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Yannarell SM, Beaudoin ES, Talley HS, Schoenborn AA, Orr G, Anderton CR, Chrisler WB, Shank EA. Extensive cellular multi-tasking within Bacillus subtilis biofilms. mSystems 2023; 8:e0089122. [PMID: 37527273 PMCID: PMC10469600 DOI: 10.1128/msystems.00891-22] [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: 09/13/2022] [Accepted: 03/08/2023] [Indexed: 08/03/2023] Open
Abstract
Bacillus subtilis is a soil-dwelling bacterium that can form biofilms, or communities of cells surrounded by a self-produced extracellular matrix. In biofilms, genetically identical cells often exhibit heterogeneous transcriptional phenotypes, so that subpopulations of cells carry out essential yet costly cellular processes that allow the entire population to thrive. Surprisingly, the extent of phenotypic heterogeneity and the relationships between subpopulations of cells within biofilms of even in well-studied bacterial systems like B. subtilis remains largely unknown. To determine relationships between these subpopulations of cells, we created 182 strains containing pairwise combinations of fluorescent transcriptional reporters for the expression state of 14 different genes associated with potential cellular subpopulations. We determined the spatial organization of the expression of these genes within biofilms using confocal microscopy, which revealed that many reporters localized to distinct areas of the biofilm, some of which were co-localized. We used flow cytometry to quantify reporter co-expression, which revealed that many cells "multi-task," simultaneously expressing two reporters. These data indicate that prior models describing B. subtilis cells as differentiating into specific cell types, each with a specific task or function, were oversimplified. Only a few subpopulations of cells, including surfactin and plipastatin producers, as well as sporulating and competent cells, appear to have distinct roles based on the set of genes examined here. These data will provide us with a framework with which to further study and make predictions about the roles of diverse cellular phenotypes in B. subtilis biofilms. IMPORTANCE Many microbes differentiate, expressing diverse phenotypes to ensure their survival in various environments. However, studies on phenotypic differentiation have typically examined only a few phenotypes at one time, thus limiting our knowledge about the extent of differentiation and phenotypic overlap in the population. We investigated the spatial organization and gene expression relationships for genes important in B. subtilis biofilms. In doing so, we mapped spatial gene expression patterns and expanded the number of cell populations described in the B. subtilis literature. It is likely that other bacteria also display complex differentiation patterns within their biofilms. Studying the extent of cellular differentiation in other microbes may be important when designing therapies for disease-causing bacteria, where studying only a single phenotype may be masking underlying phenotypic differentiation relevant to infection outcomes.
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Affiliation(s)
- Sarah M. Yannarell
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Eric S. Beaudoin
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Hunter S. Talley
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alexi A. Schoenborn
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - William B. Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Elizabeth A. Shank
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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2
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Schoenborn AA, Yannarell SM, MacVicar CT, Barriga-Medina NN, Bonham KS, Leon-Reyes A, Riveros-Iregui D, Klepac-Ceraj V, Shank EA. Microclimate is a strong predictor of the native and invasive plant-associated soil microbiome on San Cristóbal Island, Galápagos archipelago. Environ Microbiol 2023. [PMID: 36883264 DOI: 10.1111/1462-2920.16361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/26/2023] [Indexed: 03/09/2023]
Abstract
Understanding the drivers that affect soil bacterial and fungal communities is essential to understanding and mitigating the impacts of human activity on vulnerable ecosystems like those on the Galápagos Islands. The volcanic slopes of these Islands lead to steep elevation gradients that generate distinct microclimates across small spatial scales. Although much is known about the impacts of invasive plant species on the above-ground biodiversity of the Galápagos Islands, little is known about their resident soil microbial communities and the factors shaping them. Here, we investigate the bacterial and fungal soil communities associated with invasive and native plant species across three distinct microclimates on San Cristóbal Island (arid, transition zone and humid). At each site, we collected soil at three depths (rhizosphere, 5 cm and 15 cm) from multiple plants. Sampling location was the strongest driver of both bacterial and fungal communities, explaining 73% and 43% of variation in the bacterial and fungal community structure, respectively, with additional minor but significant impacts from soil depth and plant type (invasive vs. native). This study highlights the continued need to explore microbial communities across diverse environments and demonstrates how both abiotic and biotic factors impact soil microbial communities in the Galápagos archipelago.
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Affiliation(s)
- Alexi A Schoenborn
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah M Yannarell
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Caroline T MacVicar
- Department of Biological Sciences, Wellesley College, Wellesley, Massachusetts, USA
| | - Noelia N Barriga-Medina
- Galápagos Science Center, San Cristóbal Island, Galápagos Archipelago, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos-Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Kevin S Bonham
- Department of Biological Sciences, Wellesley College, Wellesley, Massachusetts, USA
| | - Antonio Leon-Reyes
- Galápagos Science Center, San Cristóbal Island, Galápagos Archipelago, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos-Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Diego Riveros-Iregui
- Galápagos Science Center, San Cristóbal Island, Galápagos Archipelago, Ecuador
- Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Center for Galápagos Studies, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, Massachusetts, USA
| | - Elizabeth A Shank
- Department of Systems Biology, UMass Chan Medical School, Worcester, Massachusetts, USA
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3
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Viladomiu M, Khounlotham M, Dogan B, Lima SF, Elsaadi A, Cardakli E, Castellanos JG, Ng C, Herzog J, Schoenborn AA, Ellermann M, Liu B, Zhang S, Gulati AS, Sartor RB, Simpson KW, Lipkin SM, Longman RS. Agr2-associated ER stress promotes adherent-invasive E. coli dysbiosis and triggers CD103 + dendritic cell IL-23-dependent ileocolitis. Cell Rep 2022; 41:111637. [PMID: 36384110 PMCID: PMC9805753 DOI: 10.1016/j.celrep.2022.111637] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/06/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Endoplasmic reticulum (ER) stress is associated with Crohn's disease (CD), but its impact on host-microbe interaction in disease pathogenesis is not well defined. Functional deficiency in the protein disulfide isomerase anterior gradient 2 (AGR2) has been linked with CD and leads to epithelial cell ER stress and ileocolitis in mice and humans. Here, we show that ileal expression of AGR2 correlates with mucosal Enterobactericeae abundance in human inflammatory bowel disease (IBD) and that Agr2 deletion leads to ER-stress-dependent expansion of mucosal-associated adherent-invasive Escherichia coli (AIEC), which drives Th17 cell ileocolitis in mice. Mechanistically, our data reveal that AIEC-induced epithelial cell ER stress triggers CD103+ dendritic cell production of interleukin-23 (IL-23) and that IL-23R is required for ileocolitis in Agr2-/- mice. Overall, these data reveal a specific and reciprocal interaction of the expansion of the CD pathobiont AIEC with ER-stress-associated ileocolitis and highlight a distinct cellular mechanism for IL-23-dependent ileocolitis.
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Affiliation(s)
- Monica Viladomiu
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Manirath Khounlotham
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Belgin Dogan
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Svetlana F. Lima
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ahmed Elsaadi
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Emre Cardakli
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jim G. Castellanos
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Charles Ng
- Department of Pathology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jeremy Herzog
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexi A. Schoenborn
- Department of Pediatrics, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melissa Ellermann
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Present address: Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Bo Liu
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shiying Zhang
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ajay S. Gulati
- Department of Pediatrics, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - R. Balfour Sartor
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenneth W. Simpson
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA,College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Steven M. Lipkin
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA,Correspondence: (S.M.L.), (R.S.L.)
| | - Randy S. Longman
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA,Jill Roberts Center for IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA,Lead contact,Correspondence: (S.M.L.), (R.S.L.)
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Schoenborn AA, Yannarell SM, Wallace ED, Clapper H, Weinstein IC, Shank EA. Defining the Expression, Production, and Signaling Roles of Specialized Metabolites during Bacillus subtilis Differentiation. J Bacteriol 2021; 203:e0033721. [PMID: 34460312 PMCID: PMC8544424 DOI: 10.1128/jb.00337-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial specialized (or secondary) metabolites are structurally diverse molecules that mediate intra- and interspecies interactions by altering growth and cellular physiology and differentiation. Bacillus subtilis, a Gram-positive model bacterium commonly used to study biofilm formation and sporulation, has the capacity to produce more than 10 specialized metabolites. Some of these B. subtilis specialized metabolites have been investigated for their role in facilitating cellular differentiation, but only rarely has the behavior of multiple metabolites been simultaneously investigated. In this study, we explored the interconnectivity of differentiation (biofilm and sporulation) and specialized metabolites in B. subtilis. Specifically, we interrogated how development influences specialized metabolites and vice versa. Using the sporulation-inducing medium DSM, we found that the majority of the specialized metabolites examined are expressed and produced during biofilm formation and sporulation. Additionally, we found that six of these metabolites (surfactin, ComX, bacillibactin, bacilysin, subtilosin A, and plipastatin) are necessary signaling molecules for proper progression of B. subtilis differentiation. This study further supports the growing body of work demonstrating that specialized metabolites have essential physiological functions as cell-cell communication signals in bacteria. IMPORTANCE Bacterially produced specialized metabolites are frequently studied for their potential use as antibiotics and antifungals. However, a growing body of work has suggested that the antagonistic potential of specialized metabolites is not their only function. Here, using Bacillus subtilis as our model bacterium, we demonstrated that developmental processes such as biofilm formation and sporulation are tightly linked to specialized metabolite gene expression and production. Additionally, under our differentiation-inducing conditions, six out of the nine specialized metabolites investigated behave as intraspecific signals that impact B. subtilis physiology and influence biofilm formation and sporulation. Our work supports the viewpoint that specialized metabolites have a clear role as cell-cell signaling molecules within differentiated populations of bacteria.
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Affiliation(s)
- Alexi A. Schoenborn
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah M. Yannarell
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E. Diane Wallace
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Haley Clapper
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ilon C. Weinstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Elizabeth A. Shank
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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5
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Taylor GA, Huang HI, Fee BE, Youssef N, Jewell ML, Cantillana V, Schoenborn AA, Rogala AR, Buckley AF, Feng CG, Vallance BA, Gulati AS, Hammer GE. Irgm1-deficiency leads to myeloid dysfunction in colon lamina propria and susceptibility to the intestinal pathogen Citrobacter rodentium. PLoS Pathog 2020; 16:e1008553. [PMID: 32453761 PMCID: PMC7274479 DOI: 10.1371/journal.ppat.1008553] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 03/19/2019] [Revised: 06/05/2020] [Accepted: 04/15/2020] [Indexed: 01/09/2023] Open
Abstract
IRGM and its mouse orthologue Irgm1 are dynamin-like proteins that regulate vesicular remodeling, intracellular microbial killing, and pathogen immunity. IRGM dysfunction is linked to inflammatory bowel disease (IBD), and while it is thought that defective intracellular killing of microbes underscores IBD susceptibility, studies have yet to address how IRGM/Irgm1 regulates immunity to microbes relevant to intestinal inflammation. Here we find that loss of Irgm1 confers marked susceptibility to Citrobacter rodentium, a noninvasive intestinal pathogen that models inflammatory responses to intestinal bacteria. Irgm1-deficient mice fail to control C. rodentium outgrowth in the intestine, leading to systemic pathogen spread and host mortality. Surprisingly, susceptibility due to loss of Irgm1 function was not linked to defective intracellular killing of C. rodentium or exaggerated inflammation, but was instead linked to failure to remodel specific colon lamina propria (C-LP) myeloid cells that expand in response to C. rodentium infection and are essential for C. rodentium immunity. Defective immune remodeling was most striking in C-LP monocytes, which were successfully recruited to the infected C-LP, but subsequently underwent apoptosis. Apoptotic susceptibility was induced by C. rodentium infection and was specific to this setting of pathogen infection, and was not apparent in other settings of intestinal inflammation. These studies reveal a novel role for Irgm1 in host defense and suggest that deficiencies in survival and remodeling of C-LP myeloid cells that control inflammatory intestinal bacteria may underpin IBD pathogenesis linked to IRGM dysfunction.
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Affiliation(s)
- Gregory A. Taylor
- Geriatric Research, Education, and Clinical Center, VA Health Care Center, Durham, North Carolina, United States of America
- Departments of Medicine, Division of Geriatrics, and Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (GAT); (GEH)
| | - Hsin-I Huang
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Brian E. Fee
- Geriatric Research, Education, and Clinical Center, VA Health Care Center, Durham, North Carolina, United States of America
| | - Nourhan Youssef
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Mark L. Jewell
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Viviana Cantillana
- Departments of Medicine, Division of Geriatrics, and Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Alexi A. Schoenborn
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Allison R. Rogala
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Anne F. Buckley
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Carl G. Feng
- Department of Infectious Diseases and Immunology, University of Sydney, Sydney, NSW, Australia
| | - Bruce A. Vallance
- Department of Pediatrics, Division of Gastroenterology, BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Ajay S. Gulati
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gianna E. Hammer
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (GAT); (GEH)
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6
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Schoenborn AA, von Furstenberg RJ, Valsaraj S, Hussain FS, Stein M, Shanahan MT, Henning SJ, Gulati AS. The enteric microbiota regulates jejunal Paneth cell number and function without impacting intestinal stem cells. Gut Microbes 2018; 10:45-58. [PMID: 29883265 PMCID: PMC6363071 DOI: 10.1080/19490976.2018.1474321] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 06/27/2017] [Revised: 04/06/2018] [Accepted: 05/01/2018] [Indexed: 02/03/2023] Open
Abstract
Paneth cells (PCs) are epithelial cells found in the small intestine, next to intestinal stem cells (ISCs) at the base of the crypts. PCs secrete antimicrobial peptides (AMPs) that regulate the commensal gut microbiota. In contrast, little is known regarding how the enteric microbiota reciprocally influences PC function. In this study, we sought to characterize the impact of the enteric microbiota on PC biology in the mouse small intestine. This was done by first enumerating jejunal PCs in germ-free (GF) versus conventionally raised (CR) mice. We next evaluated the possible functional consequences of altered PC biology in these experimental groups by assessing epithelial proliferation, ISC numbers, and the production of AMPs. We found that PC numbers were significantly increased in CR versus GF mice; however, there were no differences in ISC numbers or cycling activity between groups. Of the AMPs assessed, only Reg3γ transcript expression was significantly increased in CR mice. Intriguingly, this increase was abrogated in cultured CR versus GF enteroids, and could not be re-induced with various bacterial ligands. Our findings demonstrate the enteric microbiota regulates PC function by increasing PC numbers and inducing Reg3γ expression, though the latter effect may not involve direct interactions between bacteria and the intestinal epithelium. In contrast, the enteric microbiota does not appear to regulate jejunal ISC census and proliferation. These are critical findings for investigators using GF mice and the enteroid system to study PC and ISC biology.
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Affiliation(s)
- Alexi A Schoenborn
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Richard J von Furstenberg
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Smrithi Valsaraj
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Farah S Hussain
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Molly Stein
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Michael T Shanahan
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Susan J Henning
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- c Department of Medicine, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- d Department of Cellular and Molecular Physiology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Ajay S Gulati
- a Center for Gastrointestinal Biology and Disease , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- b Department of Pediatrics, Division of Gastroenterology , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
- e Department of Pathology and Laboratory Medicine , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
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7
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Rogala AR, Schoenborn AA, Fee BE, Cantillana VA, Joyce MJ, Gharaibeh RZ, Roy S, Fodor AA, Sartor RB, Taylor GA, Gulati AS. Environmental factors regulate Paneth cell phenotype and host susceptibility to intestinal inflammation in Irgm1-deficient mice. Dis Model Mech 2018; 11:dmm.031070. [PMID: 29361512 PMCID: PMC5894938 DOI: 10.1242/dmm.031070] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/14/2017] [Indexed: 12/29/2022] Open
Abstract
Crohn's disease (CD) represents a chronic inflammatory disorder of the intestinal tract. Several susceptibility genes have been linked to CD, though their precise role in the pathogenesis of this disorder remains unclear. Immunity-related GTPase M (IRGM) is an established risk allele in CD. We have shown previously that conventionally raised (CV) mice lacking the IRGM ortholog, Irgm1 exhibit abnormal Paneth cells (PCs) and increased susceptibility to intestinal injury. In the present study, we sought to utilize this model system to determine if environmental conditions impact these phenotypes, as is thought to be the case in human CD. To accomplish this, wild-type and Irgm1−/− mice were rederived into specific pathogen-free (SPF) and germ-free (GF) conditions. We next assessed how these differential housing environments influenced intestinal injury patterns, and epithelial cell morphology and function in wild-type and Irgm1−/− mice. Remarkably, in contrast to CV mice, SPF Irgm1−/− mice showed only a slight increase in susceptibility to dextran sodium sulfate-induced inflammation. SPF Irgm1−/− mice also displayed minimal abnormalities in PC number and morphology, and in antimicrobial peptide expression. Goblet cell numbers and epithelial proliferation were also unaffected by Irgm1 in SPF conditions. No microbial differences were observed between wild-type and Irgm1−/− mice, but gut bacterial communities differed profoundly between CV and SPF mice. Specifically, Helicobacter sequences were significantly increased in CV mice; however, inoculating SPF Irgm1−/− mice with Helicobacter hepaticus was not sufficient to transmit a pro-inflammatory phenotype. In summary, our findings suggest the impact of Irgm1-deficiency on susceptibility to intestinal inflammation and epithelial function is critically dependent on environmental influences. This work establishes the importance of Irgm1−/− mice as a model to elucidate host-environment interactions that regulate mucosal homeostasis and intestinal inflammatory responses. Defining such interactions will be essential for developing novel preventative and therapeutic strategies for human CD. Summary: In this study, we rederived conventionally raised Irgm1-deficient mice into specific pathogen-free and germ-free conditions. We show that these environments determine how Irgm1 regulates Paneth cell function and gut inflammation susceptibility.
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Affiliation(s)
- Allison R Rogala
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexi A Schoenborn
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian E Fee
- Geriatric Research, Education, and Clinical Center, VA Medical Center, Durham, NC 27705, USA
| | - Viviana A Cantillana
- Departments of Medicine; Molecular Genetics and Microbiology; and Immunology; Division of Geriatrics, and Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, NC 27710, USA
| | - Maria J Joyce
- Department of Medicine, Division of Infectious Disease, Duke University Medical Center, Durham, NC 27710, USA
| | - Raad Z Gharaibeh
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Sayanty Roy
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anthony A Fodor
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gregory A Taylor
- Geriatric Research, Education, and Clinical Center, VA Medical Center, Durham, NC 27705, USA.,Departments of Medicine; Molecular Genetics and Microbiology; and Immunology; Division of Geriatrics, and Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, NC 27710, USA
| | - Ajay S Gulati
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA .,Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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8
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Greer RL, Dong X, Moraes ACF, Zielke RA, Fernandes GR, Peremyslova E, Vasquez-Perez S, Schoenborn AA, Gomes EP, Pereira AC, Ferreira SRG, Yao M, Fuss IJ, Strober W, Sikora AE, Taylor GA, Gulati AS, Morgun A, Shulzhenko N. Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism. Nat Commun 2016; 7:13329. [PMID: 27841267 PMCID: PMC5114536 DOI: 10.1038/ncomms13329] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/23/2016] [Indexed: 12/19/2022] Open
Abstract
Cross-talk between the gut microbiota and the host immune system regulates host metabolism, and its dysregulation can cause metabolic disease. Here, we show that the gut microbe Akkermansia muciniphila can mediate negative effects of IFNγ on glucose tolerance. In IFNγ-deficient mice, A. muciniphila is significantly increased and restoration of IFNγ levels reduces A. muciniphila abundance. We further show that IFNγ-knockout mice whose microbiota does not contain A. muciniphila do not show improvement in glucose tolerance and adding back A. muciniphila promoted enhanced glucose tolerance. We go on to identify Irgm1 as an IFNγ-regulated gene in the mouse ileum that controls gut A. muciniphila levels. A. muciniphila is also linked to IFNγ-regulated gene expression in the intestine and glucose parameters in humans, suggesting that this trialogue between IFNγ, A. muciniphila and glucose tolerance might be an evolutionally conserved mechanism regulating metabolic health in mice and humans. Mice deficient in the pro-inflammatory cytokine IFNγ have improved glucose tolerance. Here, the authors show that this effect depends on the gut microbe Akkermansia muciniphila, whose abundance increases in the absence IFNγ, and which is known to have beneficial effects on host metabolism.
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Affiliation(s)
- Renee L Greer
- College of Veterinary Medicine, Oregon State University, 105 Dryden Hall, 450 SW 30th Street, Corvallis, Oregon 97331, USA
| | - Xiaoxi Dong
- College of Pharmacy, Oregon State University, 1601 SW Jefferson Way, Corvallis, Oregon 97331, USA
| | - Ana Carolina F Moraes
- Department of Epidemiology, School of Public Health, University of São Paulo, Av. Dr Arnaldo, 715, São Paulo, SP 01246-904, Brazil
| | - Ryszard A Zielke
- College of Pharmacy, Oregon State University, 1601 SW Jefferson Way, Corvallis, Oregon 97331, USA
| | - Gabriel R Fernandes
- Oswaldo Cruz Foundation, René Rachou Research Center, Av. Augusto de Lima, 1715, Belo Horizonte, MG 30190-002, Brazil
| | - Ekaterina Peremyslova
- College of Pharmacy, Oregon State University, 1601 SW Jefferson Way, Corvallis, Oregon 97331, USA
| | - Stephany Vasquez-Perez
- College of Veterinary Medicine, Oregon State University, 105 Dryden Hall, 450 SW 30th Street, Corvallis, Oregon 97331, USA
| | - Alexi A Schoenborn
- Division of Pediatric Gastroenterology, University of North Carolina at Chapel Hill, 260 MacNider Building, CB# 7220, Chapel Hill, North Carolina 27599, USA
| | - Everton P Gomes
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, Av. Dr Eneas de Carvalho Aguiar, 44, São Paulo, SP 05403-000, Brazil
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, Av. Dr Eneas de Carvalho Aguiar, 44, São Paulo, SP 05403-000, Brazil
| | - Sandra R G Ferreira
- Department of Epidemiology, School of Public Health, University of São Paulo, Av. Dr Arnaldo, 715, São Paulo, SP 01246-904, Brazil
| | - Michael Yao
- Mucosal Immunity Section, Laboratory of Immune Defenses, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, USA
| | - Ivan J Fuss
- Mucosal Immunity Section, Laboratory of Immune Defenses, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, USA
| | - Warren Strober
- Mucosal Immunity Section, Laboratory of Immune Defenses, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, USA
| | - Aleksandra E Sikora
- College of Pharmacy, Oregon State University, 1601 SW Jefferson Way, Corvallis, Oregon 97331, USA
| | - Gregory A Taylor
- Geriatric Research, Education and Clinical Center, VA Medical Center, Departments of Medicine, Molecular Genetics and Microbiology and Immunology, Division of Geriatrics and Center for the Study of Aging and Human Development, Duke Box 3003, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Ajay S Gulati
- Division of Pediatric Gastroenterology, University of North Carolina at Chapel Hill, 260 MacNider Building, CB# 7220, Chapel Hill, North Carolina 27599, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, 1601 SW Jefferson Way, Corvallis, Oregon 97331, USA
| | - Natalia Shulzhenko
- College of Veterinary Medicine, Oregon State University, 105 Dryden Hall, 450 SW 30th Street, Corvallis, Oregon 97331, USA
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9
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Kumar P, Monin L, Castillo P, Elsegeiny W, Horne W, Eddens T, Vikram A, Good M, Schoenborn AA, Bibby K, Montelaro RC, Metzger DW, Gulati AS, Kolls JK. Intestinal Interleukin-17 Receptor Signaling Mediates Reciprocal Control of the Gut Microbiota and Autoimmune Inflammation. Immunity 2016; 44:659-671. [PMID: 26982366 DOI: 10.1016/j.immuni.2016.02.007] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/17/2015] [Accepted: 12/03/2015] [Indexed: 12/18/2022]
Abstract
Interleukin-17 (IL-17) and IL-17 receptor (IL-17R) signaling are essential for regulating mucosal host defense against many invading pathogens. Commensal bacteria, especially segmented filamentous bacteria (SFB), are a crucial factor that drives T helper 17 (Th17) cell development in the gastrointestinal tract. In this study, we demonstrate that Th17 cells controlled SFB burden. Disruption of IL-17R signaling in the enteric epithelium resulted in SFB dysbiosis due to reduced expression of α-defensins, Pigr, and Nox1. When subjected to experimental autoimmune encephalomyelitis, IL-17R-signaling-deficient mice demonstrated earlier disease onset and worsened severity that was associated with increased intestinal Csf2 expression and elevated systemic GM-CSF cytokine concentrations. Conditional deletion of IL-17R in the enteric epithelium demonstrated that there was a reciprocal relationship between the gut microbiota and enteric IL-17R signaling that controlled dysbiosis, constrained Th17 cell development, and regulated the susceptibility to autoimmune inflammation.
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Affiliation(s)
- Pawan Kumar
- Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Leticia Monin
- Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Patricia Castillo
- Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Waleed Elsegeiny
- Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - William Horne
- Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Taylor Eddens
- Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Amit Vikram
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Misty Good
- Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Alexi A Schoenborn
- Division of Pediatric Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ronald C Montelaro
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Dennis W Metzger
- Center for Immunology & Microbial Disease, Albany Medical College, Albany, NY 12208, USA
| | - Ajay S Gulati
- Division of Pediatric Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jay K Kolls
- Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA.
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10
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Randell RL, Gulati AS, Cook SF, Martin CF, Chen W, Jaeger EL, Schoenborn AA, Basta PV, Dejong H, Luo J, Gallant M, Sandler RS, Long MD, Kappelman MD. Collecting Biospecimens From an Internet-Based Prospective Cohort Study of Inflammatory Bowel Disease (CCFA Partners): A Feasibility Study. JMIR Res Protoc 2016; 5:e3. [PMID: 26732016 PMCID: PMC4719077 DOI: 10.2196/resprot.5171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/01/2015] [Indexed: 12/27/2022] Open
Abstract
Background The Internet has successfully been used for patient-oriented survey research. Internet-based translational research may also be possible. Objective Our aim was to study the feasibility of collecting biospecimens from CCFA Partners, an Internet-based inflammatory bowel disease (IBD) cohort. Methods From August 20, 2013, to January 4, 2014, we randomly sampled 412 participants, plus 179 from a prior validation study, and invited them to contribute a biospecimen. Participants were randomized to type (blood, saliva), incentive (none, US $20, or US $50), and collection method for blood. The first 82 contributors were also invited to contribute stool. We used descriptive statistics and t tests for comparisons. Results Of the 591 participants, 239 (40.4%) indicated interest and 171 (28.9%) contributed a biospecimen. Validation study participants were more likely to contribute than randomly selected participants (44% versus 23%, P<.001). The return rate for saliva was higher than blood collected by mobile phlebotomist and at doctors’ offices (38%, 31%, and 17% respectively, P<.001). For saliva, incentives were associated with higher return rates (43-44% versus 26%, P=.04); 61% contributed stool. Fourteen IBD-associated single nucleotide polymorphisms were genotyped, and risk allele frequencies were comparable to other large IBD populations. Bacterial DNA was successfully extracted from stool samples and was of sufficient quality to permit quantitative polymerase chain reaction for total bacteria. Conclusions Participants are willing to contribute and it is feasible to collect biospecimens from an Internet-based IBD cohort. Home saliva kits yielded the highest return rate, though mobile phlebotomy was also effective. All samples were sufficient for genetic testing. These data support the feasibility of developing a centralized collection of biospecimens from this cohort to facilitate IBD translational studies.
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Affiliation(s)
- Rachel L Randell
- Department of Pediatrics, Duke University School of Medicine, Duke University, Durham, NC, United States.
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Liu B, Gulati AS, Cantillana V, Henry SC, Schmidt EA, Daniell X, Grossniklaus E, Schoenborn AA, Sartor RB, Taylor GA. Irgm1-deficient mice exhibit Paneth cell abnormalities and increased susceptibility to acute intestinal inflammation. Am J Physiol Gastrointest Liver Physiol 2013; 305:G573-84. [PMID: 23989005 PMCID: PMC3798734 DOI: 10.1152/ajpgi.00071.2013] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [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: 01/31/2023]
Abstract
Crohn's disease (CD) is a chronic, immune-mediated, inflammatory disorder of the intestine that has been linked to numerous susceptibility genes, including the immunity-related GTPase (IRG) M (IRGM). IRGs comprise a family of proteins known to confer resistance to intracellular infections through various mechanisms, including regulation of phagosome processing, cell motility, and autophagy. However, despite its association with CD, the role of IRGM and other IRGs in regulating intestinal inflammation is unclear. We investigated the involvement of Irgm1, an ortholog of IRGM, in the genesis of murine intestinal inflammation. After dextran sodium sulfate exposure, Irgm1-deficient [Irgm1 knockout (KO)] mice showed increased acute inflammation in the colon and ileum, with worsened clinical responses. Marked alterations of Paneth cell location and granule morphology were present in Irgm1 KO mice, even without dextran sodium sulfate exposure, and were associated with impaired mitophagy and autophagy in Irgm1 KO intestinal cells (including Paneth cells). This was manifested by frequent tubular and swollen mitochondria and increased LC3-positive autophagic structures. Interestingly, these LC3-positive structures often contained Paneth cell granules. These results suggest that Irgm1 modulates acute inflammatory responses in the mouse intestine, putatively through the regulation of gut autophagic processes, that may be pivotal for proper Paneth cell functioning.
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Affiliation(s)
- Bo Liu
- PO Box 3003, Duke Univ. Medical Center, Durham, NC 27710.
| | - Ajay S. Gulati
- 3Department of Pediatrics/Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina;
| | - Viviana Cantillana
- 4Departments of Medicine, Molecular Genetics and Microbiology, and Immunology, Division of Geriatrics, and Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina; and
| | - Stanley C. Henry
- 5Geriatric Research, Education, and Clinical Center, VA Medical Center, Durham, North Carolina
| | - Elyse A. Schmidt
- 4Departments of Medicine, Molecular Genetics and Microbiology, and Immunology, Division of Geriatrics, and Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina; and
| | - Xiaoju Daniell
- 4Departments of Medicine, Molecular Genetics and Microbiology, and Immunology, Division of Geriatrics, and Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina; and
| | - Emily Grossniklaus
- 3Department of Pediatrics/Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina;
| | - Alexi A. Schoenborn
- 3Department of Pediatrics/Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina;
| | - R. Balfour Sartor
- 2Departments of Medicine, Microbiology, and Immunology, Division of Gastroenterology and Hepatology, and Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina;
| | - Gregory A. Taylor
- 4Departments of Medicine, Molecular Genetics and Microbiology, and Immunology, Division of Geriatrics, and Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina; and ,5Geriatric Research, Education, and Clinical Center, VA Medical Center, Durham, North Carolina
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12
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Smits BMG, Haag JD, Rissman AI, Sharma D, Tran A, Schoenborn AA, Baird RC, Peiffer DS, Leinweber DQ, Muelbl MJ, Meilahn AL, Eichelberg MR, Leng N, Kendziorski C, John MC, Powers PA, Alexander CM, Gould MN. The gene desert mammary carcinoma susceptibility locus Mcs1a regulates Nr2f1 modifying mammary epithelial cell differentiation and proliferation. PLoS Genet 2013; 9:e1003549. [PMID: 23785296 PMCID: PMC3681674 DOI: 10.1371/journal.pgen.1003549] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [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: 11/15/2012] [Accepted: 04/23/2013] [Indexed: 12/28/2022] Open
Abstract
Genome-wide association studies have revealed that many low-penetrance breast cancer susceptibility loci are located in non-protein coding genomic regions; however, few have been characterized. In a comparative genetics approach to model such loci in a rat breast cancer model, we previously identified the mammary carcinoma susceptibility locus Mcs1a. We now localize Mcs1a to a critical interval (277 Kb) within a gene desert. Mcs1a reduces mammary carcinoma multiplicity by 50% and acts in a mammary cell-autonomous manner. We developed a megadeletion mouse model, which lacks 535 Kb of sequence containing the Mcs1a ortholog. Global gene expression analysis by RNA-seq revealed that in the mouse mammary gland, the orphan nuclear receptor gene Nr2f1/Coup-tf1 is regulated by Mcs1a. In resistant Mcs1a congenic rats, as compared with susceptible congenic control rats, we found Nr2f1 transcript levels to be elevated in mammary gland, epithelial cells, and carcinoma samples. Chromatin looping over ∼820 Kb of sequence from the Nr2f1 promoter to a strongly conserved element within the Mcs1a critical interval was identified. This element contains a 14 bp indel polymorphism that affects a human-rat-mouse conserved COUP-TF binding motif and is a functional Mcs1a candidate. In both the rat and mouse models, higher Nr2f1 transcript levels are associated with higher abundance of luminal mammary epithelial cells. In both the mouse mammary gland and a human breast cancer global gene expression data set, we found Nr2f1 transcript levels to be strongly anti-correlated to a gene cluster enriched in cell cycle-related genes. We queried 12 large publicly available human breast cancer gene expression studies and found that the median NR2F1 transcript level is consistently lower in 'triple-negative' (ER-PR-HER2-) breast cancers as compared with 'receptor-positive' breast cancers. Our data suggest that the non-protein coding locus Mcs1a regulates Nr2f1, which is a candidate modifier of differentiation, proliferation, and mammary cancer risk.
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Affiliation(s)
- Bart M. G. Smits
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Jill D. Haag
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Anna I. Rissman
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Deepak Sharma
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Ann Tran
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Alexi A. Schoenborn
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Rachael C. Baird
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Dan S. Peiffer
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - David Q. Leinweber
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Matthew J. Muelbl
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Amanda L. Meilahn
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Mark R. Eichelberg
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Ning Leng
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Manorama C. John
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Patricia A. Powers
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Caroline M. Alexander
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Michael N. Gould
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- * E-mail:
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