuclear factor 4 family nuclear receptors are liganded transcription factors that are critical for the development and function of multiple digestive organs in vertebrates, including the intestinal epithelium. Zebrafish have 3 hepatocyte nuclear factor 4 homologs, of which, hnf4a was previously shown to mediate intestinal responses to microbiota in zebrafish larvae. To discern the functions of other hepatocyte nuclear factor 4 family members in zebrafish development and intestinal function, we created and characterized mutations in hnf4g and hnf4b. We addressed the possibility of genetic redundancy amongst these factors by creating double and triple mutants which showed different rates of survival, including apparent early lethality in hnf4a; hnf4b double mutants and triple mutants. RNA sequencing performed on digestive tracts from single and double mutant larvae revealed extensive changes in intestinal gene expression in hnf4a mutants that were amplified in hnf4a; hnf4g mutants, but limited in hnf4g mutants. Changes in hnf4a and hnf4a; hnf4g mutants were reminiscent of those seen in mice including decreased expression of genes involved in intestinal function and increased expression of cell proliferation genes, and were validated using transgenic reporters and EdU labeling in the intestinal epithelium. Gnotobiotics combined with RNA sequencing also showed hnf4g has subtler roles than hnf4a in host responses to microbiota. Overall, phenotypic changes in hnf4a single mutants were strongly enhanced in hnf4a; hnf4g double mutants, suggesting a conserved partial genetic redundancy between hnf4a and hnf4g in the vertebrate intestine.
Collapse
Affiliation(s)
- Jennifer K Heppert
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Colin R Lickwar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthew C Tillman
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Briana R Davis
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - James M Davison
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hsiu-Yi Lu
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wei Chen
- Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - David L Corcoran
- Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| |
Collapse
|
8
|
Tong W, Hannou SA, Wang Y, Astapova I, Sargsyan A, Monn R, Thiriveedi V, Li D, McCann JR, Rawls JF, Roper J, Zhang GF, Herman MA. The intestine is a major contributor to circulating succinate in mice. FASEB J 2022; 36:e22546. [PMID: 36106538 PMCID: PMC9523828 DOI: 10.1096/fj.202200135rr] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 10/03/2023]
Abstract
The tricarboxylic acid (TCA) cycle is the epicenter of cellular aerobic metabolism. TCA cycle intermediates facilitate energy production and provide anabolic precursors, but also function as intra- and extracellular metabolic signals regulating pleiotropic biological processes. Despite the importance of circulating TCA cycle metabolites as signaling molecules, the source of circulating TCA cycle intermediates remains uncertain. We observe that in mice, the concentration of TCA cycle intermediates in the portal blood exceeds that in tail blood indicating that the gut is a major contributor to circulating TCA cycle metabolites. With a focus on succinate as a representative of a TCA cycle intermediate with signaling activities and using a combination of gut microbiota depletion mouse models and isotopomer tracing, we demonstrate that intestinal microbiota is not a major contributor to circulating succinate. Moreover, we demonstrate that endogenous succinate production is markedly higher than intestinal succinate absorption in normal physiological conditions. Altogether, these results indicate that endogenous succinate production within the intestinal tissue is a major physiological source of circulating succinate. These results provide a foundation for an investigation into the role of the intestine in regulating circulating TCA cycle metabolites and their potential signaling effects on health and disease.
Collapse
Affiliation(s)
- Wenxin Tong
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Sarah A. Hannou
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - You Wang
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Inna Astapova
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
- Division of Endocrinology, Metabolism, and Nutrition, Duke University, Durham, North Carolina, USA
| | - Ashot Sargsyan
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Ruby Monn
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | | | - Diana Li
- Division of Gastroenterology, Duke University, Durham, North Carolina, USA
| | - Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University, Durham, NC, USA
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Jatin Roper
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
- Division of Gastroenterology, Duke University, Durham, North Carolina, USA
| | - Guo-fang Zhang
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Mark A. Herman
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
- Division of Endocrinology, Metabolism, and Nutrition, Duke University, Durham, North Carolina, USA
| |
Collapse
|
9
|
Levraud JP, Rawls JF, Clatworthy AE. Using zebrafish to understand reciprocal interactions between the nervous and immune systems and the microbial world. J Neuroinflammation 2022; 19:170. [PMID: 35765004 PMCID: PMC9238045 DOI: 10.1186/s12974-022-02506-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Jean-Pierre Levraud
- Université Paris-Saclay, CNRS, Institut Pasteur, Université Paris-Cité, Institut des Neurosciences Paris-Saclay, 91400, Saclay, France.
| | - John F. Rawls
- grid.26009.3d0000 0004 1936 7961Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, 213 Research Drive, Durham, NC 27710 USA
| | - Anne E. Clatworthy
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114 USA
| |
Collapse
|
10
|
Suarez L, Skinner AC, Truong T, McCann JR, Rawls JF, Seed PC, Armstrong SC. Advanced Obesity Treatment Selection among Adolescents in a Pediatric Weight Management Program. Child Obes 2022; 18:237-245. [PMID: 34757829 PMCID: PMC9145572 DOI: 10.1089/chi.2021.0190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
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.
Collapse
Affiliation(s)
- Lilianna Suarez
- Duke University School of Medicine, Durham, NC, USA.,Address correspondence to: Lilianna Suarez, MPH, Duke University School of Medicine, 4020 N Roxboro Street, Durham, NC 27704, USA
| | - Asheley C. Skinner
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA.,Duke Clinical Research Institute, Duke University, Durham, NC, USA
| | - Tracy Truong
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Patrick C. Seed
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sarah C. Armstrong
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA.,Duke Clinical Research Institute, Duke University, Durham, NC, USA
| |
Collapse
|
11
|
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. Starvation causes changes in the intestinal transcriptome and microbiome that are reversed upon refeeding. BMC Genomics 2022; 23:225. [PMID: 35317738 PMCID: PMC8941736 DOI: 10.1186/s12864-022-08447-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/07/2022] [Indexed: 12/16/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Jayanth Jawahar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Alexander W McCumber
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708, USA
| | - Colin R Lickwar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Caroline R Amoroso
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA
| | - Sol Gomez de la Torre Canny
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Sandi Wong
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Margaret Morash
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, 27710, USA
| | - James H Thierer
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Steven A Farber
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, 27710, USA.
| |
Collapse
|
12
|
Hurst JH, McCumber AW, Aquino JN, Rodriguez J, Heston SM, Lugo DJ, Rotta AT, Turner NA, Pfeiffer TS, Gurley TC, Moody MA, Denny TN, Rawls JF, Clark JS, Woods CW, Kelly MS. Age-Related Changes in the Nasopharyngeal Microbiome Are Associated With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and Symptoms Among Children, Adolescents, and Young Adults. Clin Infect Dis 2022; 75:e928-e937. [PMID: 35247047 PMCID: PMC8903463 DOI: 10.1093/cid/ciac184] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Children are less susceptible to SARS-CoV-2 infection and typically have milder illness courses than adults, but the factors underlying these age-associated differences are not well understood. The upper respiratory microbiome undergoes substantial shifts during childhood and is increasingly recognized to influence host defense against respiratory pathogens. Thus, we sought to identify upper respiratory microbiome features associated with SARS-CoV-2 infection susceptibility and illness severity. METHODS We collected clinical data and nasopharyngeal swabs from 285 children, adolescents, and young adults (<21 years) with documented SARS-CoV-2 exposure. We used 16S ribosomal RNA gene sequencing to characterize the nasopharyngeal microbiome and evaluated for age-adjusted associations between microbiome characteristics and SARS-CoV-2 infection status and respiratory symptoms. RESULTS Nasopharyngeal microbiome composition varied with age (PERMANOVA, P < .001; R2 = 0.06) and between SARS-CoV-2-infected individuals with and without respiratory symptoms (PERMANOVA, P = .002; R2 = 0.009). SARS-CoV-2-infected participants with Corynebacterium/Dolosigranulum-dominant microbiome profiles were less likely to have respiratory symptoms than infected participants with other nasopharyngeal microbiome profiles (OR: .38; 95% CI: .18-.81). Using generalized joint attributed modeling, we identified 9 bacterial taxa associated with SARS-CoV-2 infection and 6 taxa differentially abundant among SARS-CoV-2-infected participants with respiratory symptoms; the magnitude of these associations was strongly influenced by age. CONCLUSIONS We identified interactive relationships between age and specific nasopharyngeal microbiome features that are associated with SARS-CoV-2 infection susceptibility and symptoms in children, adolescents, and young adults. Our data suggest that the upper respiratory microbiome may be a mechanism by which age influences SARS-CoV-2 susceptibility and illness severity.
Collapse
Affiliation(s)
| | | | - Jhoanna N Aquino
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Javier Rodriguez
- Children’s Clinical Research Unit, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sarah M Heston
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Debra J Lugo
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandre T Rotta
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas A Turner
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Trevor S Pfeiffer
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Thaddeus C Gurley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - M Anthony Moody
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA,Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USAand
| | - James S Clark
- Nicholas School of the Environment, Duke University, Durham, North Carolina, USA
| | - Christopher W Woods
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Matthew S Kelly
- Correspondence: M. S. Kelly, 2301 Erwin Road, Durham, NC 27710 USA ()
| |
Collapse
|
13
|
Kelly MS, Plunkett C, Yu Y, Aquino JN, Patel SM, Hurst JH, Young RR, Smieja M, Steenhoff AP, Arscott-Mills T, Feemster KA, Boiditswe S, Leburu T, Mazhani T, Patel MZ, Rawls JF, Jawahar J, Shah SS, Polage CR, Cunningham CK, Seed PC. Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy. ISME J 2022; 16:655-665. [PMID: 34511605 PMCID: PMC8857224 DOI: 10.1038/s41396-021-01108-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/22/2021] [Accepted: 09/03/2021] [Indexed: 02/08/2023]
Abstract
Streptococcus pneumoniae (pneumococcus) is a leading cause of severe infections among children and adults. Interactions between commensal microbes in the upper respiratory tract and S. pneumoniae are poorly described. In this study, we sought to identify interspecies interactions that modify the risk of S. pneumoniae colonization during infancy and to describe development of the upper respiratory microbiome during infancy in a sub-Saharan African setting. We collected nasopharyngeal swabs monthly (0-6 months of age) or bimonthly (6-12 months of age) from 179 mother-infant dyads in Botswana. We used 16S ribosomal RNA gene sequencing to characterize the nasopharyngeal microbiome and identified S. pneumoniae colonization using a species-specific PCR assay. We detect S. pneumoniae colonization in 144 (80%) infants at a median age of 71 days and identify a strong negative association between the relative abundance of the bacterial genera Corynebacterium within the infant nasopharyngeal microbiome and the risk of S. pneumoniae colonization. Using in vitro cultivation experiments, we demonstrate growth inhibition of S. pneumoniae by secreted factors from strains of several Corynebacterium species isolated from these infants. Finally, we demonstrate that antibiotic exposures and the winter season are associated with a decline in the relative abundance of Corynebacterium within the nasopharyngeal microbiome, while breastfeeding is associated with an increase in the Corynebacterium relative abundance. Our findings provide novel insights into the interspecies interactions that contribute to colonization resistance to S. pneumoniae and suggest that the nasopharyngeal microbiome may be a previously unrecognized mechanism by which environmental factors influence the risk of pneumococcal infections during childhood. Moreover, this work lays the foundation for future studies seeking to use targeted manipulation of the nasopharyngeal microbiome to prevent infections caused by S. pneumoniae.
Collapse
Affiliation(s)
- Matthew S. Kelly
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana ,grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Catherine Plunkett
- grid.16753.360000 0001 2299 3507Division of Pediatric Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - Yahe Yu
- grid.40803.3f0000 0001 2173 6074Department of Mathematics, North Carolina State University, Raleigh, NC USA
| | - Jhoanna N. Aquino
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Sweta M. Patel
- grid.26009.3d0000 0004 1936 7961Division of Pulmonary Allergy, and Critical Care Medicine, Duke University, Durham, NC USA
| | - Jillian H. Hurst
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Rebecca R. Young
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Marek Smieja
- grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada
| | - Andrew P. Steenhoff
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana ,grid.239552.a0000 0001 0680 8770Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.239552.a0000 0001 0680 8770Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Tonya Arscott-Mills
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana ,grid.239552.a0000 0001 0680 8770Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Kristen A. Feemster
- grid.239552.a0000 0001 0680 8770Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Sefelani Boiditswe
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Tirayaone Leburu
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Tiny Mazhani
- grid.7621.20000 0004 0635 5486University of Botswana School of Medicine, Gaborone, Botswana
| | - Mohamed Z. Patel
- grid.7621.20000 0004 0635 5486University of Botswana School of Medicine, Gaborone, Botswana
| | - John F. Rawls
- grid.26009.3d0000 0004 1936 7961Department of Molecular Genetics and Microbiology, Duke University, Durham, NC USA
| | - Jayanth Jawahar
- grid.26009.3d0000 0004 1936 7961Department of Molecular Genetics and Microbiology, Duke University, Durham, NC USA
| | - Samir S. Shah
- grid.239573.90000 0000 9025 8099Divisions of Hospital Medicine and Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Christopher R. Polage
- grid.26009.3d0000 0004 1936 7961Department of Pathology, Duke University, Durham, NC USA
| | - Coleen K. Cunningham
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Patrick C. Seed
- grid.16753.360000 0001 2299 3507Division of Pediatric Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| |
Collapse
|
14
|
Abstract
The developmental programs that build and sustain animal forms also encode the capacity to sense and adapt to the microbial world within which they evolved. This is abundantly apparent in the development of the digestive tract, which typically harbors the densest microbial communities of the body. Here, we review studies in human, mouse, zebrafish and Drosophila that are revealing how the microbiota impacts the development of the gut and its communication with the nervous system, highlighting important implications for human and animal health.
Collapse
|
15
|
Yan C, Yang Q, Zhang S, Millar DG, Alpert EJ, Do D, Veloso A, Brunson DC, Drapkin BJ, Stanzione M, Scarfò I, Moore JC, Iyer S, Qin Q, Wei Y, McCarthy KM, Rawls JF, Dyson NJ, Cobbold M, Maus MV, Langenau DM. Single-cell imaging of T cell immunotherapy responses in vivo. J Exp Med 2021; 218:e20210314. [PMID: 34415995 PMCID: PMC8383813 DOI: 10.1084/jem.20210314] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/19/2021] [Accepted: 07/09/2021] [Indexed: 12/22/2022] Open
Abstract
T cell immunotherapies have revolutionized treatment for a subset of cancers. Yet, a major hurdle has been the lack of facile and predicative preclinical animal models that permit dynamic visualization of T cell immune responses at single-cell resolution in vivo. Here, optically clear immunocompromised zebrafish were engrafted with fluorescent-labeled human cancers along with chimeric antigen receptor T (CAR T) cells, bispecific T cell engagers (BiTEs), and antibody peptide epitope conjugates (APECs), allowing real-time single-cell visualization of T cell-based immunotherapies in vivo. This work uncovered important differences in the kinetics of T cell infiltration, tumor cell engagement, and killing between these immunotherapies and established early endpoint analysis to predict therapy responses. We also established EGFR-targeted immunotherapies as a powerful approach to kill rhabdomyosarcoma muscle cancers, providing strong preclinical rationale for assessing a wider array of T cell immunotherapies in this disease.
Collapse
Affiliation(s)
- Chuan Yan
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| | - Qiqi Yang
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| | - Songfa Zhang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
| | - David G. Millar
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
| | - Eric J. Alpert
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| | - Daniel Do
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| | - Alexandra Veloso
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| | - Dalton C. Brunson
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| | - Benjamin J. Drapkin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
| | - Marcello Stanzione
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
| | - Irene Scarfò
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
| | - John C. Moore
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| | - Sowmya Iyer
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| | - Qian Qin
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| | - Yun Wei
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| | - Karin M. McCarthy
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC
| | - Nick J. Dyson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
| | - Mark Cobbold
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Early Oncology R&D, AstraZeneca, Gaithersburg, MD
| | - Marcela V. Maus
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
| | - David M. Langenau
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
| |
Collapse
|
16
|
Wen J, Mercado GP, Volland A, Doden HL, Lickwar CR, Crooks T, Kakiyama G, Kelly C, Cocchiaro JL, Ridlon JM, Rawls JF. Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine. Sci Adv 2021; 7:eabg1371. [PMID: 34301599 PMCID: PMC8302129 DOI: 10.1126/sciadv.abg1371] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/07/2021] [Indexed: 05/02/2023]
Abstract
Bile salt synthesis, secretion into the intestinal lumen, and resorption in the ileum occur in all vertebrate classes. In mammals, bile salt composition is determined by host and microbial enzymes, affecting signaling through the bile salt-binding transcription factor farnesoid X receptor (Fxr). However, these processes in other vertebrate classes remain poorly understood. We show that key components of hepatic bile salt synthesis and ileal transport pathways are conserved and under control of Fxr in zebrafish. Zebrafish bile salts consist primarily of a C27 bile alcohol and a C24 bile acid that undergo multiple microbial modifications including bile acid deconjugation that augments Fxr activity. Using single-cell RNA sequencing, we provide a cellular atlas of the zebrafish intestinal epithelium and uncover roles for Fxr in transcriptional and differentiation programs in ileal and other cell types. These results establish zebrafish as a nonmammalian vertebrate model for studying bile salt metabolism and Fxr signaling.
Collapse
Affiliation(s)
- Jia Wen
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Gilberto Padilla Mercado
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Alyssa Volland
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Heidi L Doden
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Colin R Lickwar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Taylor Crooks
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Genta Kakiyama
- Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Cecelia Kelly
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Jordan L Cocchiaro
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Jason M Ridlon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.
- Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
- Cancer Center of Illinois, Urbana, IL, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA.
| |
Collapse
|
17
|
Hurst JH, McCumber AW, Aquino JN, Rodriguez J, Heston SM, Lugo DJ, Rotta AT, Turner NA, Pfeiffer TS, Gurley TC, Moody MA, Denny TN, Rawls JF, Woods CW, Kelly MS. Age-related changes in the upper respiratory microbiome are associated with SARS-CoV-2 susceptibility and illness severity. medRxiv 2021:2021.03.20.21252680. [PMID: 33791716 PMCID: PMC8010748 DOI: 10.1101/2021.03.20.21252680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Children are less susceptible to SARS-CoV-2 and typically have milder illness courses than adults. We studied the nasopharyngeal microbiomes of 274 children, adolescents, and young adults with SARS-CoV-2 exposure using 16S rRNA gene sequencing. We find that higher abundances of Corynebacterium species are associated with SARS-CoV-2 infection and SARS-CoV-2-associated respiratory symptoms, while higher abundances of Dolosigranulum pigrum are present in SARS-CoV-2-infected individuals without respiratory symptoms. We also demonstrate that the abundances of these bacteria are strongly, and independently, associated with age, suggesting that the nasopharyngeal microbiome may be a potentially modifiable mechanism by which age influences SARS-CoV-2 susceptibility and severity. SUMMARY Evaluation of nasopharyngeal microbiome profiles in children, adolescents, and young adults with a SARS-CoV-2-infected close contact identified specific bacterial species that vary in abundance with age and are associated with SARS-CoV-2 susceptibility and the presence of SARS-CoV-2-associated respiratory symptoms.
Collapse
|
18
|
McCann JR, Bihlmeyer NA, Roche K, Catherine C, Jawahar J, Kwee LC, Younge NE, Silverman J, Ilkayeva O, Sarria C, Zizzi A, Wootton J, Poppe L, Anderson P, Arlotto M, Wei Z, Granek JA, Valdivia RH, David LA, Dressman HK, Newgard CB, Shah SH, Seed PC, Rawls JF, Armstrong SC. The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights. Obesity (Silver Spring) 2021; 29:569-578. [PMID: 33624438 PMCID: PMC7927749 DOI: 10.1002/oby.23081] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE The purpose of this study was to establish a biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification. METHODS A total of 223 adolescents aged 10 to 18 years with BMI ≥95th percentile were enrolled, along with 71 healthy weight participants. Clinical data, fasting serum, and fecal samples were collected at repeated intervals over 6 months. Herein, the study design, data collection methods, and interim analysis-including targeted serum metabolite measurements and fecal 16S ribosomal RNA gene amplicon sequencing among adolescents with obesity (n = 27) and healthy weight controls (n = 27)-are presented. RESULTS Adolescents with obesity have higher serum alanine aminotransferase, C-reactive protein, and glycated hemoglobin, and they have lower high-density lipoprotein cholesterol when compared with healthy weight controls. Metabolomics revealed differences in branched-chain amino acid-related metabolites. Also observed was a differential abundance of specific microbial taxa and lower species diversity among adolescents with obesity when compared with the healthy weight group. CONCLUSIONS The Pediatric Metabolism and Microbiome Study (POMMS) biorepository is available as a shared resource. Early findings suggest evidence of a metabolic signature of obesity unique to adolescents, along with confirmation of previously reported findings that describe metabolic and microbiome markers of obesity.
Collapse
Affiliation(s)
- Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Nathan A. Bihlmeyer
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Kimberly Roche
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | | | - Jayanth Jawahar
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Lydia Coulter Kwee
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Noelle E. Younge
- Department of Pediatrics, Duke University, Durham, NC, USA 27710
| | | | - Olga Ilkayeva
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Charles Sarria
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Alexandra Zizzi
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Janet Wootton
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Lisa Poppe
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Paul Anderson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Michelle Arlotto
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Zhengzheng Wei
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Joshua A. Granek
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
- Duke Microbiome Center, Duke University Durham, NC, USA 27710
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
- Duke Microbiome Center, Duke University Durham, NC, USA 27710
| | - Lawrence A. David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
- Duke Microbiome Center, Duke University Durham, NC, USA 27710
| | - Holly K. Dressman
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
- Duke Microbiome Center, Duke University Durham, NC, USA 27710
| | - Christopher B. Newgard
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Svati H. Shah
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
- Duke Clinical Research Institute, Duke University, Durham, NC, USA 27710
| | - Patrick C. Seed
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Stanley Manne Children’s Research Institute, Northwestern University Medical Center, Chicago, IL, USA 60611
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
- Duke Microbiome Center, Duke University Durham, NC, USA 27710
| | - Sarah C. Armstrong
- Department of Pediatrics, Duke University, Durham, NC, USA 27710
- Duke Clinical Research Institute, Duke University, Durham, NC, USA 27710
| |
Collapse
|
19
|
Chen C, Gu Y, Philippe J, Zhang P, Bachman H, Zhang J, Mai J, Rufo J, Rawls JF, Davis EE, Katsanis N, Huang TJ. Acoustofluidic rotational tweezing enables high-speed contactless morphological phenotyping of zebrafish larvae. Nat Commun 2021; 12:1118. [PMID: 33602914 PMCID: PMC7892888 DOI: 10.1038/s41467-021-21373-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
Modern biomedical research and preclinical pharmaceutical development rely heavily on the phenotyping of small vertebrate models for various diseases prior to human testing. In this article, we demonstrate an acoustofluidic rotational tweezing platform that enables contactless, high-speed, 3D multispectral imaging and digital reconstruction of zebrafish larvae for quantitative phenotypic analysis. The acoustic-induced polarized vortex streaming achieves contactless and rapid (~1 s/rotation) rotation of zebrafish larvae. This enables multispectral imaging of the zebrafish body and internal organs from different viewing perspectives. Moreover, we develop a 3D reconstruction pipeline that yields accurate 3D models based on the multi-view images for quantitative evaluation of basic morphological characteristics and advanced combinations of metrics. With its contactless nature and advantages in speed and automation, our acoustofluidic rotational tweezing system has the potential to be a valuable asset in numerous fields, especially for developmental biology, small molecule screening in biochemistry, and pre-clinical drug development in pharmacology.
Collapse
Affiliation(s)
- Chuyi Chen
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Yuyang Gu
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Julien Philippe
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Peiran Zhang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Hunter Bachman
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Jinxin Zhang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - John Mai
- Alfred E. Mann Institute for Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Joseph Rufo
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Tony Jun Huang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA.
| |
Collapse
|
20
|
Ye L, Bae M, Cassilly CD, Jabba SV, Thorpe DW, Martin AM, Lu HY, Wang J, Thompson JD, Lickwar CR, Poss KD, Keating DJ, Jordt SE, Clardy J, Liddle RA, Rawls JF. Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways. Cell Host Microbe 2020; 29:179-196.e9. [PMID: 33352109 DOI: 10.1016/j.chom.2020.11.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/08/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022]
Abstract
The intestinal epithelium senses nutritional and microbial stimuli using epithelial sensory enteroendocrine cells (EEC). EECs communicate nutritional information to the nervous system, but whether they also relay signals from intestinal microbes remains unknown. Using in vivo real-time measurements of EEC and nervous system activity in zebrafish, we discovered that the bacteria Edwardsiella tarda activate EECs through the receptor transient receptor potential ankyrin A1 (Trpa1) and increase intestinal motility. Microbial, pharmacological, or optogenetic activation of Trpa1+EECs directly stimulates vagal sensory ganglia and activates cholinergic enteric neurons by secreting the neurotransmitter 5-hydroxytryptamine (5-HT). A subset of indole derivatives of tryptophan catabolism produced by E. tarda and other gut microbes activates zebrafish EEC Trpa1 signaling. These catabolites also directly stimulate human and mouse Trpa1 and intestinal 5-HT secretion. These results establish a molecular pathway by which EECs regulate enteric and vagal neuronal pathways in response to microbial signals.
Collapse
Affiliation(s)
- Lihua Ye
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA; Division of Gastroenterology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Munhyung Bae
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Chelsi D Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sairam V Jabba
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Daniel W Thorpe
- Flinders Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Alyce M Martin
- Flinders Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Hsiu-Yi Lu
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jinhu Wang
- Division of Cardiology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - John D Thompson
- Department of Cell Biology, Regeneration Next, Duke University School of Medicine, Durham, NC 27710, USA
| | - Colin R Lickwar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA; Division of Gastroenterology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth D Poss
- Department of Cell Biology, Regeneration Next, Duke University School of Medicine, Durham, NC 27710, USA
| | - Damien J Keating
- Flinders Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Sven-Eric Jordt
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Rodger A Liddle
- Division of Gastroenterology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Veterans Affairs, Durham, NC 27705, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA; Division of Gastroenterology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
| |
Collapse
|
21
|
Cholan PM, Han A, Woodie BR, Watchon M, Kurz AR, Laird AS, Britton WJ, Ye L, Holmes ZC, McCann JR, David LA, Rawls JF, Oehlers SH. Conserved anti-inflammatory effects and sensing of butyrate in zebrafish. Gut Microbes 2020; 12:1-11. [PMID: 33064972 PMCID: PMC7575005 DOI: 10.1080/19490976.2020.1824563] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Short-chain fatty acids (SCFAs) are produced by microbial fermentation of dietary fiber in the gut. Butyrate is a particularly important SCFA with anti-inflammatory properties and is generally present at lower levels in inflammatory diseases associated with gut microbiota dysbiosis in mammals. We aimed to determine if SCFAs are produced by the zebrafish microbiome and if SCFAs exert conserved effects on zebrafish immunity as an example of the non-mammalian vertebrate immune system. We demonstrate that bacterial communities from adult zebrafish intestines synthesize all three main SCFA in vitro, although SCFA were below our detectable limits in zebrafish intestines in vivo. Immersion in butyrate, but not acetate or propionate, reduced the recruitment of neutrophils and M1-type pro-inflammatory macrophages to wounds. We found conservation of butyrate sensing by neutrophils via orthologs of the hydroxycarboxylic acid receptor 1 (hcar1) gene. Neutrophils from Hcar1-depleted embryos were no longer responsive to the anti-inflammatory effects of butyrate, while macrophage sensitivity to butyrate was independent of Hcar1. Our data demonstrate conservation of anti-inflammatory butyrate effects and identify the presence of a conserved molecular receptor in fish.
Collapse
Affiliation(s)
- Pradeep Manuneedhi Cholan
- Tuberculosis Research Program at the Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Alvin Han
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine , Durham, NC, USA
| | - Brad R Woodie
- Tuberculosis Research Program at the Centenary Institute, The University of Sydney , Camperdown, Australia.,Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine , Durham, NC, USA
| | - Maxinne Watchon
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University , Macquarie Park, Australia.,Sydney Medical School, The University of Sydney , Camperdown, Australia
| | - Angela Rm Kurz
- Centenary Imaging and Sydney Cytometry at the Centenary Institute, The University of Sydney , Camperdown, Australia
| | - Angela S Laird
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University , Macquarie Park, Australia
| | - Warwick J Britton
- Tuberculosis Research Program at the Centenary Institute, The University of Sydney , Camperdown, Australia.,The University of Sydney, Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, And Marie Bashir Institute , Camperdown, Australia.,Department of Clinical Immunology, Royal Prince Alfred Hospital , Camperdown, Australia
| | - Lihua Ye
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine , Durham, NC, USA
| | - Zachary C Holmes
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine , Durham, NC, USA
| | - Jessica R McCann
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine , Durham, NC, USA
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine , Durham, NC, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine , Durham, NC, USA
| | - Stefan H Oehlers
- Tuberculosis Research Program at the Centenary Institute, The University of Sydney , Camperdown, Australia.,The University of Sydney, Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, And Marie Bashir Institute , Camperdown, Australia
| |
Collapse
|
22
|
Holmes ZC, Silverman JD, Dressman HK, Wei Z, Dallow EP, Armstrong SC, Seed PC, Rawls JF, David LA. Short-Chain Fatty Acid Production by Gut Microbiota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition. mBio 2020; 11:e00914-20. [PMID: 32788375 PMCID: PMC7439474 DOI: 10.1128/mbio.00914-20] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/13/2020] [Indexed: 12/20/2022] Open
Abstract
Pediatric obesity remains a public health burden and continues to increase in prevalence. The gut microbiota plays a causal role in obesity and is a promising therapeutic target. Specifically, the microbial production of short-chain fatty acids (SCFA) from the fermentation of otherwise indigestible dietary carbohydrates may protect against pediatric obesity and metabolic syndrome. Still, it has not been demonstrated that therapies involving microbiota-targeting carbohydrates, known as prebiotics, will enhance gut bacterial SCFA production in children and adolescents with obesity (age, 10 to 18 years old). Here, we used an in vitro system to examine the SCFA production by fecal microbiota from 17 children with obesity when exposed to five different commercially available over-the-counter (OTC) prebiotic supplements. We found microbiota from all 17 patients actively metabolized most prebiotics. Still, supplements varied in their acidogenic potential. Significant interdonor variation also existed in SCFA production, which 16S rRNA sequencing supported as being associated with differences in the host microbiota composition. Last, we found that neither fecal SCFA concentration, microbiota SCFA production capacity, nor markers of obesity positively correlated with one another. Together, these in vitro findings suggest the hypothesis that OTC prebiotic supplements may be unequal in their ability to stimulate SCFA production in children and adolescents with obesity and that the most acidogenic prebiotic may differ across individuals.IMPORTANCE Pediatric obesity remains a major public health problem in the United States, where 17% of children and adolescents are obese, and rates of pediatric "severe obesity" are increasing. Children and adolescents with obesity face higher health risks, and noninvasive therapies for pediatric obesity often have limited success. The human gut microbiome has been implicated in adult obesity, and microbiota-directed therapies can aid weight loss in adults with obesity. However, less is known about the microbiome in pediatric obesity, and microbiota-directed therapies are understudied in children and adolescents. Our research has two important findings: (i) dietary prebiotics (fiber) result in the microbiota from adolescents with obesity producing more SCFA, and (ii) the effectiveness of each prebiotic is donor dependent. Together, these findings suggest that prebiotic supplements could help children and adolescents with obesity, but that these therapies may not be "one size fits all."
Collapse
Affiliation(s)
- Zachary C Holmes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Justin D Silverman
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, USA
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina, USA
| | - Holly K Dressman
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Microbiome Shared Resource, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Zhengzheng Wei
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Eric P Dallow
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sarah C Armstrong
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Patrick C Seed
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, USA
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| |
Collapse
|
23
|
Armstrong SC, Windom M, Bihlmeyer NA, Li JS, Shah SH, Story M, Zucker N, Kraus WE, Pagidipati N, Peterson E, Wong C, Wiedemeier M, Sibley L, Berchuck SI, Merrill P, Zizzi A, Sarria C, Dressman HK, Rawls JF, Skinner AC. Rationale and design of "Hearts & Parks": study protocol for a pragmatic randomized clinical trial of an integrated clinic-community intervention to treat pediatric obesity. BMC Pediatr 2020; 20:308. [PMID: 32590958 PMCID: PMC7318397 DOI: 10.1186/s12887-020-02190-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/02/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The prevalence of child and adolescent obesity and severe obesity continues to increase despite decades of policy and research aimed at prevention. Obesity strongly predicts cardiovascular and metabolic disease risk; both begin in childhood. Children who receive intensive behavioral interventions can reduce body mass index (BMI) and reverse disease risk. However, delivering these interventions with fidelity at scale remains a challenge. Clinic-community partnerships offer a promising strategy to provide high-quality clinical care and deliver behavioral treatment in local park and recreation settings. The Hearts & Parks study has three broad objectives: (1) evaluate the effectiveness of the clinic-community model for the treatment of child obesity, (2) define microbiome and metabolomic signatures of obesity and response to lifestyle change, and (3) inform the implementation of similar models in clinical systems. METHODS Methods are designed for a pragmatic randomized, controlled clinical trial (n = 270) to test the effectiveness of an integrated clinic-community child obesity intervention as compared with usual care. We are powered to detect a difference in body mass index (BMI) between groups at 6 months, with follow up to 12 months. Secondary outcomes include changes in biomarkers for cardiovascular disease, psychosocial risk, and quality of life. Through collection of biospecimens (serum and stool), additional exploratory outcomes include microbiome and metabolomics biomarkers of response to lifestyle modification. DISCUSSION We present the study design, enrollment strategy, and intervention details for a randomized clinical trial to measure the effectiveness of a clinic-community child obesity treatment intervention. This study will inform a critical area in child obesity and cardiovascular risk research-defining outcomes, implementation feasibility, and identifying potential molecular mechanisms of treatment response. CLINICAL TRIAL REGISTRATION NCT03339440 .
Collapse
Affiliation(s)
- Sarah C Armstrong
- Department of Pediatrics, Duke University, Durham, NC, 27710, USA.,Duke Clinical Research Institute, Duke University, Durham, NC, 27710, USA
| | | | - Nathan A Bihlmeyer
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27710, USA
| | - Jennifer S Li
- Department of Pediatrics, Duke University, Durham, NC, 27710, USA
| | - Svati H Shah
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27710, USA.,Department of Medicine, Duke University, Durham, NC, 27710, USA
| | - Mary Story
- Department of Family Medicine and Community Health, Duke University, Durham, NC, 27710, USA
| | - Nancy Zucker
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, 27710, USA
| | - William E Kraus
- Department of Medicine, Duke University, Durham, NC, 27710, USA
| | - Neha Pagidipati
- Duke Clinical Research Institute, Duke University, Durham, NC, 27710, USA.,Department of Medicine, Duke University, Durham, NC, 27710, USA
| | - Eric Peterson
- Duke Clinical Research Institute, Duke University, Durham, NC, 27710, USA.,Department of Medicine, Duke University, Durham, NC, 27710, USA
| | - Charlene Wong
- Department of Pediatrics, Duke University, Durham, NC, 27710, USA.,Duke Clinical Research Institute, Duke University, Durham, NC, 27710, USA
| | - Manuela Wiedemeier
- Duke Clinical Research Institute, Duke University, Durham, NC, 27710, USA
| | - Lauren Sibley
- University of North Carolina School of Medicine, Chapel Hill, NC, 27516, USA
| | - Samuel I Berchuck
- Department of Statistical Science, Duke University, Durham, NC, 27710, USA
| | - Peter Merrill
- Duke Clinical Research Institute, Duke University, Durham, NC, 27710, USA
| | - Alexandra Zizzi
- Department of Pediatrics, Duke University, Durham, NC, 27710, USA
| | - Charles Sarria
- Department of Pediatrics, Duke University, Durham, NC, 27710, USA
| | - Holly K Dressman
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27708, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27708, USA
| | - Asheley C Skinner
- Duke Clinical Research Institute, Duke University, Durham, NC, 27710, USA. .,Department of Population Health Sciences, Duke University, 215 Morris Street, Suite 210, Durham, NC, 27701, USA.
| |
Collapse
|
24
|
Wen J, Rawls JF. Feeling the Burn: Intestinal Epithelial Cells Modify Their Lipid Metabolism in Response to Bacterial Fermentation Products. Cell Host Microbe 2020; 27:314-316. [PMID: 32164841 DOI: 10.1016/j.chom.2020.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intestinal epithelial absorption of dietary lipids is a major determinant of animal energy balance and metabolic health. Recent studies uncovered significant roles for intestinal microbiota in this process, but underlying mechanisms remain unresolved. Araújo et al. (2020) identify two end-products of bacterial fermentation that regulate intestinal lipid absorption and metabolism.
Collapse
Affiliation(s)
- Jia Wen
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA.
| |
Collapse
|
25
|
Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert J, Hofmockel KS, Holtz ML, Knight R, Mark Welch DB, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL. The emergence of microbiome centres. Nat Microbiol 2019; 5:2-3. [DOI: 10.1038/s41564-019-0644-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
26
|
Ye L, Mueller O, Bagwell J, Bagnat M, Liddle RA, Rawls JF. High fat diet induces microbiota-dependent silencing of enteroendocrine cells. eLife 2019; 8:48479. [PMID: 31793875 PMCID: PMC6937151 DOI: 10.7554/elife.48479] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022] Open
Abstract
Enteroendocrine cells (EECs) are specialized sensory cells in the intestinal epithelium that sense and transduce nutrient information. Consumption of dietary fat contributes to metabolic disorders, but EEC adaptations to high fat feeding were unknown. Here, we established a new experimental system to directly investigate EEC activity in vivo using a zebrafish reporter of EEC calcium signaling. Our results reveal that high fat feeding alters EEC morphology and converts them into a nutrient insensitive state that is coupled to endoplasmic reticulum (ER) stress. We called this novel adaptation 'EEC silencing'. Gnotobiotic studies revealed that germ-free zebrafish are resistant to high fat diet induced EEC silencing. High fat feeding altered gut microbiota composition including enrichment of Acinetobacter bacteria, and we identified an Acinetobacter strain sufficient to induce EEC silencing. These results establish a new mechanism by which dietary fat and gut microbiota modulate EEC nutrient sensing and signaling.
Collapse
Affiliation(s)
- Lihua Ye
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States.,Division of Gastroenterology, Department of Medicine, Duke University School of Medicine, Durham, United States
| | - Olaf Mueller
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States
| | - Jennifer Bagwell
- Department of Cell Biology, Duke University School of Medicine, Durham, United States
| | - Michel Bagnat
- Department of Cell Biology, Duke University School of Medicine, Durham, United States
| | - Rodger A Liddle
- Division of Gastroenterology, Department of Medicine, Duke University School of Medicine, Durham, United States
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States.,Division of Gastroenterology, Department of Medicine, Duke University School of Medicine, Durham, United States
| |
Collapse
|
27
|
Casadei E, Tacchi L, Lickwar CR, Espenschied ST, Davison JM, Muñoz P, Rawls JF, Salinas I. Commensal Bacteria Regulate Gene Expression and Differentiation in Vertebrate Olfactory Systems Through Transcription Factor REST. Chem Senses 2019; 44:615-630. [PMID: 31403159 PMCID: PMC6796929 DOI: 10.1093/chemse/bjz050] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Sensory systems such as the olfactory system detect chemical stimuli and thereby determine the relationships between the animal and its surroundings. Olfaction is one of the most conserved and ancient sensory systems in vertebrates. The vertebrate olfactory epithelium is colonized by complex microbial communities, but microbial contribution to host olfactory gene expression remains unknown. In this study, we show that colonization of germ-free zebrafish and mice with microbiota leads to widespread transcriptional responses in olfactory organs as measured in bulk tissue transcriptomics and RT-qPCR. Germ-free zebrafish olfactory epithelium showed defects in pseudostratification; however, the size of the olfactory pit and the length of the cilia were not different from that of colonized zebrafish. One of the mechanisms by which microbiota control host transcriptional programs is by differential expression and activity of specific transcription factors (TFs). REST (RE1 silencing transcription factor, also called NRSF) is a zinc finger TF that binds to the conserved motif repressor element 1 found in the promoter regions of many neuronal genes with functions in neuronal development and differentiation. Colonized zebrafish and mice showed increased nasal expression of REST, and genes with reduced expression in colonized animals were strongly enriched in REST-binding motifs. Nasal commensal bacteria promoted in vitro differentiation of Odora cells by regulating the kinetics of REST expression. REST knockdown resulted in decreased Odora cell differentiation in vitro. Our results identify a conserved mechanism by which microbiota regulate vertebrate olfactory transcriptional programs and reveal a new role for REST in sensory organs.
Collapse
Affiliation(s)
- Elisa Casadei
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM, USA
| | - Luca Tacchi
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM, USA
| | - Colin R Lickwar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Scott T Espenschied
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - James M Davison
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Pilar Muñoz
- Departamento de Sanidad Animal, Facultad de Veterinaria, Campus de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, Murcia, Spain
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM, USA
| |
Collapse
|
28
|
Abstract
Microbial communities populate the mucosal surfaces of all animals. Metazoans have co-evolved with these microorganisms, forming symbioses that affect the molecular and cellular underpinnings of animal physiology. These microorganisms, collectively referred to as the microbiota, are found on many distinct body sites (including the skin, nasal cavity, and urogenital tract), however the most densely colonized host tissue is the intestinal tract. Although spatially confined within the intestinal lumen, the microbiota and associated products shape the development and function of the host immune system. Studies comparing gnotobiotic animals devoid of any microbes (germ free) with counterparts colonized with selected microbial communities have demonstrated that commensal microorganisms are required for the proper development and function of the immune system at homeostasis and following infectious challenge or injury. Animal model systems have been essential for defining microbiota-dependent shifts in innate immune cell function and intestinal physiology during infection and disease. In particular, the zebrafish has emerged as a powerful vertebrate model organism with unparalleled capacity for in vivo imaging, a full complement of genetic approaches, and facile methods to experimentally manipulate microbial communities. Here we review key insights afforded by the zebrafish into the impact of microbiota on innate immunity, including evidence that the perception of and response to the microbiota is evolutionarily conserved. We also highlight opportunities to strengthen the zebrafish model system, and to gain new insights into microbiota-innate immune interactions that would be difficult to achieve in mammalian models.
Collapse
Affiliation(s)
- Caitlin C Murdoch
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, United States
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, United States
| |
Collapse
|
29
|
Espenschied ST, Cronan MR, Matty MA, Mueller O, Redinbo MR, Tobin DM, Rawls JF. Epithelial delamination is protective during pharmaceutical-induced enteropathy. Proc Natl Acad Sci U S A 2019; 116:16961-16970. [PMID: 31391308 PMCID: PMC6708343 DOI: 10.1073/pnas.1902596116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Intestinal epithelial cell (IEC) shedding is a fundamental response to intestinal damage, yet underlying mechanisms and functions have been difficult to define. Here we model chronic intestinal damage in zebrafish larvae using the nonsteroidal antiinflammatory drug (NSAID) Glafenine. Glafenine induced the unfolded protein response (UPR) and inflammatory pathways in IECs, leading to delamination. Glafenine-induced inflammation was augmented by microbial colonization and associated with changes in intestinal and environmental microbiotas. IEC shedding was a UPR-dependent protective response to Glafenine that restricts inflammation and promotes animal survival. Other NSAIDs did not induce IEC delamination; however, Glafenine also displays off-target inhibition of multidrug resistance (MDR) efflux pumps. We found a subset of MDR inhibitors also induced IEC delamination, implicating MDR efflux pumps as cellular targets underlying Glafenine-induced enteropathy. These results implicate IEC delamination as a protective UPR-mediated response to chemical injury, and uncover an essential role for MDR efflux pumps in intestinal homeostasis.
Collapse
Affiliation(s)
- Scott T Espenschied
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710
| | - Mark R Cronan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710
| | - Molly A Matty
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710
| | - Olaf Mueller
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biochemistry, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599
| | - David M Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710;
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710
| |
Collapse
|
30
|
Yan C, Brunson DC, Tang Q, Do D, Iftimia NA, Moore JC, Hayes MN, Welker AM, Garcia EG, Dubash TD, Hong X, Drapkin BJ, Myers DT, Phat S, Volorio A, Marvin DL, Ligorio M, Dershowitz L, McCarthy KM, Karabacak MN, Fletcher JA, Sgroi DC, Iafrate JA, Maheswaran S, Dyson NJ, Haber DA, Rawls JF, Langenau DM. Visualizing Engrafted Human Cancer and Therapy Responses in Immunodeficient Zebrafish. Cell 2019; 177:1903-1914.e14. [PMID: 31031007 PMCID: PMC6570580 DOI: 10.1016/j.cell.2019.04.004] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 02/19/2019] [Accepted: 03/31/2019] [Indexed: 01/06/2023]
Abstract
Xenograft cell transplantation into immunodeficient mice has become the gold standard for assessing pre-clinical efficacy of cancer drugs, yet direct visualization of single-cell phenotypes is difficult. Here, we report an optically-clear prkdc-/-, il2rga-/- zebrafish that lacks adaptive and natural killer immune cells, can engraft a wide array of human cancers at 37°C, and permits the dynamic visualization of single engrafted cells. For example, photoconversion cell-lineage tracing identified migratory and proliferative cell states in human rhabdomyosarcoma, a pediatric cancer of muscle. Additional experiments identified the preclinical efficacy of combination olaparib PARP inhibitor and temozolomide DNA-damaging agent as an effective therapy for rhabdomyosarcoma and visualized therapeutic responses using a four-color FUCCI cell-cycle fluorescent reporter. These experiments identified that combination treatment arrested rhabdomyosarcoma cells in the G2 cell cycle prior to induction of apoptosis. Finally, patient-derived xenografts could be engrafted into our model, opening new avenues for developing personalized therapeutic approaches in the future.
Collapse
Affiliation(s)
- Chuan Yan
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Dalton C Brunson
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Qin Tang
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Daniel Do
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Nicolae A Iftimia
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - John C Moore
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Madeline N Hayes
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Alessandra M Welker
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Elaine G Garcia
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Taronish D Dubash
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Xin Hong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Benjamin J Drapkin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - David T Myers
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sarah Phat
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Angela Volorio
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Dieuwke L Marvin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Matteo Ligorio
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lyle Dershowitz
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Karin M McCarthy
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Murat N Karabacak
- Shriners Hospitals for Children-Boston, MA 02114, USA; Center for Engineering in Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02114, USA
| | - Jonathan A Fletcher
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dennis C Sgroi
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - John A Iafrate
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Nick J Dyson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - David M Langenau
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA.
| |
Collapse
|
31
|
Murdoch CC, Espenschied ST, Matty MA, Mueller O, Tobin DM, Rawls JF. Intestinal Serum amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization. PLoS Pathog 2019; 15:e1007381. [PMID: 30845179 PMCID: PMC6405052 DOI: 10.1371/journal.ppat.1007381] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/09/2019] [Indexed: 12/25/2022] Open
Abstract
The intestinal microbiota influences the development and function of myeloid lineages such as neutrophils, but the underlying molecular mechanisms are unresolved. Using gnotobiotic zebrafish, we identified the immune effector Serum amyloid A (Saa) as one of the most highly induced transcripts in digestive tissues following microbiota colonization. Saa is a conserved secreted protein produced in the intestine and liver with described effects on neutrophils in vitro, however its in vivo functions remain poorly defined. We engineered saa mutant zebrafish to test requirements for Saa on innate immunity in vivo. Zebrafish mutant for saa displayed impaired neutrophil responses to wounding but augmented clearance of pathogenic bacteria. At baseline, saa mutants exhibited moderate neutrophilia and altered neutrophil tissue distribution. Molecular and functional analyses of isolated neutrophils revealed that Saa suppresses expression of pro-inflammatory markers and bactericidal activity. Saa's effects on neutrophils depended on microbiota colonization, suggesting this protein mediates the microbiota's effects on host innate immunity. To test tissue-specific roles of Saa on neutrophil function, we over-expressed saa in the intestine or liver and found that sufficient to partially complement neutrophil phenotypes observed in saa mutants. These results indicate Saa produced by the intestine in response to microbiota serves as a systemic signal to neutrophils to restrict aberrant activation, decreasing inflammatory tone and bacterial killing potential while simultaneously enhancing their ability to migrate to wounds.
Collapse
Affiliation(s)
- Caitlin C. Murdoch
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Scott T. Espenschied
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Molly A. Matty
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Olaf Mueller
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - David M. Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| |
Collapse
|
32
|
Minchin JEN, Scahill CM, Staudt N, Busch-Nentwich EM, Rawls JF. Deep phenotyping in zebrafish reveals genetic and diet-induced adiposity changes that may inform disease risk. J Lipid Res 2018; 59:1536-1545. [PMID: 29794036 DOI: 10.1194/jlr.d084525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/22/2018] [Indexed: 02/06/2023] Open
Abstract
The regional distribution of adipose tissues is implicated in a wide range of diseases. For example, proportional increases in visceral adipose tissue increase the risk for insulin resistance, diabetes, and CVD. Zebrafish offer a tractable model system by which to obtain unbiased and quantitative phenotypic information on regional adiposity, and deep phenotyping can explore complex disease-related adiposity traits. To facilitate deep phenotyping of zebrafish adiposity traits, we used pairwise correlations between 67 adiposity traits to generate stage-specific adiposity profiles that describe changing adiposity patterns and relationships during growth. Linear discriminant analysis classified individual fish according to an adiposity profile with 87.5% accuracy. Deep phenotyping of eight previously uncharacterized zebrafish mutants identified neuropilin 2b as a novel gene that alters adipose distribution. When we applied deep phenotyping to identify changes in adiposity during diet manipulations, zebrafish that underwent food restriction and refeeding had widespread adiposity changes when compared with continuously fed, equivalently sized control animals. In particular, internal adipose tissues (e.g., visceral adipose) exhibited a reduced capacity to replenish lipid following food restriction. Together, these results in zebrafish establish a new deep phenotyping technique as an unbiased and quantitative method to help uncover new relationships between genotype, diet, and adiposity.
Collapse
Affiliation(s)
- James E N Minchin
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom, EH16 4TJ .,Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
| | - Catherine M Scahill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom, CB10 1SA
| | - Nicole Staudt
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom, CB10 1SA
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom, CB10 1SA.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom, CB2 0QQ
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom, CB2 0QQ
| |
Collapse
|
33
|
Williamson IA, Arnold JW, Samsa LA, Gaynor L, DiSalvo M, Cocchiaro JL, Carroll I, Azcarate-Peril MA, Rawls JF, Allbritton NL, Magness ST. A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology. Cell Mol Gastroenterol Hepatol 2018; 6:301-319. [PMID: 30123820 PMCID: PMC6092482 DOI: 10.1016/j.jcmgh.2018.05.004] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022]
Abstract
Background & Aims The human gut microbiota is becoming increasingly recognized as a key factor in homeostasis and disease. The lack of physiologically relevant in vitro models to investigate host-microbe interactions is considered a substantial bottleneck for microbiota research. Organoids represent an attractive model system because they are derived from primary tissues and embody key properties of the native gut lumen; however, access to the organoid lumen for experimental perturbation is challenging. Here, we report the development and validation of a high-throughput organoid microinjection system for cargo delivery to the organoid lumen and high-content sampling. Methods A microinjection platform was engineered using off-the-shelf and 3-dimensional printed components. Microinjection needles were modified for vertical trajectories and reproducible injection volumes. Computer vision (CVis) and microfabricated CellRaft Arrays (Cell Microsystems, Research Triangle Park, NC) were used to increase throughput and enable high-content sampling of mock bacterial communities. Modeling preformed using the COMSOL Multiphysics platform predicted a hypoxic luminal environment that was functionally validated by transplantation of fecal-derived microbial communities and monocultures of a nonsporulating anaerobe. Results CVis identified and logged locations of organoids suitable for injection. Reproducible loads of 0.2 nL could be microinjected into the organoid lumen at approximately 90 organoids/h. CVis analyzed and confirmed retention of injected cargos in approximately 500 organoids over 18 hours and showed the requirement to normalize for organoid growth for accurate assessment of barrier function. CVis analyzed growth dynamics of a mock community of green fluorescent protein- or Discosoma sp. red fluorescent protein-expressing bacteria, which grew within the organoid lumen even in the presence of antibiotics to control media contamination. Complex microbiota communities from fecal samples survived and grew in the colonoid lumen without appreciable changes in complexity. Conclusions High-throughput microinjection into organoids represents a next-generation in vitro approach to investigate gastrointestinal luminal physiology and the gastrointestinal microbiota.
Collapse
Key Words
- 2D, 2-dimensional
- 3D, 3-dimensional
- Anaerobic
- Barrier Function
- CAG, chicken beta-actin promoter with CMV enhancer
- CFU, colony-forming unit
- CRA, CellRaft Array
- CVis, computer vision
- EGFP, enhanced green fluorescent protein
- FITC, fluorescein isothiocyanate
- Fecal Microbiota
- GFP, green fluorescent protein
- GI, gastrointestinal
- HF, hydrogen fluoride
- High-Content Sampling
- High-Throughput
- Microinjection
- OUT, operational taxonomic unit
- Organoid
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- QIIME, Quantitative Insights Into Microbial Ecology
- WT, wild-type
- hiPS, Human Induced Pluripotent Stem Cell
- rRNA, ribosomal RNA
Collapse
Affiliation(s)
- Ian A. Williamson
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Jason W. Arnold
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Leigh Ann Samsa
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Liam Gaynor
- Graduate Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Matthew DiSalvo
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Jordan L. Cocchiaro
- Department of Molecular Genetics and Microbiology Medicine, Duke University, Durham, North Carolina
| | - Ian Carroll
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - M. Andrea Azcarate-Peril
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology Medicine, Duke University, Durham, North Carolina
| | - Nancy L. Allbritton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Scott T. Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| |
Collapse
|
34
|
King J, Foster J, Davison JM, Rawls JF, Breton G. Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation. Zebrafish 2017; 15:202-205. [PMID: 29173090 DOI: 10.1089/zeb.2017.1486] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The completion of the zebrafish genome sequence and advances in miniaturization and multiplexing were essential to the creation of techniques such as RNA-seq, ChIP-seq, and high-throughput behavioral and chemical screens. Multiplexing was also instrumental in the recent enhancement of the classic yeast one-hybrid interaction techniques to provide unprecedented discovery capabilities for protein-DNA interactions. Unfortunately its use for zebrafish research is currently hampered by the lack of an open reading frame (ORF) clone collection. As a first step toward a complete collection, we describe a small library of transcriptional regulatory proteins comprising 142 ORFs and its potential applications.
Collapse
Affiliation(s)
- Justin King
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
| | - Justin Foster
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
| | - James M Davison
- 2 Department of Molecular Genetics and Microbiology, Duke University School of Medicine , Durham, North Carolina
| | - John F Rawls
- 2 Department of Molecular Genetics and Microbiology, Duke University School of Medicine , Durham, North Carolina
| | - Ghislain Breton
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
| |
Collapse
|
35
|
Abstract
Non-communicable diseases (NCDs) such as cardiovascular disease, diabetes and cancer were responsible for 68% of all deaths worldwide in 2012. The regional distribution of lipid deposited within adipose tissue (AT) - so called body fat distribution (BFD) - is a strong risk factor for NCDs. BFD is highly heritable; however, the genetic basis of BFD is almost entirely unknown. Genome-wide association studies have identified several loci associated with BFD, including at Plexin D1 (PLXND1) - a gene known to modulate angiogenesis. We recently demonstrated that zebrafish homozygous for a null mutation in plxnd1 had a reduced capacity to store lipid in visceral AT (VAT) leading to altered BFD. Moreover, we found that type V collagens were upregulated in plxnd1 mutants, and mediated the inhibitory effect of Plxnd1 on VAT growth. These results strengthen evidence that Plxnd1 influences BFD in human populations, and validate zebrafish as a model to study BFD. However, many pertinent questions remain unanswered. Here we outline potential Plxnd1 mechanisms of action in AT, and describe the genetic architecture at human PLXND1 that is associated with BFD and NCD susceptibility.
Collapse
Affiliation(s)
- James E. N. Minchin
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| |
Collapse
|
36
|
Lickwar CR, Camp JG, Weiser M, Cocchiaro JL, Kingsley DM, Furey TS, Sheikh SZ, Rawls JF. Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells. PLoS Biol 2017; 15:e2002054. [PMID: 28850571 PMCID: PMC5574553 DOI: 10.1371/journal.pbio.2002054] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/31/2017] [Indexed: 12/17/2022] Open
Abstract
The intestinal epithelium serves critical physiologic functions that are shared among all vertebrates. However, it is unknown how the transcriptional regulatory mechanisms underlying these functions have changed over the course of vertebrate evolution. We generated genome-wide mRNA and accessible chromatin data from adult intestinal epithelial cells (IECs) in zebrafish, stickleback, mouse, and human species to determine if conserved IEC functions are achieved through common transcriptional regulation. We found evidence for substantial common regulation and conservation of gene expression regionally along the length of the intestine from fish to mammals and identified a core set of genes comprising a vertebrate IEC signature. We also identified transcriptional start sites and other putative regulatory regions that are differentially accessible in IECs in all 4 species. Although these sites rarely showed sequence conservation from fish to mammals, surprisingly, they drove highly conserved IEC expression in a zebrafish reporter assay. Common putative transcription factor binding sites (TFBS) found at these sites in multiple species indicate that sequence conservation alone is insufficient to identify much of the functionally conserved IEC regulatory information. Among the rare, highly sequence-conserved, IEC-specific regulatory regions, we discovered an ancient enhancer upstream from her6/HES1 that is active in a distinct population of Notch-positive cells in the intestinal epithelium. Together, these results show how combining accessible chromatin and mRNA datasets with TFBS prediction and in vivo reporter assays can reveal tissue-specific regulatory information conserved across 420 million years of vertebrate evolution. We define an IEC transcriptional regulatory network that is shared between fish and mammals and establish an experimental platform for studying how evolutionarily distilled regulatory information commonly controls IEC development and physiology. The epithelium lining the intestine is an ancient animal tissue that serves as a primary site of nutrient absorption and interaction with microbiota. Its formation and function require complex patterns of gene transcription that vary along the intestine and in specialized intestinal epithelial cell (IEC) subtypes. However, it is unknown how the underlying transcriptional regulatory mechanisms have changed over the course of vertebrate evolution. Here, we used genome-wide profiling of mRNA levels and chromatin accessibility to identify conserved IEC genes and regulatory regions in 4 vertebrate species (zebrafish, stickleback, mouse, and human) separated from a common ancestor by 420 million years. We identified substantial similarities in genes expressed along the vertebrate intestine. These data disclosed putative conserved transcription factor binding sites (TFBS) enriched in accessible chromatin near IEC genes and in regulatory sites with accessibility restricted to IECs. Fluorescent reporter assays in transparent zebrafish showed that these regions, which frequently lacked sequence conservation, were still capable of driving conserved expression patterns. We also found a highly conserved region near mammalian and fish hes1 sufficient to drive expression in a specific population of IECs with active Notch signaling. These results establish a platform to define the conserved transcriptional networks underlying vertebrate IEC physiology.
Collapse
Affiliation(s)
- Colin R. Lickwar
- Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University, Durham, North Carolina, United States of America
- Department of Cell Biology and Physiology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - J. Gray Camp
- Department of Cell Biology and Physiology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Matthew Weiser
- Departments of Genetics and Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jordan L. Cocchiaro
- Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University, Durham, North Carolina, United States of America
- Department of Cell Biology and Physiology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David M. Kingsley
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Terrence S. Furey
- Departments of Genetics and Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Shehzad Z. Sheikh
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University, Durham, North Carolina, United States of America
- Department of Cell Biology and Physiology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
37
|
Davison JM, Lickwar CR, Song L, Breton G, Crawford GE, Rawls JF. Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha. Genome Res 2017; 27:1195-1206. [PMID: 28385711 PMCID: PMC5495071 DOI: 10.1101/gr.220111.116] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/30/2017] [Indexed: 02/07/2023]
Abstract
Microbiota influence diverse aspects of intestinal physiology and disease in part by controlling tissue-specific transcription of host genes. However, host genomic mechanisms mediating microbial control of intestinal gene expression are poorly understood. Hepatocyte nuclear factor 4 (HNF4) is the most ancient family of nuclear receptor transcription factors with important roles in human metabolic and inflammatory bowel diseases, but a role in host response to microbes is unknown. Using an unbiased screening strategy, we found that zebrafish Hnf4a specifically binds and activates a microbiota-suppressed intestinal epithelial transcriptional enhancer. Genetic analysis revealed that zebrafish hnf4a activates nearly half of the genes that are suppressed by microbiota, suggesting microbiota negatively regulate Hnf4a. In support, analysis of genomic architecture in mouse intestinal epithelial cells disclosed that microbiota colonization leads to activation or inactivation of hundreds of enhancers along with drastic genome-wide reduction of HNF4A and HNF4G occupancy. Interspecies meta-analysis suggested interactions between HNF4A and microbiota promote gene expression patterns associated with human inflammatory bowel diseases. These results indicate a critical and conserved role for HNF4A in maintaining intestinal homeostasis in response to microbiota.
Collapse
Affiliation(s)
- James M Davison
- Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University, Durham, North Carolina 27710, USA.,Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Colin R Lickwar
- Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University, Durham, North Carolina 27710, USA
| | - Lingyun Song
- Department of Pediatrics, Division of Medical Genetics, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Ghislain Breton
- Department of Integrative Biology and Pharmacology, McGovern Medical School, Houston, Texas 77030, USA
| | - Gregory E Crawford
- Department of Pediatrics, Division of Medical Genetics, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University, Durham, North Carolina 27710, USA
| |
Collapse
|
38
|
Abstract
The zebrafish model system offers significant utility for in vivo imaging of adipose tissue (AT) dynamics and for screening to identify chemical and genetic modifiers of adiposity. In particular, AT can be quantified accurately in live zebrafish using fluorescent lipophilic dyes. Although this methodology offers considerable promise, the comprehensive identification and classification of zebrafish ATs has not been performed. Here, we use fluorescent lipophilic dyes and in vivo imaging systematically to identify, classify and quantify the zebrafish AT pool. We identify 34 regionally distinct zebrafish ATs, including five visceral ATs and 22 subcutaneous ATs. For each of these ATs, we describe detailed morphological characteristics to aid their identification in future studies. Furthermore, we quantify the areas for each AT and construct regression models to allow prediction of expected AT size and variation across a range of developmental stages. Finally, we demonstrate the utility of this resource for identifying effects of strain variation and high-fat diet on AT growth. Altogether, this resource provides foundational information on the identity, dynamics and expected quantities of zebrafish ATs for use as a reference for future studies. Summary: A standardized nomenclature and classification system for zebrafish adipose tissues and regression models to predict expected adipose size during the course of zebrafish development.
Collapse
Affiliation(s)
- James E N Minchin
- Department of Molecular Genetics & Microbiology, Duke University, Durham, NC 27710, USA .,Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - John F Rawls
- Department of Molecular Genetics & Microbiology, Duke University, Durham, NC 27710, USA.,Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
39
|
Leulier F, MacNeil LT, Lee WJ, Rawls JF, Cani PD, Schwarzer M, Zhao L, Simpson SJ. Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health. Cell Metab 2017; 25:522-534. [PMID: 28273475 PMCID: PMC6200423 DOI: 10.1016/j.cmet.2017.02.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 02/07/2023]
Abstract
Nutrition is paramount in shaping all aspects of animal biology. In addition, the influence of the intestinal microbiota on physiology is now widely recognized. Given that diet also shapes the intestinal microbiota, this raises the question of how the nutritional environment and microbial assemblages together influence animal physiology. This research field constitutes a new frontier in the field of organismal biology that needs to be addressed. Here we review recent studies using animal models and humans and propose an integrative framework within which to define the study of the diet-physiology-microbiota systems and ultimately link it to human health. Nutritional Geometry sits centrally in the proposed framework and offers means to define diet compositions that are optimal for individuals and populations.
Collapse
Affiliation(s)
- François Leulier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon Cedex 07, France.
| | - Lesley T MacNeil
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S4K1, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S4K1, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Won-Jae Lee
- School of Biological Science, Institute of Molecular Biology and Genetics, National Creative Research Initiative Center for Hologenomics, Seoul National University, Seoul 151-742, South Korea
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University School of Medicine, Durham, NC 27710, USA
| | - Patrice D Cani
- Université Catholique de Louvain, Louvain Drug Research Institute, WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Metabolism and Nutrition Research Group, B-1200 Brussels, Belgium
| | - Martin Schwarzer
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon Cedex 07, France
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Stephen J Simpson
- Charles Perkins Centre, University of Sydney, Sydney 2006, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney 2006, Australia
| |
Collapse
|
40
|
Melancon E, Gomez De La Torre Canny S, Sichel S, Kelly M, Wiles TJ, Rawls JF, Eisen JS, Guillemin K. Best practices for germ-free derivation and gnotobiotic zebrafish husbandry. Methods Cell Biol 2017; 138:61-100. [PMID: 28129860 DOI: 10.1016/bs.mcb.2016.11.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
All animals are ecosystems with resident microbial communities, referred to as microbiota, which play profound roles in host development, physiology, and evolution. Enabled by new DNA sequencing technologies, there is a burgeoning interest in animal-microbiota interactions, but dissecting the specific impacts of microbes on their hosts is experimentally challenging. Gnotobiology, the study of biological systems in which all members are known, enables precise experimental analysis of the necessity and sufficiency of microbes in animal biology by deriving animals germ-free (GF) and inoculating them with defined microbial lineages. Mammalian host models have long dominated gnotobiology, but we have recently adapted gnotobiotic approaches to the zebrafish (Danio rerio), an important aquatic model. Zebrafish offer several experimental attributes that enable rapid, large-scale gnotobiotic experimentation with high replication rates and exquisite optical resolution. Here we describe detailed protocols for three procedures that form the foundation of zebrafish gnotobiology: derivation of GF embryos, microbial association of GF animals, and long-term, GF husbandry. Our aim is to provide sufficient guidance in zebrafish gnotobiotic methodology to expand and enrich this exciting field of research.
Collapse
Affiliation(s)
- E Melancon
- University of Oregon, Eugene, OR, Unites States
| | | | - S Sichel
- University of Oregon, Eugene, OR, Unites States
| | - M Kelly
- University of Oregon, Eugene, OR, Unites States
| | - T J Wiles
- University of Oregon, Eugene, OR, Unites States
| | - J F Rawls
- Duke University, Durham, NC, United States
| | - J S Eisen
- University of Oregon, Eugene, OR, Unites States
| | - K Guillemin
- University of Oregon, Eugene, OR, Unites States; Canadian Institute for Advanced Research, Toronto, ON, Canada
| |
Collapse
|
41
|
Abstract
Adipose tissues (ATs) are lipid-rich structures that supply and sequester energy-dense lipid in response to the energy status of an organism. As such, ATs provide an organism energetic insurance during periods of adverse physiological burden. ATs are deposited in diverse anatomical locations, and excessive accumulation of particular regional ATs modulates disease risk. Therefore, a model system that facilitates the visualization and quantification of regional adiposity holds significant biomedical promise. The zebrafish (Danio rerio) has emerged as a new model system for AT research in which the entire complement of regional ATs can be imaged and quantified in live individuals. Here we present detailed methods for labeling adipocytes in live zebrafish using fluorescent lipophilic dyes, and for identifying and quantifying regional zebrafish ATs.
Collapse
Affiliation(s)
- J E N Minchin
- University of Edinburgh, Edinburgh, United Kingdom; Duke University, Durham, NC, United States
| | - J F Rawls
- Duke University, Durham, NC, United States
| |
Collapse
|
42
|
Abstract
When exposed to cold temperatures, mammals undergo remarkable physiological adaptations including thermogenesis, increased intake of dietary energy, and enhanced capacity for intestinal absorption. In a recent Cell paper, Chevalier, Stojanović, and colleagues reveal that these key adaptations to life in the cold are facilitated by the intestinal microbiota (Chevalier et al., 2015).
Collapse
Affiliation(s)
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA.
| |
Collapse
|
43
|
Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, Guy CD, Seed PC, Rawls JF, David LA, Hunault G, Oberti F, Calès P, Diehl AM. The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. Hepatology 2016; 63:764-75. [PMID: 4975935 PMCID: PMC4975935 DOI: 10.1002/hep.28356] [Citation(s) in RCA: 865] [Impact Index Per Article: 108.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/20/2015] [Indexed: 12/12/2022]
Abstract
UNLABELLED Several animal studies have emphasized the role of gut microbiota in nonalcoholic fatty liver disease (NAFLD). However, data about gut dysbiosis in human NAFLD remain scarce in the literature, especially studies including the whole spectrum of NAFLD lesions. We aimed to evaluate the association between gut dysbiosis and severe NAFLD lesions, that is, nonalcoholic steatohepatitis (NASH) and fibrosis, in a well-characterized population of adult NAFLD. Fifty-seven patients with biopsy-proven NAFLD were enrolled. Taxonomic composition of gut microbiota was determined using 16S ribosomal RNA gene sequencing of stool samples. Thirty patients had F0/F1 fibrosis stage at liver biopsy (10 with NASH), and 27 patients had significant F≥2 fibrosis (25 with NASH). Bacteroides abundance was significantly increased in NASH and F≥2 patients, whereas Prevotella abundance was decreased. Ruminococcus abundance was significantly higher in F≥2 patients. By multivariate analysis, Bacteroides abundance was independently associated with NASH and Ruminococcus with F≥2 fibrosis. Stratification according to the abundance of these two bacteria generated three patient subgroups with increasing severity of NAFLD lesions. Based on imputed metagenomic profiles, Kyoto Encyclopedia of Genes and Genomes pathways significantly related to NASH and fibrosis F≥2 were mostly related to carbohydrate, lipid, and amino acid metabolism. CONCLUSION NAFLD severity associates with gut dysbiosis and a shift in metabolic function of the gut microbiota. We identified Bacteroides as independently associated with NASH and Ruminococcus with significant fibrosis. Thus, gut microbiota analysis adds information to classical predictors of NAFLD severity and suggests novel metabolic targets for pre-/probiotics therapies.
Collapse
Affiliation(s)
- Jérôme Boursier
- Hepato-Gastroenterology Department, University Hospital, Angers, France, HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - Olaf Mueller
- Center for Genomics of Microbial Systems, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Matthieu Barret
- INRA, UMR1345 Institut de Recherches en Horticulture et Semences, SFR4207 QUASAV, F-49071, Beaucouzé, France
| | - Mariana Machado
- Division of Gastroenterology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Lionel Fizanne
- HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - Felix Araujo-Perez
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Cynthia D. Guy
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Patrick C. Seed
- Center for Genomics of Microbial Systems, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America, INRA, UMR1345 Institut de Recherches en Horticulture et Semences, SFR4207 QUASAV, F-49071, Beaucouzé, France, Division of Gastroenterology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - John F. Rawls
- Center for Genomics of Microbial Systems, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Lawrence A. David
- Center for Genomics of Microbial Systems, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Gilles Hunault
- HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - Frédéric Oberti
- Hepato-Gastroenterology Department, University Hospital, Angers, France, HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - Paul Calès
- Hepato-Gastroenterology Department, University Hospital, Angers, France, HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - Anna Mae Diehl
- Division of Gastroenterology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| |
Collapse
|
44
|
Burns AR, Stephens WZ, Stagaman K, Wong S, Rawls JF, Guillemin K, Bohannan BJM. Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. ISME J 2016; 10:655-64. [PMID: 26296066 PMCID: PMC4817674 DOI: 10.1038/ismej.2015.142] [Citation(s) in RCA: 413] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/19/2015] [Accepted: 07/05/2015] [Indexed: 01/22/2023]
Abstract
Despite their importance to host health and development, the communities of microorganisms associated with humans and other animals are characterized by a large degree of unexplained variation across individual hosts. The processes that drive such inter-individual variation are not well understood. To address this, we surveyed the microbial communities associated with the intestine of the zebrafish, Danio rerio, over developmental time. We compared our observations of community composition and distribution across hosts with that predicted by a neutral assembly model, which assumes that community assembly is driven solely by chance and dispersal. We found that as hosts develop from larvae to adults, the fit of the model to observed microbial distributions decreases, suggesting that the relative importance of non-neutral processes, such as microbe-microbe interactions, active dispersal, or selection by the host, increases as hosts mature. We also observed that taxa which depart in their distributions from the neutral prediction form ecologically distinct sub-groups, which are phylogenetically clustered with respect to the full metacommunity. These results demonstrate that neutral processes are sufficient to generate substantial variation in microbiota composition across individual hosts, and suggest that potentially unique or important taxa may be identified by their divergence from neutral distributions.
Collapse
Affiliation(s)
- Adam R Burns
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - W Zac Stephens
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Keaton Stagaman
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Sandi Wong
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | | |
Collapse
|
45
|
Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, Guy CD, Seed PC, Rawls JF, David LA, Hunault G, Oberti F, Calès P, Diehl AM. The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. Hepatology 2016. [PMID: 26600078 DOI: 10.1002/hep.28356 doi: 10.1002/hep.28356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
UNLABELLED Several animal studies have emphasized the role of gut microbiota in nonalcoholic fatty liver disease (NAFLD). However, data about gut dysbiosis in human NAFLD remain scarce in the literature, especially studies including the whole spectrum of NAFLD lesions. We aimed to evaluate the association between gut dysbiosis and severe NAFLD lesions, that is, nonalcoholic steatohepatitis (NASH) and fibrosis, in a well-characterized population of adult NAFLD. Fifty-seven patients with biopsy-proven NAFLD were enrolled. Taxonomic composition of gut microbiota was determined using 16S ribosomal RNA gene sequencing of stool samples. Thirty patients had F0/F1 fibrosis stage at liver biopsy (10 with NASH), and 27 patients had significant F≥2 fibrosis (25 with NASH). Bacteroides abundance was significantly increased in NASH and F≥2 patients, whereas Prevotella abundance was decreased. Ruminococcus abundance was significantly higher in F≥2 patients. By multivariate analysis, Bacteroides abundance was independently associated with NASH and Ruminococcus with F≥2 fibrosis. Stratification according to the abundance of these two bacteria generated three patient subgroups with increasing severity of NAFLD lesions. Based on imputed metagenomic profiles, Kyoto Encyclopedia of Genes and Genomes pathways significantly related to NASH and fibrosis F≥2 were mostly related to carbohydrate, lipid, and amino acid metabolism. CONCLUSION NAFLD severity associates with gut dysbiosis and a shift in metabolic function of the gut microbiota. We identified Bacteroides as independently associated with NASH and Ruminococcus with significant fibrosis. Thus, gut microbiota analysis adds information to classical predictors of NAFLD severity and suggests novel metabolic targets for pre-/probiotics therapies.
Collapse
Affiliation(s)
- Jérôme Boursier
- Hepato-Gastroenterology Department, University Hospital, Angers, France.,HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - Olaf Mueller
- Center for Genomics of Microbial Systems, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC
| | - Matthieu Barret
- INRA, UMR1345 Institut de Recherches en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France
| | - Mariana Machado
- Division of Gastroenterology, Department of Medicine, Duke University Medical Center, Durham, NC
| | - Lionel Fizanne
- HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | | | - Cynthia D Guy
- Department of Pathology, Duke University Medical Center, Durham, NC
| | - Patrick C Seed
- Center for Genomics of Microbial Systems, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC.,Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - John F Rawls
- Center for Genomics of Microbial Systems, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC
| | - Lawrence A David
- Center for Genomics of Microbial Systems, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC
| | - Gilles Hunault
- HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - Frédéric Oberti
- Hepato-Gastroenterology Department, University Hospital, Angers, France.,HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - Paul Calès
- Hepato-Gastroenterology Department, University Hospital, Angers, France.,HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - Anna Mae Diehl
- Division of Gastroenterology, Department of Medicine, Duke University Medical Center, Durham, NC
| |
Collapse
|
46
|
Williamson LL, McKenney EA, Holzknecht ZE, Belliveau C, Rawls JF, Poulton S, Parker W, Bilbo SD. Got worms? Perinatal exposure to helminths prevents persistent immune sensitization and cognitive dysfunction induced by early-life infection. Brain Behav Immun 2016; 51:14-28. [PMID: 26162711 DOI: 10.1016/j.bbi.2015.07.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/06/2015] [Accepted: 07/06/2015] [Indexed: 02/08/2023] Open
Abstract
The incidence of autoimmune and inflammatory diseases has risen dramatically in post-industrial societies. "Biome depletion" - loss of commensal microbial and multicellular organisms such as helminths (intestinal worms) that profoundly modulate the immune system - may contribute to these increases. Hyperimmune-associated disorders also affect the brain, especially neurodevelopment, and increasing evidence links early-life infection to cognitive and neurodevelopmental disorders. We have demonstrated previously that rats infected with bacteria as newborns display life-long vulnerabilities to cognitive dysfunction, a vulnerability that is specifically linked to long-term hypersensitivity of microglial cell function, the resident immune cells of the brain. Here, we demonstrate that helminth colonization of pregnant dams attenuated the exaggerated brain cytokine response of their offspring to bacterial infection, and that combined with post-weaning colonization of offspring with helminths (consistent with their mothers treatment) completely prevented enduring microglial sensitization and cognitive dysfunction in adulthood. Importantly, helminths had no overt impact on adaptive immune cell subsets, whereas exaggerated innate inflammatory responses in splenic macrophages were prevented. Finally, helminths altered the effect of neonatal infection on the gut microbiome; neonatal infection with Escherichia coli caused a shift from genera within the Actinobacteria and Tenericutes phyla to genera in the Bacteroidetes phylum in rats not colonized with helminths, but helminths attenuated this effect. In sum, these data point toward an inter-relatedness of various components of the biome, and suggest potential mechanisms by which this helminth might exert therapeutic benefits in the treatment of neuroinflammatory and cognitive disorders.
Collapse
Affiliation(s)
- Lauren L Williamson
- Department of Psychology & Neuroscience, Duke Institute for Brain Sciences, Duke University, United States
| | | | - Zoie E Holzknecht
- Department of Surgery, Duke University Medical Center, United States
| | - Christine Belliveau
- Department of Psychology & Neuroscience, Duke Institute for Brain Sciences, Duke University, United States
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, United States
| | - Susan Poulton
- Department of Surgery, Duke University Medical Center, United States
| | - William Parker
- Department of Surgery, Duke University Medical Center, United States
| | - Staci D Bilbo
- Department of Psychology & Neuroscience, Duke Institute for Brain Sciences, Duke University, United States.
| |
Collapse
|
47
|
Wang L, Oehlers SH, Espenschied ST, Rawls JF, Tobin DM, Ko DC. CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation. Genome Biol 2015; 16:190. [PMID: 26374098 PMCID: PMC4570686 DOI: 10.1186/s13059-015-0722-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/09/2015] [Indexed: 12/31/2022] Open
Abstract
Meta-analyses of genome-wide association studies (GWAS) have demonstrated that the same genetic variants can be associated with multiple diseases and other complex traits. We present software called CPAG (Cross-Phenotype Analysis of GWAS) to look for similarities between 700 traits, build trees with informative clusters, and highlight underlying pathways. Clusters are consistent with pre-defined groups and literature-based validation but also reveal novel connections. We report similarity between plasma palmitoleic acid and Crohn's disease and find that specific fatty acids exacerbate enterocolitis in zebrafish. CPAG will become increasingly powerful as more genetic variants are uncovered, leading to a deeper understanding of complex traits. CPAG is freely available at www.sourceforge.net/projects/CPAG/.
Collapse
Affiliation(s)
- Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA.
| | - Stefan H Oehlers
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA.
| | - Scott T Espenschied
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA.
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA.
| | - David M Tobin
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA.
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA. .,Department of Medicine and the Center for Human Genome Variation, School of Medicine, Duke University, Durham, NC, 27710, USA.
| |
Collapse
|
48
|
Abstract
The microbiome is now widely recognized as being important in health and disease, and makes up a substantial subset of the biome within the ecosystem of the vertebrate body. At the same time, multicellular, eukaryotic organisms such as helminths are being recognized as an important component of the biome that shaped the evolution of our genes. The absence of these macroscopic organisms during the early development and life of humans in Western culture probably leads to a wide range of human immunological diseases. However, the interaction between the microbiome and macroscopic components of the biome remains poorly characterized. In this study, the microbiome of the cecum in rats colonized for 2 generations with the small intestinal helminth Hymenolepis diminuta was evaluated. The introduction of this benign helminth, which is of considerable therapeutic interest, led to several changes in the cecal microbiome. Most of the changes were within the Firmicutes phylum, involved about 20% of the total bacteria, and generally entailed a shift from Bacilli to Clostridia species in the presence of the helminth. The results point toward ecological relationships between various components of the biome, with the observed shifts in the microbiome suggesting potential mechanisms by which this helminth might exert therapeutic effects.
Collapse
Affiliation(s)
| | | | - Anne D Yoder
- Departments of Biology; Duke University; Durham, NC, USA,Evolutionary Anthropology; Duke University; Durham, NC, USA
| | - John F Rawls
- Molecular Genetics and Microbiology; Duke University; Durham, NC, USA
| | - Staci D Bilbo
- Psychology & Neuroscience; Duke University; Durham, NC, USA
| | - William Parker
- Department of Surgery; Duke University Medical Center; Durham, NC, USA,Correspondence to: William Parker;
| |
Collapse
|
49
|
Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res 2014; 24:1504-16. [PMID: 24963153 PMCID: PMC4158762 DOI: 10.1101/gr.165845.113] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microbiota regulate intestinal physiology by modifying host gene expression along the length of the intestine, but the underlying regulatory mechanisms remain unresolved. Transcriptional specificity occurs through interactions between transcription factors (TFs) and cis-regulatory regions (CRRs) characterized by nucleosome-depleted accessible chromatin. We profiled transcriptome and accessible chromatin landscapes in intestinal epithelial cells (IECs) from mice reared in the presence or absence of microbiota. We show that regional differences in gene transcription along the intestinal tract were accompanied by major alterations in chromatin accessibility. Surprisingly, we discovered that microbiota modify host gene transcription in IECs without significantly impacting the accessible chromatin landscape. Instead, microbiota regulation of host gene transcription might be achieved by differential expression of specific TFs and enrichment of their binding sites in nucleosome-depleted CRRs near target genes. Our results suggest that the chromatin landscape in IECs is preprogrammed by the host in a region-specific manner to permit responses to microbiota through binding of open CRRs by specific TFs.
Collapse
Affiliation(s)
- J Gray Camp
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Department of Developmental Biology, Stanford University, Stanford, California 94305, USA; Computer Science Department, Stanford University, Stanford, California 94305, USA
| | - Christopher L Frank
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710, USA
| | - Colin R Lickwar
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710, USA
| | - Harendra Guturu
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - Tomas Rube
- Physics Department, Stanford University, Stanford, California 94305, USA
| | - Aaron M Wenger
- Computer Science Department, Stanford University, Stanford, California 94305, USA
| | - Jenny Chen
- Biomedical Informatics Program, Stanford University, Stanford, California 94305, USA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University, Stanford, California 94305, USA; Computer Science Department, Stanford University, Stanford, California 94305, USA
| | - Gregory E Crawford
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA; Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina 27708, USA
| | - John F Rawls
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710, USA;
| |
Collapse
|
50
|
Kanther M, Tomkovich S, Xiaolun S, Grosser MR, Koo J, Flynn EJ, Jobin C, Rawls JF. Commensal microbiota stimulate systemic neutrophil migration through induction of serum amyloid A. Cell Microbiol 2014; 16:1053-67. [PMID: 24373309 DOI: 10.1111/cmi.12257] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 12/18/2022]
Abstract
Neutrophils serve critical roles in inflammatory responses to infection and injury, and mechanisms governing their activity represent attractive targets for controlling inflammation. The commensal microbiota is known to regulate the activity of neutrophils and other leucocytes in the intestine, but the systemic impact of the microbiota on neutrophils remains unknown. Here we utilized in vivo imaging in gnotobiotic zebrafish to reveal diverse effects of microbiota colonization on systemic neutrophil development and function. The presence of a microbiota resulted in increased neutrophil number and myeloperoxidase expression, and altered neutrophil localization and migratory behaviours. These effects of the microbiota on neutrophil homeostasis were accompanied by an increased recruitment of neutrophils to injury. Genetic analysis identified the microbiota-induced acute phase protein serum amyloid A (Saa) as a host factor mediating microbial stimulation of tissue-specific neutrophil migratory behaviours. In vitro studies revealed that zebrafish cells respond to Saa exposure by activating NF-κB, and that Saa-dependent neutrophil migration requires NF-κB-dependent gene expression. These results implicate the commensal microbiota as an important environmental factor regulating diverse aspects of systemic neutrophil development and function, and reveal a critical role for a Saa-NF-κB signalling axis in mediating neutrophil migratory responses.
Collapse
Affiliation(s)
- Michelle Kanther
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | | | | | | | | | | | | |
Collapse
|