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Greigert V, Saraav I, Son J, Zhu Y, Dayao D, Antia A, Tzipori S, Witola WH, Stappenbeck TS, Ding S, Sibley LD. Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon and impairs infectivity of Rotavirus. Gut Microbes 2024; 16:2297897. [PMID: 38189373 PMCID: PMC10793699 DOI: 10.1080/19490976.2023.2297897] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024] Open
Abstract
Cryptosporidiosis is a major cause of severe diarrheal disease in infants from resource poor settings. The majority of infections are caused by the human-specific pathogen C. hominis and absence of in vitro growth platforms has limited our understanding of host-pathogen interactions and development of effective treatments. To address this problem, we developed a stem cell-derived culture system for C. hominis using human enterocytes differentiated under air-liquid interface (ALI) conditions. Human ALI cultures supported robust growth and complete development of C. hominis in vitro including all life cycle stages. Cryptosporidium infection induced a strong interferon response from enterocytes, possibly driven, in part, by an endogenous dsRNA virus in the parasite. Prior infection with Cryptosporidium induced type III IFN secretion and consequently blunted infection with Rotavirus, including live attenuated vaccine strains. The development of hALI provides a platform for further studies on human-specific pathogens, including clinically important coinfections that may alter vaccine efficacy.
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Affiliation(s)
- Valentin Greigert
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Iti Saraav
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Juhee Son
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yinxing Zhu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Denise Dayao
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Avan Antia
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - William H. Witola
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Thaddeus S. Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
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2
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Zhang S, Han Y, Schofield W, Nicosia M, Karell PE, Newhall KP, Zhou JY, Musich RJ, Pan S, Valujskikh A, Sangwan N, Dwidar M, Lu Q, Stappenbeck TS. Select symbionts drive high IgA levels in the mouse intestine. Cell Host Microbe 2023; 31:1620-1638.e7. [PMID: 37776865 DOI: 10.1016/j.chom.2023.09.001] [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: 02/27/2023] [Revised: 07/14/2023] [Accepted: 09/01/2023] [Indexed: 10/02/2023]
Abstract
Immunoglobulin A (IgA) is an important factor in maintaining homeostasis at mucosal surfaces, yet luminal IgA levels vary widely. Total IgA levels are thought to be driven by individual immune responses to specific microbes. Here, we found that the prebiotic, pectin oligosaccharide (pec-oligo), induced high IgA levels in the small intestine in a T cell-dependent manner. Surprisingly, this IgA-high phenotype was retained after cessation of pec-oligo treatment, and microbiome transmission either horizontally or vertically was sufficient to retain high IgA levels in the absence of pec-oligo. Interestingly, the bacterial taxa enriched in the overall pec-oligo bacterial community differed from IgA-coated microbes in this same community. Rather, a group of ethanol-resistant microbes, highly enriched for Lachnospiraceae bacterium A2, drove the IgA-high phenotype. These findings support a model of intestinal adaptive immunity in which a limited number of microbes can promote durable changes in IgA directed to many symbionts.
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Affiliation(s)
- Shanshan Zhang
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan 250000, P.R. China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yi Han
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Michael Nicosia
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul E Karell
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kevin P Newhall
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Julie Y Zhou
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ryan J Musich
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Siyi Pan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Anna Valujskikh
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Mohammed Dwidar
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Qiuhe Lu
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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3
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Greigert V, Saraav I, Son J, Dayao D, Antia A, Tzipori S, Witola WH, Stappenbeck TS, Ding S, Sibley LD. Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon and impairs infectivity of Rotavirus. bioRxiv 2023:2023.08.30.555581. [PMID: 37693422 PMCID: PMC10491271 DOI: 10.1101/2023.08.30.555581] [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: 09/12/2023]
Abstract
Cryptosporidiosis is a major cause of severe diarrheal disease in infants from resource poor settings. The majority of infections are caused by the human-specific pathogen C. hominis and absence of in vitro growth platforms has limited our understanding of host-pathogen interactions and development of effective treatments. To address this problem, we developed a stem cell-derived culture system for C. hominis using human enterocytes differentiated under air-liquid interface (ALI) conditions. Human ALI cultures supported robust growth and complete development of C. hominis in vitro including all life cycle stages. C. hominis infection induced a strong interferon response from enterocytes, likely driven by an endogenous dsRNA virus in the parasite. Prior infection with Cryptosporidium induced type III IFN secretion and consequently blunted infection with Rotavirus, including live attenuated vaccine strains. The development of hALI provides a platform for further studies on human-specific pathogens, including clinically important coinfections that may alter vaccine efficacy.
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Affiliation(s)
- Valentin Greigert
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Iti Saraav
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Juhee Son
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Denise Dayao
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, 01536, USA
| | - Avan Antia
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, 01536, USA
| | - William H. Witola
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Thaddeus S. Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA
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Funkhouser-Jones LJ, Xu R, Wilke G, Fu Y, Schriefer LA, Makimaa H, Rodgers R, Kennedy EA, VanDussen KL, Stappenbeck TS, Baldridge MT, Sibley LD. Microbiota-produced indole metabolites disrupt mitochondrial function and inhibit Cryptosporidium parvum growth. Cell Rep 2023; 42:112680. [PMID: 37384526 PMCID: PMC10530208 DOI: 10.1016/j.celrep.2023.112680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 12/12/2022] [Revised: 05/08/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
Cryptosporidiosis is a leading cause of life-threatening diarrhea in young children in resource-poor settings. To explore microbial influences on susceptibility, we screened 85 microbiota-associated metabolites for their effects on Cryptosporidium parvum growth in vitro. We identify eight inhibitory metabolites in three main classes: secondary bile salts/acids, a vitamin B6 precursor, and indoles. Growth restriction of C. parvum by indoles does not depend on the host aryl hydrocarbon receptor (AhR) pathway. Instead, treatment impairs host mitochondrial function and reduces total cellular ATP, as well as directly reducing the membrane potential in the parasite mitosome, a degenerate mitochondria. Oral administration of indoles, or reconstitution of the gut microbiota with indole-producing bacteria, delays life cycle progression of the parasite in vitro and reduces the severity of C. parvum infection in mice. Collectively, these findings indicate that microbiota metabolites impair mitochondrial function and contribute to colonization resistance to Cryptosporidium infection.
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Affiliation(s)
- Lisa J Funkhouser-Jones
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rui Xu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Georgia Wilke
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yong Fu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lawrence A Schriefer
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Heyde Makimaa
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel Rodgers
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Elizabeth A Kennedy
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
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5
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Funkhouser-Jones LJ, Xu R, Wilke G, Fu Y, Shriefer LA, Makimaa H, Rodgers R, Kennedy EA, VanDussen KL, Stappenbeck TS, Baldridge MT, Sibley LD. Microbiota produced indole metabolites disrupt host cell mitochondrial energy production and inhibit Cryptosporidium parvum growth. bioRxiv 2023:2023.05.25.542157. [PMID: 37292732 PMCID: PMC10245909 DOI: 10.1101/2023.05.25.542157] [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: 06/10/2023]
Abstract
Cryptosporidiosis is a leading cause of life-threatening diarrhea in young children in resource-poor settings. Susceptibility rapidly declines with age, associated with changes in the microbiota. To explore microbial influences on susceptibility, we screened 85 microbiota- associated metabolites enriched in the adult gut for their effects on C. parvum growth in vitro. We identified eight inhibitory metabolites in three main classes: secondary bile salts/acids, a vitamin B 6 precursor, and indoles. Growth restriction of C. parvum by indoles did not depend on the host aryl hydrocarbon receptor (AhR) pathway. Instead, treatment impaired host mitochondrial function and reduced total cellular ATP, as well as directly reduced the membrane potential in the parasite mitosome, a degenerate mitochondria. Oral administration of indoles, or reconstitution of the gut microbiota with indole producing bacteria, delayed life cycle progression of the parasite in vitro and reduced severity of C. parvum infection in mice. Collectively, these findings indicate that microbiota metabolites contribute to colonization resistance to Cryptosporidium infection.
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Affiliation(s)
- Lisa J. Funkhouser-Jones
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Rui Xu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Georgia Wilke
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Yong Fu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Lawrence A. Shriefer
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Heyde Makimaa
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel Rodgers
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Elizabeth A. Kennedy
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Kelli L. VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Thaddeus S. Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Megan T. Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
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6
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Russell SK, Harrison JK, Olson BS, Lee HJ, O'Brien VP, Xing X, Livny J, Yu L, Roberson EDO, Bomjan R, Fan C, Sha M, Estfanous S, Amer AO, Colonna M, Stappenbeck TS, Wang T, Hannan TJ, Hultgren SJ. Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome. Nat Microbiol 2023; 8:875-888. [PMID: 37037942 PMCID: PMC10159856 DOI: 10.1038/s41564-023-01346-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 04/12/2023]
Abstract
Previous urinary tract infections (UTIs) can predispose one to future infections; however, the underlying mechanisms affecting recurrence are poorly understood. We previously found that UTIs in mice cause differential bladder epithelial (urothelial) remodelling, depending on disease outcome, that impacts susceptibility to recurrent UTI. Here we compared urothelial stem cell (USC) lines isolated from mice with a history of either resolved or chronic uropathogenic Escherichia coli (UPEC) infection, elucidating evidence of molecular imprinting that involved epigenetic changes, including differences in chromatin accessibility, DNA methylation and histone modification. Epigenetic marks in USCs from chronically infected mice enhanced caspase-1-mediated cell death upon UPEC infection, promoting bacterial clearance. Increased Ptgs2os2 expression also occurred, potentially contributing to sustained cyclooxygenase-2 expression, bladder inflammation and mucosal wounding-responses associated with severe recurrent cystitis. Thus, UPEC infection acts as an epi-mutagen reprogramming the urothelial epigenome, leading to urothelial-intrinsic remodelling and training of the innate response to subsequent infection.
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Affiliation(s)
- Seongmi K Russell
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Jessica K Harrison
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Benjamin S Olson
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Valerie P O'Brien
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
- Fred Hutchinson Cancer Center, Human Biology Division, Seattle, WA, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Lu Yu
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Elisha D O Roberson
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St Louis, MO, USA
| | - Rajdeep Bomjan
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Changxu Fan
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Marina Sha
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shady Estfanous
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy Helwan University, Cairo, Egypt
| | - Amal O Amer
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
| | - Thomas J Hannan
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
| | - Scott J Hultgren
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA.
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7
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Liu JJ, Abraham BP, Adamson P, Barnes EL, Brister KA, Damas OM, Glover SC, Hooks K, Ingram A, Kaplan GG, Loftus EV, McGovern DPB, Narain-Blackwell M, Odufalu FD, Quezada S, Reeves V, Shen B, Stappenbeck TS, Ward L. The Current State of Care for Black and Hispanic Inflammatory Bowel Disease Patients. Inflamm Bowel Dis 2023; 29:297-307. [PMID: 35816130 DOI: 10.1093/ibd/izac124] [Citation(s) in RCA: 3] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Indexed: 02/03/2023]
Abstract
Research on the care of inflammatory bowel disease (IBD) patients has been primarily in populations of European ancestry. However, the incidence of IBD, which comprises Crohn's disease and ulcerative colitis, is increasing in different populations around the world. In this comprehensive review, we examine the epidemiology, clinical presentations, disease phenotypes, treatment outcomes, social determinants of health, and genetic and environmental factors in the pathogenesis of IBD in Black and Hispanic patients in the United States. To improve health equity of underserved minorities with IBD, we identified the following priority areas: access to care, accurate assessment of treatment outcomes, incorporation of Black and Hispanic patients in therapeutic clinical trials, and investigation of environmental factors that lead to the increase in disease incidence.
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Affiliation(s)
- Julia J Liu
- Division of Gastroenterology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Bincy P Abraham
- Division of Gastroenterology and Hepatology, Houston Methodist Academic Institute, Houston, TX, USA
| | - Paula Adamson
- Division of Gastroenterology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Edward L Barnes
- Division of Gastroenterology and Hepatology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Kelly A Brister
- Department of Surgery, University of Mississippi Medical Center, Jackson, MS, USA
| | - Oriana M Damas
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sarah C Glover
- Division of Gastroenterology and Hepatology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Kimberly Hooks
- Color of Crohn's and Chronic Illness, Glenarden, MD, USA
| | - Ana Ingram
- Color of Crohn's and Chronic Illness, Glenarden, MD, USA
| | - Gilaad G Kaplan
- Division of Gastroenterology and Hepatology, Department of Medicine and Community Health Sciences, University of Calgary, Calgary, AB, Canada
| | - Edward V Loftus
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Florence-Damilola Odufalu
- Division of Gastroenterology and Liver Diseases, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Sandra Quezada
- Division of Gastroenterology and Hepatology, University of Maryland, College Park, College Park, MD, USA
| | - Vonda Reeves
- GI Associates and Endoscopy Center, Jackson, MS, USA
| | - Bo Shen
- Inflammatory Bowel Disease Center, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center, New York, NY, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Latonia Ward
- Color of Crohn's and Chronic Illness, Glenarden, MD, USA
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8
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Abstract
We are entering an era of medicine where increasingly sophisticated data will be obtained from patients to determine proper diagnosis, predict outcomes and direct therapies. We predict that the most valuable data will be produced by systems that are highly dynamic in both time and space. Three-dimensional (3D) organoids are poised to be such a highly valuable system for a variety of gastrointestinal (GI) diseases. In the lab, organoids have emerged as powerful systems to model molecular and cellular processes orchestrating natural and pathophysiological human tissue formation in remarkable detail. Preclinical studies have impressively demonstrated that these organs-in-a-dish can be used to model immunological, neoplastic, metabolic or infectious GI disorders by taking advantage of patient-derived material. Technological breakthroughs now allow to study cellular communication and molecular mechanisms of interorgan cross-talk in health and disease including communication along for example, the gut-brain axis or gut-liver axis. Despite considerable success in culturing classical 3D organoids from various parts of the GI tract, some challenges remain to develop these systems to best help patients. Novel platforms such as organ-on-a-chip, engineered biomimetic systems including engineered organoids, micromanufacturing, bioprinting and enhanced rigour and reproducibility will open improved avenues for tissue engineering, as well as regenerative and personalised medicine. This review will highlight some of the established methods and also some exciting novel perspectives on organoids in the fields of gastroenterology. At present, this field is poised to move forward and impact many currently intractable GI diseases in the form of novel diagnostics and therapeutics.
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Affiliation(s)
- Claudia Günther
- Department of Medicine 1, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Beate Winner
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Stem Cell Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Center of Rare Diseases Erlangen (ZSEER), University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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9
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Lai CW, Bagadia P, Barisas DAG, Jarjour NN, Wong R, Ohara T, Muegge BD, Lu Q, Xiong S, Edelson BT, Murphy KM, Stappenbeck TS. Mesothelium-Derived Factors Shape GATA6-Positive Large Cavity Macrophages. The Journal of Immunology 2022; 209:742-750. [DOI: 10.4049/jimmunol.2200278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/15/2022] [Indexed: 01/04/2023]
Abstract
Abstract
The local microenvironment shapes macrophage differentiation in each tissue. We hypothesized that in the peritoneum, local factors in addition to retinoic acid can support GATA6-driven differentiation and function of peritoneal large cavity macrophages (LCMs). We found that soluble proteins produced by mesothelial cells lining the peritoneal cavity maintained GATA6 expression in cultured LCMs. Analysis of global gene expression of isolated mesothelial cells highlighted mesothelin (Msln) and its binding partner mucin 16 (Muc16) as candidate secreted ligands that potentially regulate GATA6 expression in peritoneal LCMs. Mice deficient for either of these molecules showed diminished GATA6 expression in peritoneal and pleural LCMs that was most prominent in aged mice. The more robust phenotype in older mice suggested that monocyte-derived macrophages were the target of Msln and Muc16. Cell transfer and bone marrow chimera experiments supported this hypothesis. We found that lethally irradiated Msln−/− and Muc16−/− mice reconstituted with wild-type bone marrow had lower levels of GATA6 expression in peritoneal and pleural LCMs. Similarly, during the resolution of zymosan-induced inflammation, repopulated peritoneal LCMs lacking expression of Msln or Muc16 expressed diminished GATA6. These data support a role for mesothelial cell–produced Msln and Muc16 in local macrophage differentiation within large cavity spaces such as the peritoneum. The effect appears to be most prominent on monocyte-derived macrophages that enter into this location as the host ages and also in response to infection.
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Affiliation(s)
- Chin-Wen Lai
- Department of Pathology and Immunology, Washington University Medical School, St. Louis, MO
| | - Prachi Bagadia
- Department of Pathology and Immunology, Washington University Medical School, St. Louis, MO
| | - Derek A. G. Barisas
- Department of Pathology and Immunology, Washington University Medical School, St. Louis, MO
| | - Nicholas N. Jarjour
- Department of Pathology and Immunology, Washington University Medical School, St. Louis, MO
| | - Rachel Wong
- Department of Pathology and Immunology, Washington University Medical School, St. Louis, MO
| | - Takahiro Ohara
- Department of Pathology and Immunology, Washington University Medical School, St. Louis, MO
| | - Brian D. Muegge
- Department of Pathology and Immunology, Washington University Medical School, St. Louis, MO
| | - Qiuhe Lu
- Department of Pathology and Immunology, Washington University Medical School, St. Louis, MO
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University Medical School, St. Louis, MO
| | - Brian T. Edelson
- Department of Pathology and Immunology, Washington University Medical School, St. Louis, MO
| | - Kenneth M. Murphy
- Department of Pathology and Immunology, Washington University Medical School, St. Louis, MO
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10
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Xiong S, Whitehurst CE, Li L, Heo GS, Lai CW, Jain U, Muegge BD, Espenschied ST, Musich RJ, Chen M, Liu Y, Liu TC, Stappenbeck TS. Reverse translation approach generates a signature of penetrating fibrosis in Crohn's disease that is associated with anti-TNF response. Gut 2022; 71:1289-1301. [PMID: 34261752 DOI: 10.1136/gutjnl-2020-323405] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 06/28/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Fibrosis is a common feature of Crohn's disease (CD) which can involve the mesenteric fat. However, the molecular signature of this process remains unclear. Our goal was to define the transcriptional signature of mesenteric fibrosis in CD subjects and to model mesenteric fibrosis in mice to improve our understanding of CD pathogenesis. DESIGN We performed histological and transcriptional analysis of fibrosis in CD samples. We modelled a CD-like fibrosis phenotype by performing repeated colonic biopsies in mice and analysed the model by histology, type I collagen-targeted positron emission tomography (PET) and global gene expression. We generated a gene set list of essential features of mesenteric fibrosis and compared it to mucosal biopsy datasets from inflammatory bowel disease patients to identify a refined gene set that correlated with clinical outcomes. RESULTS Mesenteric fibrosis in CD was interconnected to areas of fibrosis in all layers of the intestine, defined as penetrating fibrosis. We found a transcriptional signature of differentially expressed genes enriched in areas of the mesenteric fat of CD subjects with high levels of fibrosis. Mice subjected to repeated colonic biopsies showed penetrating fibrosis as shown by histology, PET imaging and transcriptional analysis. Finally, we composed a composite 24-gene set list that was linked to inflammatory fibroblasts and correlated with treatment response. CONCLUSION We linked histopathological and molecular features of CD penetrating fibrosis to a mouse model of repeated biopsy injuries. This experimental system provides an innovative approach for functional investigations of underlying profibrotic mechanisms and therapeutic concepts in CD.
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Affiliation(s)
- Shanshan Xiong
- Department of Gastroenterology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, China
| | - Charles E Whitehurst
- Department of Immunology and Respiratory Diseases Research, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, Connecticut, USA
| | - Li Li
- Department of Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, Connecticut, USA
| | - Gyu Seong Heo
- Washington University in St Louis, St Louis, Missouri, USA
| | - Chin-Wen Lai
- Washington University in St Louis, St Louis, Missouri, USA
| | - Umang Jain
- Washington University in St Louis, St Louis, Missouri, USA
| | - Brian D Muegge
- Washington University in St Louis, St Louis, Missouri, USA
| | | | - Ryan J Musich
- Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
| | - Minhu Chen
- Department of Gastroenterology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, China
| | - Yongjian Liu
- Washington University in St Louis, St Louis, Missouri, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
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11
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Abstract
Associations between the dynamic community of microbes (the microbiota) and the host they colonize appear to be vital for ensuring host health. Microbe-host communication is actively maintained across physiological barriers of various body sites and is mediated by a range of bidirectional secreted proteins and small molecules. So far, a range of "omics" methods have succeeded in revealing the multiplicity of associations between members of a microbiota and a wide range of host processes and diseases. Although these advances point to possibilities for treating disease, there has not been much translational success thus far. We know little about which organisms are key contributors to host health, the importance of strain differences, and the activities of much of the chemical "soup" that is produced by the microbiota. Adding to this complexity are emerging hints of the role of interkingdom interactions between bacteria, phages, protozoa, and/or fungi in regulating the microbiota-host interactions. Functional approaches, although experimentally challenging, could be the next step to unlocking the power of the microbiota.
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Affiliation(s)
- Qiuhe Lu
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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12
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Ohara TE, Colonna M, Stappenbeck TS. Adaptive differentiation promotes intestinal villus recovery. Dev Cell 2022; 57:166-179.e6. [PMID: 35016013 PMCID: PMC9092613 DOI: 10.1016/j.devcel.2021.12.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 05/18/2021] [Revised: 09/28/2021] [Accepted: 12/10/2021] [Indexed: 01/26/2023]
Abstract
Loss of differentiated cells to tissue damage is a hallmark of many diseases. In slow-turnover tissues, long-lived differentiated cells can re-enter the cell cycle or transdifferentiate to another cell type to promote repair. Here, we show that in a high-turnover tissue, severe damage to the differentiated compartment induces progenitors to transiently acquire a unique transcriptional and morphological postmitotic state. We highlight this in an acute villus injury model in the mouse intestine, where we identified a population of progenitor-derived cells that covered injured villi. These atrophy-induced villus epithelial cells (aVECs) were enriched for fetal markers but were differentiated and lineage committed. We further established a role for aVECs in maintaining barrier integrity through the activation of yes-associated protein (YAP). Notably, loss of YAP activity led to impaired villus regeneration. Thus, we define a key repair mechanism involving the activation of a fetal-like program during injury-induced differentiation, a process we term "adaptive differentiation."
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Affiliation(s)
- Takahiro E Ohara
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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13
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Liu TC, Kern JT, Jain U, Sonnek NM, Xiong S, Simpson KF, VanDussen KL, Winkler ES, Haritunians T, Malique A, Lu Q, Sasaki Y, Storer C, Diamond MS, Head RD, McGovern DPB, Stappenbeck TS. Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation. Cell Host Microbe 2021; 29:988-1001.e6. [PMID: 34010595 DOI: 10.1016/j.chom.2021.04.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [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: 05/18/2020] [Revised: 12/22/2020] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
Intestinal Paneth cells modulate innate immunity and infection. In Crohn's disease, genetic mutations together with environmental triggers can disable Paneth cell function. Here, we find that a western diet (WD) similarly leads to Paneth cell dysfunction through mechanisms dependent on the microbiome and farnesoid X receptor (FXR) and type I interferon (IFN) signaling. Analysis of multiple human cohorts suggests that obesity is associated with Paneth cell dysfunction. In mouse models, consumption of a WD for as little as 4 weeks led to Paneth cell dysfunction. WD consumption in conjunction with Clostridium spp. increased the secondary bile acid deoxycholic acid levels in the ileum, which in turn inhibited Paneth cell function. The process required excess signaling of both FXR and IFN within intestinal epithelial cells. Our findings provide a mechanistic link between poor diet and inhibition of gut innate immunity and uncover an effect of FXR activation in gut inflammation.
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Affiliation(s)
- Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Justin T Kern
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Naomi M Sonnek
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Katherine F Simpson
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Emma S Winkler
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Talin Haritunians
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles 90048, USA
| | - Atika Malique
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Qiuhe Lu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yo Sasaki
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chad Storer
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Dermot P B McGovern
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles 90048, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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14
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Jain U, Ver Heul AM, Xiong S, Gregory MH, Demers EG, Kern JT, Lai CW, Muegge BD, Barisas DAG, Leal-Ekman JS, Deepak P, Ciorba MA, Liu TC, Hogan DA, Debbas P, Braun J, McGovern DPB, Underhill DM, Stappenbeck TS. Debaryomyces is enriched in Crohn's disease intestinal tissue and impairs healing in mice. Science 2021; 371:1154-1159. [PMID: 33707263 PMCID: PMC10114606 DOI: 10.1126/science.abd0919] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 11/15/2020] [Accepted: 01/15/2021] [Indexed: 12/13/2022]
Abstract
Alterations of the mycobiota composition associated with Crohn's disease (CD) are challenging to link to defining elements of pathophysiology, such as poor injury repair. Using culture-dependent and -independent methods, we discovered that Debaryomyces hansenii preferentially localized to and was abundant within incompletely healed intestinal wounds of mice and inflamed mucosal tissues of CD human subjects. D. hansenii cultures from injured mice and inflamed CD tissues impaired colonic healing when introduced into injured conventionally raised or gnotobiotic mice. We reisolated D. hansenii from injured areas of these mice, fulfilling Koch's postulates. Mechanistically, D. hansenii impaired mucosal healing through the myeloid cell-specific type 1 interferon-CCL5 axis. Taken together, we have identified a fungus that inhabits inflamed CD tissue and can lead to dysregulated mucosal healing.
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Affiliation(s)
- Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Aaron M Ver Heul
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Martin H Gregory
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elora G Demers
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Justin T Kern
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chin-Wen Lai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Inflammation and Oncology, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Brian D Muegge
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Medicine, VA Medical Center, St. Louis, MO 63106, USA
| | - Derek A G Barisas
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - J Steven Leal-Ekman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Parakkal Deepak
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew A Ciorba
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Philip Debbas
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jonathan Braun
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - David M Underhill
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. .,Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
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15
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Desai P, Janova H, White JP, Reynoso GV, Hickman HD, Baldridge MT, Urban JF, Stappenbeck TS, Thackray LB, Diamond MS. Enteric helminth coinfection enhances host susceptibility to neurotropic flaviviruses via a tuft cell-IL-4 receptor signaling axis. Cell 2021; 184:1214-1231.e16. [PMID: 33636133 PMCID: PMC7962748 DOI: 10.1016/j.cell.2021.01.051] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 08/01/2020] [Revised: 12/15/2020] [Accepted: 01/26/2021] [Indexed: 12/17/2022]
Abstract
Although enteric helminth infections modulate immunity to mucosal pathogens, their effects on systemic microbes remain less established. Here, we observe increased mortality in mice coinfected with the enteric helminth Heligmosomoides polygyrus bakeri (Hpb) and West Nile virus (WNV). This enhanced susceptibility is associated with altered gut morphology and transit, translocation of commensal bacteria, impaired WNV-specific T cell responses, and increased virus infection in the gastrointestinal tract and central nervous system. These outcomes were due to type 2 immune skewing, because coinfection in Stat6-/- mice rescues mortality, treatment of helminth-free WNV-infected mice with interleukin (IL)-4 mirrors coinfection, and IL-4 receptor signaling in intestinal epithelial cells mediates the susceptibility phenotypes. Moreover, tuft cell-deficient mice show improved outcomes with coinfection, whereas treatment of helminth-free mice with tuft cell-derived cytokine IL-25 or ligand succinate worsens WNV disease. Thus, helminth activation of tuft cell-IL-4-receptor circuits in the gut exacerbates infection and disease of a neurotropic flavivirus.
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Affiliation(s)
- Pritesh Desai
- Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA
| | - Hana Janova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA
| | - James P White
- Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA
| | - Glennys V Reynoso
- Viral Immunity and Pathogenesis Unit, Laboratory of Clinical Microbiology and Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Heather D Hickman
- Viral Immunity and Pathogenesis Unit, Laboratory of Clinical Microbiology and Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Megan T Baldridge
- Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA
| | - Joseph F Urban
- US Department of Agriculture, Agricultural Research Services, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, and Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705-2350, USA
| | | | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA.
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16
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den Hartog G, Butcher LD, Ablack AL, Pace LA, Ablack JNG, Xiong R, Das S, Stappenbeck TS, Eckmann L, Ernst PB, Crowe SE. Apurinic/Apyrimidinic Endonuclease 1 Restricts the Internalization of Bacteria Into Human Intestinal Epithelial Cells Through the Inhibition of Rac1. Front Immunol 2021; 11:553994. [PMID: 33603730 PMCID: PMC7884313 DOI: 10.3389/fimmu.2020.553994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/01/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Pathogenic intestinal bacteria lead to significant disease in humans. Here we investigated the role of the multifunctional protein, Apurinic/apyrimidinic endonuclease 1 (APE1), in regulating the internalization of bacteria into the intestinal epithelium. Intestinal tumor-cell lines and primary human epithelial cells were infected with Salmonella enterica serovar Typhimurium or adherent-invasive Escherichia coli. The effects of APE1 inhibition on bacterial internalization, the regulation of Rho GTPase Rac1 as well as the epithelial cell barrier function were assessed. Increased numbers of bacteria were present in APE1-deficient colonic tumor cell lines and primary epithelial cells. Activation of Rac1 was augmented following infection but negatively regulated by APE1. Pharmacological inhibition of Rac1 reversed the increase in intracellular bacteria in APE1-deficient cells whereas overexpression of constitutively active Rac1 augmented the numbers in APE1-competent cells. Enhanced numbers of intracellular bacteria resulted in the loss of barrier function and a delay in its recovery. Our data demonstrate that APE1 inhibits the internalization of invasive bacteria into human intestinal epithelial cells through its ability to negatively regulate Rac1. This activity also protects epithelial cell barrier function.
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Affiliation(s)
- Gerco den Hartog
- Department of Medicine, Division of Gastroenterology, University of California San Diego, La Jolla, CA, United States
| | - Lindsay D Butcher
- Department of Medicine, Division of Gastroenterology, University of California San Diego, La Jolla, CA, United States
| | - Amber L Ablack
- Department of Medicine, Division of Gastroenterology, University of California San Diego, La Jolla, CA, United States
| | - Laura A Pace
- Department of Medicine, Division of Gastroenterology, University of California San Diego, La Jolla, CA, United States
| | - Jailal N G Ablack
- Department of Medicine, Division of Rheumatology, University of California San Diego, La Jolla, CA, United States
| | - Richard Xiong
- Department of Medicine, Division of Gastroenterology, University of California San Diego, La Jolla, CA, United States
| | - Soumita Das
- Division of Comparative Pathology and Medicine, Department of Pathology, University of California San Diego, La Jolla, CA, United States
| | | | - Lars Eckmann
- Department of Medicine, Division of Gastroenterology, University of California San Diego, La Jolla, CA, United States
| | - Peter B Ernst
- Division of Comparative Pathology and Medicine, Department of Pathology, University of California San Diego, La Jolla, CA, United States.,Center for Mucosal Immunology, Allergy and Vaccine Development, Department of Pathology, University of California San Diego, La Jolla, CA, United States.,Department of Immunology, Chiba University, Chiba, Japan
| | - Sheila E Crowe
- Department of Medicine, Division of Gastroenterology, University of California San Diego, La Jolla, CA, United States.,Division of ImmunoBiology, Washington University, St. Louis, MO, United States
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17
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Potdar AA, Dube S, Naito T, Li K, Botwin G, Haritunians T, Li D, Casero D, Yang S, Bilsborough J, Perrigoue JG, Denson LA, Daly M, Targan SR, Fleshner P, Braun J, Kugathasan S, Stappenbeck TS, McGovern DP. Altered Intestinal ACE2 Levels Are Associated With Inflammation, Severe Disease, and Response to Anti-Cytokine Therapy in Inflammatory Bowel Disease. Gastroenterology 2021; 160:809-822.e7. [PMID: 33160965 PMCID: PMC9671555 DOI: 10.1053/j.gastro.2020.10.041] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/14/2020] [Accepted: 10/24/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIMS The host receptor for severe acute respiratory syndrome coronavirus 2, angiotensin-converting enzyme 2 (ACE2), is highly expressed in small bowel (SB). Our aim was to identify factors influencing intestinal ACE2 expression in Crohn's disease (CD), ulcerative colitis (UC), and non-inflammatory bowel disease (IBD) controls. METHODS Using bulk RNA sequencing or microarray transcriptomics from tissue samples (4 SB and 2 colonic cohorts; n = 495; n = 387 UC; n = 94 non-IBD), we analyzed the relationship between ACE2 with demographics and disease activity and prognosis. We examined the outcome of anti-tumor necrosis factor and anti-interleukin-12/interleukin-23 treatment on SB and colonic ACE2 expression in 3 clinical trials. Univariate and multivariate regression models were fitted. RESULTS ACE2 levels were consistently reduced in SB CD and elevated in colonic UC compared with non-IBD controls. Elevated SB ACE2 was also associated with demographic features (age and elevated body mass index) associated with poor coronavirus disease 2019 outcomes. Within CD, SB ACE2 was reduced in patients subsequently developing complicated disease. Within UC, colonic ACE2 was elevated in active disease and in patients subsequently requiring anti-tumor necrosis factor rescue therapy. SB and colonic ACE2 expression in active CD and UC were restored by anti-cytokine therapy, most notably in responders. CONCLUSIONS Reduced SB but elevated colonic ACE2 levels in IBD are associated with inflammation and severe disease, but normalized after anti-cytokine therapy, suggesting compartmentalization of ACE2-related biology in SB and colonic inflammation. The restoration of ACE2 expression with anti-cytokine therapy might be important in the context of severe acute respiratory syndrome coronavirus 2 infection and potentially explain reports of reduced morbidity from coronavirus disease 2019 in IBD patients treated with anti-cytokines.
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Affiliation(s)
- Alka A. Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shishir Dube
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Takeo Naito
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Katherine Li
- Janssen Research and Development, LLC, Spring House, Pennsylvania
| | - Gregory Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - David Casero
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shaohong Yang
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Janine Bilsborough
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Lee A. Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Mark Daly
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Phillip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Atlanta, Georgia
| | | | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California,Correspondence Address correspondence to: Dermot P. B. McGovern, MD, PhD, FRCP(Lon), F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, 8730 Alden Drive, Los Angeles, California 90048
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18
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Murray E, Cheng X, Krishna A, Jin X, Ohara TE, Stappenbeck TS, Bose R. HER2 and APC Mutations Promote Altered Crypt-Villus Morphology and Marked Hyperplasia in the Intestinal Epithelium. Cell Mol Gastroenterol Hepatol 2021; 12:1105-1120. [PMID: 33930605 PMCID: PMC8350008 DOI: 10.1016/j.jcmgh.2021.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/26/2020] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS The Cancer Genome Atlas (TCGA) project has identified HER2 mutations or amplification in 7% of colon cancers. In addition to HER2 mutations, colon cancer patients also possess co-occurring mutations in genes such as APC. Here, we investigated the role of HER2 and APC mutations on the crypt-villus architecture of the intestinal epithelium, localization of secretory cells, and expression of intestinal stem cell markers. METHODS We generated a HER2 transgenic mouse (HER2V777L Tg) possessing an activating mutation commonly found in colorectal cancer patients, HER2V777L, using transcription activator-like effector nucleases-based gene editing technology. We expressed the HER2V777L transgene in mouse small intestine and colon using Lgr5-Cre and Villin-Cre recombinases. In addition, we analyzed Lgr5-Cre; APCmin; HER2V777L Tg mice by morphologic and gene expression assays on intestinal sections and organoids derived from the epithelium. RESULTS HER2V777L expression resulted in hypertrophic crypt formation with expanded zones of proliferation. Proximal intestinal villi showed increased abundance of multiple differentiated lineages including extensive intermediate cell differentiation, as evidenced by MUC2/MMP7 co-immunofluorescence and transmission electron microscopy. HER2V777L expression in the context of APC loss resulted in further enhancement and expansion of the proliferative crypt compartment. CONCLUSIONS We established an epithelial intrinsic role for HER2V777L on enhanced cellular proliferation. Additionally, we determined that HER2 and APC mutations, when combined, promote enhanced proliferation of intestinal crypts.
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Affiliation(s)
- Elisa Murray
- Division of Biology and Biomedical Sciences, Department of Biochemistry, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Division of Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Xiaoqing Cheng
- Division of Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Anagha Krishna
- Division of Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Xiaohua Jin
- Division of Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Takahiro E Ohara
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Ron Bose
- Division of Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Alvin J. Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri.
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19
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Osterman MT, VanDussen KL, Gordon IO, Davis EM, Li K, Simpson K, Ciorba M, Glover SC, Abraham B, Guo X, Yee EU, Allard FD, Perrigoue JG, Claggett B, Shen B, Stappenbeck TS, Liu JJ. Epithelial Cell Biomarkers Are Predictive of Response to Biologic Agents in Crohn's Disease. Inflamm Bowel Dis 2020; 27:677-685. [PMID: 32964238 PMCID: PMC8047859 DOI: 10.1093/ibd/izaa251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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] [Received: 04/28/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Therapeutic efficacy of biologics has remained at about 50% for 2 decades. In Crohn's disease (CD) patients, we examined the predictive value of an epithelial cell biomarker, ileal microvillar length (MVL), for clinical response to ustekinumab (UST) and vedolizumab (VDZ) and its relationship to another biomarker, intestinal epithelial cell (IEC) pyroptosis, with respect to response to VDZ. METHOD Ileal biopsies from the UNITI-2 randomized controlled trial were analyzed for MVL as a predictor of clinical response to UST. In a 5-center academic retrospective cohort of CD patients, ileal MVL was analyzed to determine its predictive value for response to VDZ. Correlation between ileal MVL and IEC pyroptosis was determined, and the discriminant ability of the combination of 2 biomarkers to VDZ was examined. RESULTS Clinical response in UST was significantly higher than placebo (65% vs 39%; P = 0.03), with patients with normal MVL (>1.7 µm) having the greatest therapeutic effect: 85% vs 20% (P = 0.02). For VDZ, clinical response with MVL of 1.35 to 1.55 µm was 82% vs 44% (<1.35 µm) and 40% (>1.55 µm; P = 0.038). There was no correlation between ileal MVL and IEC pyroptosis. The combination criteria of ileal pyroptosis <14 positive cells/1000 IECs or MVL of 1.35 to 1.55 µm could identify 84% of responders and 67% of nonresponders (P = 0.001). CONCLUSION Ileal MVL was predictive of response to UST and VDZ in prospective and retrospective CD cohorts. It was independent of ileal IEC pyroptosis, and combination of the 2 biomarkers enhanced the discriminate ability of responders from nonresponders to VDZ.
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Affiliation(s)
- Mark T Osterman
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kelli L VanDussen
- Divisions of Gastroenterology, Hepatology, and Nutrition and of Developmental Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ilyssa O Gordon
- Department of Pathology, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Elisabeth M Davis
- Division of Gastroenterology and Hepatology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Katherine Li
- Janssen Research and Development, Spring House, PA, USA
| | - Kate Simpson
- Departments of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew Ciorba
- Division of Gastroenterology and Hepatology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sarah C Glover
- Division of Gastroenterology and Hepatology, University of Florida, Gainesville, FL, USA
| | - Bincy Abraham
- Division of Gastroenterology and Hepatology, Houston Methodist Hospital, Houston, TX, USA
| | - Xueyan Guo
- Division of Gastroenterology and Hepatology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Eric U Yee
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Felicia D Allard
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Brian Claggett
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Bo Shen
- Department of Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Thaddeus S Stappenbeck
- Departments of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Julia J Liu
- Division of Gastroenterology and Hepatology, University of Arkansas for Medical Sciences, Little Rock, AR, USA,Address correspondence to: Julia J. Liu, MD, MSc, Division of Gastroenterology and Hepatology, University of Arkansas for Medical Sciences, 4301 W. Markham St. #567, Little Rock, AR 72205, USA. E-mail:
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20
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Winkler ES, Shrihari S, Hykes BL, Handley SA, Andhey PS, Huang YJS, Swain A, Droit L, Chebrolu KK, Mack M, Vanlandingham DL, Thackray LB, Cella M, Colonna M, Artyomov MN, Stappenbeck TS, Diamond MS. The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid-Type I IFN Signaling Axis. Cell 2020; 182:901-918.e18. [PMID: 32668198 DOI: 10.1016/j.cell.2020.06.029] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/09/2020] [Accepted: 06/17/2020] [Indexed: 12/31/2022]
Abstract
Chikungunya virus (CHIKV), an emerging alphavirus, has infected millions of people. However, the factors modulating disease outcome remain poorly understood. Here, we show in germ-free mice or in oral antibiotic-treated conventionally housed mice with depleted intestinal microbiomes that greater CHIKV infection and spread occurs within 1 day of virus inoculation. Alteration of the microbiome alters TLR7-MyD88 signaling in plasmacytoid dendritic cells (pDCs) and blunts systemic production of type I interferon (IFN). Consequently, circulating monocytes express fewer IFN-stimulated genes and become permissive for CHIKV infection. Reconstitution with a single bacterial species, Clostridium scindens, or its derived metabolite, the secondary bile acid deoxycholic acid, can restore pDC- and MyD88-dependent type I IFN responses to restrict systemic CHIKV infection and transmission back to vector mosquitoes. Thus, symbiotic intestinal bacteria modulate antiviral immunity and levels of circulating alphaviruses within hours of infection through a bile acid-pDC-IFN signaling axis, which affects viremia, dissemination, and potentially transmission.
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Affiliation(s)
- Emma S Winkler
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Swathi Shrihari
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barry L Hykes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Prabhakar S Andhey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yan-Jang S Huang
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Biosecurity Research Institute, Kansas State University, Manhattan, KS 66506, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lindsay Droit
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kranthi K Chebrolu
- Proteomics and Mass Spectrometry Facility, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Matthias Mack
- Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
| | - Dana L Vanlandingham
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Biosecurity Research Institute, Kansas State University, Manhattan, KS 66506, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA.
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21
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Winkler ES, Thackray LB, Hykes BL, Handley SA, Droit L, Andhey P, Mack M, Shrihari S, Swain A, Cella M, Colonna M, Artyomov M, Stappenbeck TS, Diamond MS. A commensal Clostridium species restricts systemic alphavirus dissemination through a type I interferon signaling axis. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.171.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The role of the gut microbiota in shaping antiviral immune responses at non-intestinal sites has been described in multiple models of viral pathogenesis. Although chikungunya virus (CHIKV), an emerging alphavirus, is a substantial global health threat, the impact of the microbiota in modulating immune responses to alphavirus infection is entirely unexplored. Here, we show that CHIKV infection of oral antibiotic-treated or germ-free mice resulted in increased viremia within one day of infection, and this enhanced viral dissemination. Microbiota depletion resulted in greater CHIKV infection of circulating monocytes, which was linked to dampened systemic type I interferon (IFN) responses. Differences in CHIKV tropism and replication following microbiota depletion depended on MyD88 signaling in plasmacytoid dendritic cells, which contributed to systemic type I IFN production within hours of infection. Colonization of antibiotic-treated mice with a single bacterial microbiota-derived Clostridium species resulted in MyD88-dependent type I IFN responses that restricted CHIKV infection in blood. We propose that select bacterial symbionts impact antiviral immunity to alphaviruses within hours of infection through a type I IFN signaling axis and by virtue of effects on viremia may determine disease severity and affect vector transmission and epidemic spread.
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Affiliation(s)
- Emma S Winkler
- 1Department of Medicine, Washington University School of Medicine, Saint Louis, MO
| | - Larissa B Thackray
- 1Department of Medicine, Washington University School of Medicine, Saint Louis, MO
| | - Barry L Hykes
- 2Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Scott A Handley
- 2Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Lindsay Droit
- 2Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Prabhakar Andhey
- 2Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | | | - Swathi Shrihari
- 1Department of Medicine, Washington University School of Medicine, Saint Louis, MO
| | - Amanda Swain
- 2Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Marina Cella
- 2Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Marco Colonna
- 2Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Maxim Artyomov
- 2Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Thaddeus S Stappenbeck
- 4Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Ohio
| | - Michael S Diamond
- 1Department of Medicine, Washington University School of Medicine, Saint Louis, MO
- 2Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
- 5Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO
- 6Andrew M. and Jane M. Bursky The Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO
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22
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Potdar AA, Dube S, Naito T, Botwin G, Haritunians T, Li D, Yang S, Bilsborough J, Denson LA, Daly M, Targan SR, Fleshner P, Braun J, Kugathasan S, Stappenbeck TS, McGovern DP. Reduced expression of COVID-19 host receptor, ACE2 is associated with small bowel inflammation, more severe disease, and response to anti-TNF therapy in Crohn's disease. medRxiv 2020:2020.04.19.20070995. [PMID: 32511625 PMCID: PMC7276052 DOI: 10.1101/2020.04.19.20070995] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Angiotensin-Converting Enzyme 2 ( ACE2 ) has been identified as the host receptor for SARS-coronavirus 2 (SARS-CoV-2) which has infected millions world-wide and likely caused hundreds of thousands of deaths. Utilizing transcriptomic data from four cohorts taken from Crohn's disease (CD) and non-inflammatory bowel disease (IBD) subjects, we observed evidence of increased ACE2 mRNA in ileum with demographic features that have been associated with poor outcomes in COVID-19 including age and raised BMI. ACE2 was downregulated in CD compared to controls in independent cohorts. Within CD, ACE2 expression was reduced in inflamed ileal tissue and also remarkably, from uninvolved tissue in patients with a worse prognosis in both adult and pediatric cohorts. In active CD, small bowel ACE2 expression was restored by anti-TNF therapy particularly in anti-TNF responders. Collectively our data suggest that ACE2 downregulation is associated with inflammation and worse outcomes in CD.
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Affiliation(s)
- Alka A. Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shishir Dube
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Takeo Naito
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gregory Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shaohong Yang
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Janine Bilsborough
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lee A. Denson
- Division of Pediatric Gastroenterology, Hepatology, and nutrition, Department of Pediatrics, University of Cincinnati college of Medicine and the Cincinnati children’s Hospital Medical center, Cincinnati, OH, USA
| | - Mark Daly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Phillip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA; Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | | | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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23
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Wegorzewska MM, Glowacki RWP, Hsieh SA, Donermeyer DL, Hickey CA, Horvath SC, Martens EC, Stappenbeck TS, Allen PM. Diet modulates colonic T cell responses by regulating the expression of a Bacteroides thetaiotaomicron antigen. Sci Immunol 2020; 4:4/32/eaau9079. [PMID: 30737355 DOI: 10.1126/sciimmunol.aau9079] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/10/2019] [Indexed: 12/14/2022]
Abstract
T cell responses to symbionts in the intestine drive tolerance or inflammation depending on the genetic background of the host. These symbionts in the gut sense the available nutrients and adapt their metabolic programs to use these nutrients efficiently. Here, we ask whether diet can alter the expression of a bacterial antigen to modulate adaptive immune responses. We generated a CD4+ T cell hybridoma, BθOM, specific for Bacteroides thetaiotaomicron (B. theta). Adoptively transferred transgenic T cells expressing the BθOM TCR proliferated in the colon, colon-draining lymph node, and spleen in B. theta-colonized healthy mice and differentiated into regulatory T cells (Tregs) and effector T cells (Teffs). Depletion of B. theta-specific Tregs resulted in colitis, showing that a single protein expressed by B. theta can drive differentiation of Tregs that self-regulate Teffs to prevent disease. We found that BθOM T cells recognized a peptide derived from a single B. theta protein, BT4295, whose expression is regulated by nutrients, with glucose being a strong catabolite repressor. Mice fed a high-glucose diet had a greatly reduced activation of BθOM T cells in the colon. These studies establish that the immune response to specific bacterial antigens can be modified by changes in the diet by altering antigen expression in the microbe.
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Affiliation(s)
- Marta M Wegorzewska
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA
| | - Robert W P Glowacki
- Department of Microbiology and Immunology, University of Michigan Medical School, 1500 E Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Samantha A Hsieh
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA
| | - David L Donermeyer
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA
| | - Christina A Hickey
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA.,Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA
| | - Stephen C Horvath
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, 1500 E Medical Center Drive, Ann Arbor, MI 48109, USA.
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA.
| | - Paul M Allen
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Avenue, Saint Louis, MO 63110, USA.
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24
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Kaiko GE, Chen F, Lai CW, Chiang IL, Perrigoue J, Stojmirović A, Li K, Muegge BD, Jain U, VanDussen KL, Goggins BJ, Keely S, Weaver J, Foster PS, Lawrence DA, Liu TC, Stappenbeck TS. PAI-1 augments mucosal damage in colitis. Sci Transl Med 2020; 11:11/482/eaat0852. [PMID: 30842312 DOI: 10.1126/scitranslmed.aat0852] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 10/10/2018] [Accepted: 02/12/2019] [Indexed: 12/13/2022]
Abstract
There is a major unmet clinical need to identify pathways in inflammatory bowel disease (IBD) to classify patient disease activity, stratify patients that will benefit from targeted therapies such as anti-tumor necrosis factor (TNF), and identify new therapeutic targets. In this study, we conducted global transcriptome analysis to identify IBD-related pathways using colon biopsies, which highlighted the coagulation gene pathway as one of the most enriched gene sets in patients with IBD. Using this gene-network analysis across 14 independent cohorts and 1800 intestinal biopsies, we found that, among the coagulation pathway genes, plasminogen activator inhibitor-1 (PAI-1) expression was highly enriched in active disease and in patients with IBD who did not respond to anti-TNF biologic therapy and that PAI-1 is a key link between the epithelium and inflammation. Functionally, PAI-1 and its direct target, the fibrinolytic protease tissue plasminogen activator (tPA), played an important role in regulating intestinal inflammation. Intestinal epithelial cells produced tPA, which was protective against chemical and mechanical-mediated colonic injury in mice. In contrast, PAI-1 exacerbated mucosal damage by blocking tPA-mediated cleavage and activation of anti-inflammatory TGF-β, whereas the inhibition of PAI-1 reduced both mucosal damage and inflammation. This study identifies an immune-coagulation gene axis in IBD where elevated PAI-1 may contribute to more aggressive disease.
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Affiliation(s)
- Gerard E Kaiko
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Feidi Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chin-Wen Lai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - I-Ling Chiang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | | | - Katherine Li
- Janssen Research & Development LLC, Spring House, PA 19002, USA
| | - Brian D Muegge
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Bridie J Goggins
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Jessica Weaver
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Paul S Foster
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Daniel A Lawrence
- Departments of Pathology and Internal Medicine, Division of Cardiovascular Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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25
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Hsieh S, Porter NT, Donermeyer DL, Horvath S, Strout G, Saunders BT, Zhang N, Zinselmeyer B, Martens EC, Stappenbeck TS, Allen PM. Polysaccharide Capsules Equip the Human Symbiont Bacteroides thetaiotaomicron to Modulate Immune Responses to a Dominant Antigen in the Intestine. J Immunol 2020; 204:1035-1046. [PMID: 31900343 PMCID: PMC7002182 DOI: 10.4049/jimmunol.1901206] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/26/2019] [Indexed: 01/12/2023]
Abstract
Bacteria express multiple diverse capsular polysaccharides (CPSs) for protection against environmental and host factors, including the host immune system. Using a mouse TCR transgenic CD4+ T cell, BθOM, that is specific for B. thetaiotaomicron and a complete set of single CPS-expressing B. thetaiotaomicron strains, we ask whether CPSs can modify the immune responses to specific bacterial Ags. Acapsular B. thetaiotaomicron, which lacks all B. thetaiotaomicron CPSs, stimulated BθOM T cells more strongly than wild-type B. thetaiotaomicron Despite similar levels of BθOM Ag expression, many single CPS-expressing B. thetaiotaomicron strains were antistimulatory and weakly activated BθOM T cells, but a few strains were prostimulatory and strongly activated BθOM T cells just as well or better than an acapsular strain. B. thetaiotaomicron strains that expressed an antistimulatory CPS blocked Ag delivery to the immune system, which could be rescued by Fc receptor-dependent Ab opsonization. All single CPS-expressing B. thetaiotaomicron strains stimulated the innate immune system to skew toward M1 macrophages and release inflammatory cytokines in an MyD88-dependent manner, with antistimulatory CPS activating the innate immune system in a weaker manner than prostimulatory CPS. The expression of antistimulatory versus prostimulatory CPSs on outer membrane vesicles also regulated immune responses. Moreover, antistimulatory and prostimulatory single CPS-expressing B. thetaiotaomicron strains regulated the activation of Ag-specific and polyclonal T cells as well as clearance of dominant Ag in vivo. These studies establish that the immune responses to specific bacterial Ags can be modulated by a diverse set of CPSs.
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Affiliation(s)
- Samantha Hsieh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Nathan T Porter
- Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, SE-412 96 Sweden
| | - David L Donermeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Stephen Horvath
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Gregory Strout
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110; and
| | - Brian T Saunders
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Nan Zhang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Bernd Zinselmeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Paul M Allen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
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26
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Jarjour NN, Bradstreet TR, Schwarzkopf EA, Cook ME, Lai CW, Huang SCC, Taneja R, Stappenbeck TS, Van Dyken SJ, Urban JF, Edelson BT. BHLHE40 Promotes T H2 Cell-Mediated Antihelminth Immunity and Reveals Cooperative CSF2RB Family Cytokines. J Immunol 2020; 204:923-932. [PMID: 31900338 DOI: 10.4049/jimmunol.1900978] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/24/2019] [Indexed: 11/19/2022]
Abstract
The transcription factor BHLHE40 is an emerging regulator of the immune system. Recent studies suggest that BHLHE40 regulates type 2 immunity, but this has not been demonstrated in vivo. We found that BHLHE40 is required in T cells for a protective TH2 cell response in mice infected with the helminth Heligmosomoides polygyrus bakeri H. polygyrus elicited changes in gene and cytokine expression by lamina propria CD4+ T cells, many of which were BHLHE40 dependent, including production of the common β (CSF2RB) chain family cytokines GM-CSF and IL-5. In contrast to deficiency in GM-CSF or IL-5 alone, loss of both GM-CSF and IL-5 signaling impaired protection against H. polygyrus Overall, we show that BHLHE40 regulates the TH2 cell transcriptional program during helminth infection to support normal expression of Csf2, Il5, and other genes required for protection and reveal unexpected redundancy of common β chain-dependent cytokines previously thought to possess substantially divergent functions.
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Affiliation(s)
- Nicholas N Jarjour
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Tara R Bradstreet
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Elizabeth A Schwarzkopf
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Melissa E Cook
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Chin-Wen Lai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Stanley Ching-Cheng Huang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; and
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Steven J Van Dyken
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Joseph F Urban
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705
| | - Brian T Edelson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;
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27
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Wang Y, Chiang IL, Ohara TE, Fujii S, Cheng J, Muegge BD, Ver Heul A, Han ND, Lu Q, Xiong S, Chen F, Lai CW, Janova H, Wu R, Whitehurst CE, VanDussen KL, Liu TC, Gordon JI, Sibley LD, Stappenbeck TS. Long-Term Culture Captures Injury-Repair Cycles of Colonic Stem Cells. Cell 2019; 179:1144-1159.e15. [PMID: 31708126 PMCID: PMC6904908 DOI: 10.1016/j.cell.2019.10.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/15/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023]
Abstract
The colonic epithelium can undergo multiple rounds of damage and repair, often in response to excessive inflammation. The responsive stem cell that mediates this process is unclear, in part because of a lack of in vitro models that recapitulate key epithelial changes that occur in vivo during damage and repair. Here, we identify a Hopx+ colitis-associated regenerative stem cell (CARSC) population that functionally contributes to mucosal repair in mouse models of colitis. Hopx+ CARSCs, enriched for fetal-like markers, transiently arose from hypertrophic crypts known to facilitate regeneration. Importantly, we established a long-term, self-organizing two-dimensional (2D) epithelial monolayer system to model the regenerative properties and responses of Hopx+ CARSCs. This system can reenact the "homeostasis-injury-regeneration" cycles of epithelial alterations that occur in vivo. Using this system, we found that hypoxia and endoplasmic reticulum stress, insults commonly present in inflammatory bowel diseases, mediated the cyclic switch of cellular status in this process.
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Affiliation(s)
- Yi Wang
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - I-Ling Chiang
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Takahiro E Ohara
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Satoru Fujii
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jiye Cheng
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Brian D Muegge
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Aaron Ver Heul
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Nathan D Han
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Qiuhe Lu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Feidi Chen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chin-Wen Lai
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Hana Janova
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Renee Wu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Charles E Whitehurst
- Boehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Disease Research, Ridgefield, CT 06877, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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28
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Potdar AA, Li D, Haritunians T, VanDussen KL, Fiorino MF, Liu TC, Stappenbeck TS, Fleshner P, Targan SR, McGovern DPB, Bilsborough J. Ileal Gene Expression Data from Crohn's Disease Small Bowel Resections Indicate Distinct Clinical Subgroups. J Crohns Colitis 2019; 13:1055-1066. [PMID: 30877309 PMCID: PMC6939877 DOI: 10.1093/ecco-jcc/jjz021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 12/17/2022]
Abstract
BACKGROUND AND AIMS Heterogeneity in Crohn's disease [CD] provides a challenge for the development of effective therapies. Our goal was to define a unique molecular signature for severe, refractory CD to enable precision therapy approaches to disease treatment and to facilitate earlier intervention in complicated disease. METHODS We analysed clinical metadata, genetics, and transcriptomics from uninvolved ileal tissue from CD patients who underwent a single small bowel resection. We determined transcriptional risk scores, cellular signatures, and mechanistic pathways that define patient subsets in refractory CD. RESULTS Within refractory CD, we found three CD patient subgroups [CD1, CD2, and CD3]. Compared with CD1, CD3 was enriched for subjects with increased disease recurrence after first surgery [OR = 6.78, p = 0.04], enhanced occurrence of second surgery [OR = 5.07, p = 0.016], and presence of perianal CD [OR = 3.61, p = 0.036]. The proportion of patients with recurrence-free survival was smaller in CD3 than in CD1 (p = 0.02, median survival time [months] in CD1 = 10 and CD3 = 6). Overlaying differential gene expression between CD1 and CD3 on CD subgroup-associated genetic polymorphisms identified 174 genes representing both genetic and biological differences between the CD subgroups. Pathway analyses using this unique gene signature indicated eukaryotic initiation factor 2 [eIF2] and cyclic adenosine monophosphate [cAMP] signalling to be dominant pathways associated with CD3. Furthermore, the severe, refractory subset, CD3, was associated with a higher transcriptional risk score and enriched with eosinophil and natural killer T [NKT] cell gene signatures. CONCLUSION We characterized a subset of severe, refractory CD patients who may need more aggressive treatment after first resection and who are likely to benefit from targeted therapy based on their genotype and tissue gene expression signature.
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Affiliation(s)
- Alka A Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Marie F Fiorino
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Phillip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Stephan R Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Janine Bilsborough
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA,Corresponding author: Janine Bilsborough, IBD Drug Development Unit, F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, 8693 Wilshire Blvd, Beverly Hills, CA 90211, USA. Tel: 310-423-7797; Fax: 310-423-0224;
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29
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Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 2019; 569:655-662. [PMID: 31142855 PMCID: PMC6650278 DOI: 10.1038/s41586-019-1237-9] [Citation(s) in RCA: 1328] [Impact Index Per Article: 265.6] [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: 02/06/2018] [Accepted: 04/16/2019] [Indexed: 12/11/2022]
Abstract
Inflammatory bowel diseases, which include Crohn’s disease and ulcerative colitis, affect several million individuals worldwide. Crohn’s disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study’s infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi’omics Database (http://ibdmdb.org), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases. The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.
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Affiliation(s)
- Jason Lloyd-Price
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Cesar Arze
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Melanie Schirmer
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Tiffany W Poon
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nadim J Ajami
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kevin S Bonham
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
| | - David Casero
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Holly Courtney
- Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Thomas G Graeber
- Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA
| | - A Brantley Hall
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathleen Lake
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carol J Landers
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Himel Mallick
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Damian R Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mahadev Prasad
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Gholamali Rahnavard
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jenny Sauk
- Vatche and Tamar Manoukian Division of Digestive Diseases, University of California Los Angeles, Los Angeles, CA, USA
| | - Dmitry Shungin
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Odontology, Umeå University, Umeå, Sweden
| | - Yoshiki Vázquez-Baeza
- Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Richard A White
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
| | | | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | | | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joseph F Petrosino
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | | | - Harland S Winter
- Department of Pediatrics, MassGeneral Hospital for Children, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Clary B Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Gastroenterology, Massachusetts General Hospital, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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30
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Malvin NP, Kern JT, Liu TC, Brody SL, Stappenbeck TS. Autophagy proteins are required for club cell structure and function in airways. Am J Physiol Lung Cell Mol Physiol 2019; 317:L259-L270. [PMID: 31116580 DOI: 10.1152/ajplung.00394.2018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 02/06/2023] Open
Abstract
Epithelial cells that line lung airways produce and secrete proteins with important roles in barrier function and host defense. Secretion of airway goblet cells is controlled by autophagy proteins during inflammatory conditions, resulting in accumulation of mucin proteins. We hypothesized that autophagy proteins would also be important in the function of club cells, dominant secretory airway epithelial cells that are dysregulated in chronic lung disease. We found that in the absence of an inflammatory stimulus, mice with club cells deficient for the autophagy protein Atg5 had a markedly diminished expression of secreted host defense proteins secretoglobulin family 1A, member 1 (Scgb1a1) and surfactant proteins A1 and D (Sftpa1 and Sftpd), as well as abnormal club cell morphology. Adult mice with targeted loss of Atg5 also showed diminished levels of host defense proteins in regenerating cells following ablation with naphthalene. A mouse strain with global deficiency of Atg16-like 1 (Atg16l1), an Atg5 binding partner, had a similar loss of host defense proteins and abnormal club cell morphology. Cigarette smoke exposure reduced levels of Scgb1a1 in wild-type mice as expected. Smoke exposure was not required to trigger club cell abnormalities in mice bearing the human ATG16 variant Atg16l1T300A/T300A, which had low Scgb1a1 levels independent of this environmental stress. Evaluation of lung tissues from former smokers with severe chronic obstructive pulmonary disease showed evidence of reduced autophagy and SCGB1A1 expression in club cells. Thus, autophagy proteins are required for the function of club cells, independent of the cellular stress of cigarette smoke, with roles that appear to be distinct from those of other secretory cell types.
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Affiliation(s)
- Nicole P Malvin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Justin T Kern
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Steven L Brody
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
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31
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Pizarro TT, Stappenbeck TS, Rieder F, Rosen MJ, Colombel JF, Donowitz M, Towne J, Mazmanian SK, Faith JJ, Hodin RA, Garrett WS, Fichera A, Poritz LS, Cortes CJ, Shtraizent N, Honig G, Snapper SB, Hurtado-Lorenzo A, Salzman NH, Chang EB. Challenges in IBD Research: Preclinical Human IBD Mechanisms. Inflamm Bowel Dis 2019; 25:S5-S12. [PMID: 31095706 DOI: 10.1093/ibd/izz075] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [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: 03/29/2019] [Indexed: 12/21/2022]
Abstract
Preclinical human IBD mechanisms is part of five focus areas of the Challenges in IBD research document, which also include environmental triggers, novel technologies, precision medicine and pragmatic clinical research. The Challenges in IBD research document provides a comprehensive overview of current gaps in inflammatory bowel diseases (IBD) research and delivers actionable approaches to address them. It is the result of a multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient centric research prioritization. In particular, the preclinical human IBD mechanisms manuscript is focused on highlighting the main research gaps in the pathophysiological understanding of human IBD. These research gap areas include: 1) triggers of immune responses; 2) intestinal epithelial homeostasis and wound repair; 3) age-specific pathophysiology; 4) disease complications; 5) heterogeneous response to treatments; and 6) determination of disease location. As an approach to address these research gaps, the prioritization of reverse translation studies is proposed in which clinical observations are the foundation for experimental IBD research in the lab, and for the identification of new therapeutic targets and biomarkers. The use of human samples in validating basic research findings and development of precision medicine solutions is also proposed. This prioritization aims to put emphasis on relevant biochemical pathways and humanized in vitro and in vivo models that extrapolate meaningfully to human IBD, to eventually yield first-in-class and effective therapies.
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Affiliation(s)
- Theresa T Pizarro
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | | | | | - Michael J Rosen
- Cincinnati Children's Hospital and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Mark Donowitz
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | - Richard A Hodin
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wendy S Garrett
- School of Public Health, Harvard University, Boston, MA, USA
| | | | - Lisa S Poritz
- Pennsylvania State University College of Medicine, Hershey, PA, USA
| | | | | | | | - Scott B Snapper
- Harvard Medical School and Boston Children's Hospital, Boston, MA, USA
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32
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Abstract
In this issue of Cell Stem Cell, Mihaylova et al. (2018) show that short-term fasting increases serum levels of long-chain fatty acids, presumably derived from the host. This effect in turn can rescue age-related phenotypes that occur in intestinal epithelial stem cells.
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Affiliation(s)
- Derek A G Barisas
- Department of Pathology and Immunology, Washington University Medical School, Saint Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University Medical School, Saint Louis, MO 63110, USA.
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33
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Abstract
Regulation of intestinal epithelial turnover is a key component of villus maintenance in the intestine. The balance of cell turnover can be perturbed by various extrinsic factors including the cytokine TNF, a cell signaling protein that mediates both proliferative and cytotoxic outcomes. Under conditions of infection and damage, defects in autophagy are associated with TNF-mediated cell death and tissue damage in the intestinal epithelium. However, a direct role of autophagy within the context of enterocyte cell death during homeostasis is lacking. Here, we generated mice lacking ATG14 (autophagy related 14) within the intestinal epithelium [Atg14f/f Vil1-Cre (VC)+]. These mice developed spontaneous villus loss and intestinal epithelial cell death within the small intestine. Based on marker studies, the increased cell death in these mice was due to apoptosis. Atg14f/f VC+ intestinal epithelial cells demonstrated sensitivity to TNF-triggered apoptosis. Correspondingly, both TNF blocking antibody and genetic deletion of Tnfrsf1a/Tnfr1 rescued villus loss and cell death phenotype in Atg14f/f VC+ mice. Lastly, we identified a similar pattern of spontaneous villus atrophy and cell death when Rb1cc1/Fip200 was conditionally deleted from the intestinal epithelium (Rb1cc1f/f VC+). Overall, these findings are consistent with the hypothesis that factors that control entry into the autophagy pathway are also required during homeostasis to prevent TNF triggered death in the intestine. Abbreviations: ANOVA: analysis of variance; Atg14: autophagy related 14; Atg16l1: autophagy related 16-like 1 (S. cerevisiae); Atg5: autophagy related 5; cCASP3: cleaved CASP3/caspase-3; cCASP8: cleaved CASP8/caspase-8; CHX: cycloheximide; EdU: 5-ethynyl-2´-deoxyuridine thymidine; f/f: flox/flox; H&E: hematoxylin and eosin; MTT: 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide; Nec-1: necrostatin-1; Rb1cc1/Fip200: RB1-inducible coiled-coil 1; Ripk1: receptor (TNFRSF)-interacting serine-threonine kinase 1; Ripk3: receptor (TNFRSF)-interacting serine-threonine kinase 3; Tnfrsf1a/Tnfr1: tumor necrosis factor receptor superfamily, member 1a; Tnf/ Tnfsf1a: tumor necrosis factor; VC: Vil1/villin 1-Cre.
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Affiliation(s)
- Haerin Jung
- Department of Pathology and Immunology, Washington University in St. Louis , St. Louis , MO , USA
| | - J Steven Leal-Ekman
- Department of Pathology and Immunology, Washington University in St. Louis , St. Louis , MO , USA
| | - Qiuhe Lu
- Department of Pathology and Immunology, Washington University in St. Louis , St. Louis , MO , USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University in St. Louis , St. Louis , MO , USA
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Sarkar A, Tindle C, Pranadinata RF, Reed S, Eckmann L, Stappenbeck TS, Ernst PB, Das S. ELMO1 Regulates Autophagy Induction and Bacterial Clearance During Enteric Infection. J Infect Dis 2019; 216:1655-1666. [PMID: 29029244 DOI: 10.1093/infdis/jix528] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 12/15/2022] Open
Abstract
Macrophages are specialized phagocytic cells involved in clearing invading pathogens. Previously we reported that engulfment and cell motility protein 1 (ELMO1) in macrophages mediates bacterial internalization and intestinal inflammation. Here we studied the role of ELMO1 in the fate of internalized targets. ELMO1 is present in the intracellular vesicles and enhances accumulation of the protein LC3B following engulfment of Salmonella or treatment with autophagy-inducing rapamycin. The protein ATG5 and the kinase ULK1 are involved in classical autophagy, while LC3-associated phagocytosis is ULK1 independent. ATG5 but not ULK1 cooperated with ELMO1 in LC3 accumulation after infection, suggesting the ELMO1 preferentially regulated LC3-associated phagocytosis. Because LC3-associated phagocytosis delivers cargo for degradation, the contribution of ELMO1 to the lysosome degradation pathways was evaluated by studying pH and cathepsin B activity. ELMO1-depleted macrophages showed a time-dependent increase in pH and a decrease in cathepsin B activity associated with bacterial survival. Together, ELMO1 regulates LC3B accumulation and antimicrobial responses involved in the clearance of enteric pathogens. This paper investigated how innate immune pathways involving ELMO1 work in a coordinated fashion to eliminate bacterial threats. ELMO1 is present in the phagosome and enhances bacterial clearance by differential regulation of lysosomal acidification and enzymatic activity.
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Affiliation(s)
- Arup Sarkar
- Department of Pathology, University of California-San Diego
| | | | | | - Sharon Reed
- Department of Pathology, University of California-San Diego
| | - Lars Eckmann
- Department of Medicine, University of California-San Diego
| | | | - Peter B Ernst
- Department of Pathology, University of California-San Diego
| | - Soumita Das
- Department of Pathology, University of California-San Diego
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Marsh JN, Matlock MK, Kudose S, Liu TC, Stappenbeck TS, Gaut JP, Swamidass SJ. Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen Sections. IEEE Trans Med Imaging 2018; 37:2718-2728. [PMID: 29994669 PMCID: PMC6296264 DOI: 10.1109/tmi.2018.2851150] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Transplantable kidneys are in very limited supply. Accurate viability assessment prior to transplantation could minimize organ discard. Rapid and accurate evaluation of intra-operative donor kidney biopsies is essential for determining which kidneys are eligible for transplantation. The criterion for accepting or rejecting donor kidneys relies heavily on pathologist determination of the percent of glomeruli (determined from a frozen section) that are normal and sclerotic. This percentage is a critical measurement that correlates with transplant outcome. Inter- and intra-observer variability in donor biopsy evaluation is, however, significant. An automated method for determination of percent global glomerulosclerosis could prove useful in decreasing evaluation variability, increasing throughput, and easing the burden on pathologists. Here, we describe the development of a deep learning model that identifies and classifies non-sclerosed and sclerosed glomeruli in whole-slide images of donor kidney frozen section biopsies. This model extends a convolutional neural network (CNN) pre-trained on a large database of digital images. The extended model, when trained on just 48 whole slide images, exhibits slide-level evaluation performance on par with expert renal pathologists. Encouragingly, the model's performance is robust to slide preparation artifacts associated with frozen section preparation. The model substantially outperforms a model trained on image patches of isolated glomeruli, in terms of both accuracy and speed. The methodology overcomes the technical challenge of applying a pretrained CNN bottleneck model to whole-slide image classification. The traditional patch-based approach, while exhibiting deceptively good performance classifying isolated patches, does not translate successfully to whole-slide image segmentation in this setting. As the first model reported that identifies and classifies normal and sclerotic glomeruli in frozen kidney sections, and thus the first model reported in the literature relevant to kidney transplantation, it may become an essential part of donor kidney biopsy evaluation in the clinical setting.
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Liu TC, Kern JT, VanDussen KL, Xiong S, Kaiko GE, Wilen CB, Rajala MW, Caruso R, Holtzman MJ, Gao F, McGovern DP, Nunez G, Head RD, Stappenbeck TS. Interaction between smoking and ATG16L1T300A triggers Paneth cell defects in Crohn's disease. J Clin Invest 2018; 128:5110-5122. [PMID: 30137026 DOI: 10.1172/jci120453] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [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: 02/21/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022] Open
Abstract
It is suggested that subtyping of complex inflammatory diseases can be based on genetic susceptibility and relevant environmental exposure (G+E). We propose that using matched cellular phenotypes in human subjects and corresponding preclinical models with the same G+E combinations is useful to this end. As an example, defective Paneth cells can subtype Crohn's disease (CD) subjects; Paneth cell defects have been linked to multiple CD susceptibility genes and are associated with poor outcome. We hypothesized that CD susceptibility genes interact with cigarette smoking, a major CD environmental risk factor, to trigger Paneth cell defects. We found that both CD subjects and mice with ATG16L1T300A (T300A; a prevalent CD susceptibility allele) developed Paneth cell defects triggered by tobacco smoke. Transcriptional analysis of full-thickness ileum and Paneth cell-enriched crypt base cells showed the T300A-smoking combination altered distinct pathways, including proapoptosis, metabolic dysregulation, and selective downregulation of the PPARγ pathway. Pharmacologic intervention by either apoptosis inhibitor or PPARγ agonist rosiglitazone prevented smoking-induced crypt apoptosis and Paneth cell defects in T300A mice and mice with conditional Paneth cell-specific knockout of Atg16l1. This study demonstrates how explicit G+E can drive disease-relevant phenotype and provides rational strategies for identifying actionable targets.
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Affiliation(s)
- Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Justin T Kern
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Gerard E Kaiko
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Craig B Wilen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Michael W Rajala
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Roberta Caruso
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | | | - Feng Gao
- Department of Surgery, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Dermot Pb McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gabriel Nunez
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Richard D Head
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
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White JP, Xiong S, Malvin NP, Khoury-Hanold W, Heuckeroth RO, Stappenbeck TS, Diamond MS. Intestinal Dysmotility Syndromes following Systemic Infection by Flaviviruses. Cell 2018; 175:1198-1212.e12. [PMID: 30293866 DOI: 10.1016/j.cell.2018.08.069] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 05/02/2018] [Revised: 08/07/2018] [Accepted: 08/29/2018] [Indexed: 02/07/2023]
Abstract
Although chronic gastrointestinal dysmotility syndromes are a common worldwide health problem, underlying causes for these disorders are poorly understood. We show that flavivirus infection of enteric neurons leads to acute neuronal injury and cell death, inflammation, bowel dilation, and slowing of intestinal transit in mice. Flavivirus-primed CD8+ T cells promote these phenotypes, as their absence diminished enteric neuron injury and intestinal transit delays, and their adoptive transfer reestablished dysmotility after flavivirus infection. Remarkably, mice surviving acute flavivirus infection developed chronic gastrointestinal dysmotility that was exacerbated by immunization with an unrelated alphavirus vaccine or exposure to a non-infectious inflammatory stimulus. This model of chronic post-infectious gastrointestinal dysmotility in mice suggests that viral infections with tropism for enteric neurons and the ensuing immune response might contribute to the development of bowel motility disorders in humans. These results suggest an opportunity for unique approaches to diagnosis and therapy of gastrointestinal dysmotility syndromes.
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Affiliation(s)
- James P White
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole P Malvin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Robert O Heuckeroth
- Department of Pediatrics, the Children's Hospital of Philadelphia Research Institute, the Perelman School of Medicine at the University of Pennsylvania, Abramson Research Center, Philadelphia, PA 19104, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Zhao D, Kim YH, Jeong S, Greenson JK, Chaudhry MS, Hoepting M, Anderson ER, van den Brink MR, Peled JU, Gomes AL, Slingerland AE, Donovan MJ, Harris AC, Levine JE, Ozbek U, Hooper LV, Stappenbeck TS, Ver Heul A, Liu TC, Reddy P, Ferrara JL. Survival signal REG3α prevents crypt apoptosis to control acute gastrointestinal graft-versus-host disease. J Clin Invest 2018; 128:4970-4979. [PMID: 30106382 DOI: 10.1172/jci99261] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [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: 12/14/2017] [Accepted: 08/07/2018] [Indexed: 12/30/2022] Open
Abstract
Graft-versus-host disease (GVHD) in the gastrointestinal (GI) tract remains the major cause of morbidity and nonrelapse mortality after BM transplantation (BMT). The Paneth cell protein regenerating islet-derived 3α (REG3α) is a biomarker specific for GI GVHD. REG3α serum levels rose in the systematic circulation as GVHD progressively destroyed Paneth cells and reduced GI epithelial barrier function. Paradoxically, GVHD suppressed intestinal REG3γ (the mouse homolog of human REG3α), and the absence of REG3γ in BMT recipients intensified GVHD but did not change the composition of the microbiome. IL-22 administration restored REG3γ production and prevented apoptosis of both intestinal stem cells (ISCs) and Paneth cells, but this protection was completely abrogated in Reg3g-/- mice. In vitro, addition of REG3α reduced the apoptosis of colonic cell lines. Strategies that increase intestinal REG3α/γ to promote crypt regeneration may offer a novel, nonimmunosuppressive approach for GVHD and perhaps for other diseases involving the ISC niche, such as inflammatory bowel disease.
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Affiliation(s)
- Dongchang Zhao
- The Tisch Cancer Institute and Division of Hematology/Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
| | | | - Seihwan Jeong
- The Tisch Cancer Institute and Division of Hematology/Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
| | - Joel K Greenson
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Mohammed S Chaudhry
- The Tisch Cancer Institute and Division of Hematology/Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
| | - Matthias Hoepting
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Erik R Anderson
- The Tisch Cancer Institute and Division of Hematology/Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
| | - Marcel Rm van den Brink
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, New York, USA
| | - Jonathan U Peled
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, New York, USA
| | - Antonio Lc Gomes
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, New York, USA
| | - Ann E Slingerland
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, New York, USA
| | - Michael J Donovan
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
| | - Andrew C Harris
- Blood and Marrow Transplantation Program, University of Utah, Salt Lake City, Utah, USA
| | - John E Levine
- The Tisch Cancer Institute and Division of Hematology/Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
| | - Umut Ozbek
- The Tisch Cancer Institute and Division of Hematology/Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
| | - Lora V Hooper
- Howard Hughes Medical Institute, Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Aaron Ver Heul
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pavan Reddy
- Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - James Lm Ferrara
- The Tisch Cancer Institute and Division of Hematology/Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
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VanDussen KL, Stojmirović A, Li K, Liu TC, Kimes PK, Muegge BD, Simpson KF, Ciorba MA, Perrigoue JG, Friedman JR, Towne JE, Head RD, Stappenbeck TS. Abnormal Small Intestinal Epithelial Microvilli in Patients With Crohn's Disease. Gastroenterology 2018; 155:815-828. [PMID: 29782846 PMCID: PMC6378688 DOI: 10.1053/j.gastro.2018.05.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [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] [Received: 07/17/2017] [Revised: 04/16/2018] [Accepted: 05/07/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Crohn disease (CD) presents as chronic and often progressive intestinal inflammation, but the contributing pathogenic mechanisms are unclear. We aimed to identify alterations in intestinal cells that could contribute to the chronic and progressive course of CD. METHODS We took an unbiased system-wide approach by performing sequence analysis of RNA extracted from formalin-fixed paraffin-embedded ileal tissue sections from patients with CD (n = 36) and without CD (controls; n = 32). We selected relatively uninflamed samples, based on histology, before gene expression profiling; validation studies were performed using adjacent serial tissue sections. A separate set of samples (3 control and 4 CD samples) was analyzed by transmission electron microscopy. We developed methods to visualize an overlapping modular network of genes dysregulated in the CD samples. We validated our findings using biopsy samples (110 CD samples for gene expression analysis and 54 for histologic analysis) from the UNITI-2 phase 3 trial of ustekinumab for patients with CD and healthy individuals (26 samples used in gene expression analysis). RESULTS We identified gene clusters that were altered in nearly all CD samples. One cluster encoded genes associated with the enterocyte brush border, leading us to investigate microvilli. In ileal tissues from patients with CD, the microvilli were of decreased length and had ultrastructural defects compared with tissues from controls. Microvilli length correlated with expression of genes that regulate microvilli structure and function. Network analysis linked the microvilli cluster to several other down-regulated clusters associated with altered intracellular trafficking and cellular metabolism. Enrichment of a core microvilli gene set also was lower in the UNITI-2 trial CD samples compared with controls; expression of microvilli genes was correlated with microvilli length and endoscopy score and was associated with response to treatment. CONCLUSIONS In a transcriptome analysis of formalin-fixed and paraffin-embedded ileal tissues from patients with CD and controls, we associated transcriptional alterations with histologic alterations, such as differences in microvilli length. Decreased microvilli length and decreased expression of the microvilli gene set might contribute to epithelial malfunction and the chronic and progressive disease course in patients with CD.
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Affiliation(s)
- Kelli L. VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Aleksandar Stojmirović
- Department of Janssen Research and Development, LLC. 1400 McKean Rd., Spring House, PA, 19477, USA
| | - Katherine Li
- Department of Janssen Research and Development, LLC. 1400 McKean Rd., Spring House, PA, 19477, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Patrick K. Kimes
- Department of Janssen Research and Development, LLC. 1400 McKean Rd., Spring House, PA, 19477, USA
| | - Brian D. Muegge
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine F. Simpson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew A. Ciorba
- Department of Internal Medicine, Division of Gastroenterology, Inflammatory Bowel Disease Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jacqueline G. Perrigoue
- Department of Janssen Research and Development, LLC. 1400 McKean Rd., Spring House, PA, 19477, USA
| | - Joshua R. Friedman
- Department of Janssen Research and Development, LLC. 1400 McKean Rd., Spring House, PA, 19477, USA
| | - Jennifer E. Towne
- Department of Janssen Research and Development, LLC. 1400 McKean Rd., Spring House, PA, 19477, USA
| | - Richard D. Head
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S. Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Correspondence: Thaddeus S. Stappenbeck,
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40
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Jain U, Lai CW, Xiong S, Goodwin VM, Lu Q, Muegge BD, Christophi GP, VanDussen KL, Cummings BP, Young E, Hambor J, Stappenbeck TS. Temporal Regulation of the Bacterial Metabolite Deoxycholate during Colonic Repair Is Critical for Crypt Regeneration. Cell Host Microbe 2018; 24:353-363.e5. [PMID: 30122655 DOI: 10.1016/j.chom.2018.07.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/18/2018] [Accepted: 07/25/2018] [Indexed: 02/07/2023]
Abstract
Colonic wound repair is an orchestrated process, beginning with barrier re-establishment and followed by wound channel formation and crypt regeneration. Elevated levels of prostaglandin E2 (PGE2) promote barrier re-establishment; however, we found that persistently elevated PGE2 hinders subsequent repair phases. The bacterial metabolite deoxycholate (DCA) promotes transition through repair phases via PGE2 regulation. During barrier re-establishment, DCA levels are locally diminished in the wound, allowing enhanced PGE2 production and barrier re-establishment. However, during transition to the wound channel formation phase, DCA levels increase to inhibit PGE2 production and promote crypt regeneration. Altering DCA levels via antibiotic treatment enhances PGE2 levels but impairs wound repair, which is rescued with DCA treatment. DCA acts via its receptor, farnesoid X receptor, to inhibit the enzyme cPLA2 required for PGE2 synthesis. Thus, colonic wound repair requires temporally regulated signals from microbial metabolites to coordinate host-associated signaling cascades. VIDEO ABSTRACT.
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Affiliation(s)
- Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chin-Wen Lai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Victoria M Goodwin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Qiuhe Lu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian D Muegge
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - George P Christophi
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110 USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bethany P Cummings
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Erick Young
- Research Beyond Borders, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT 06877, USA
| | - John Hambor
- Research Beyond Borders, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT 06877, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Verma MS, Fink MJ, Salmon GL, Fornelos N, Ohara TE, Ryu SH, Vlamakis H, Xavier RJ, Stappenbeck TS, Whitesides GM. A Common Mechanism Links Activities of Butyrate in the Colon. ACS Chem Biol 2018; 13:1291-1298. [PMID: 29584955 DOI: 10.1021/acschembio.8b00073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Two biological activities of butyrate in the colon (suppression of proliferation of colonic epithelial stem cells and inflammation) correlate with inhibition of the activity of histone deacetylases. Cellular and biochemical studies of molecules similar in structure to butyrate, but different in molecular details (functional groups, chain-length, deuteration, oxidation level, fluorination, or degree of unsaturation), demonstrated that these activities were sensitive to molecular structure, and were compatible with the hypothesis that butyrate acts by binding to the Zn2+ in the catalytic site of histone deacetylases. Structure-activity relationships drawn from a set of 36 compounds offer a starting point for the design of new compounds targeting the inhibition of histone deacetylases. The observation that butyrate was more potent than other short-chain fatty acids is compatible with the hypothesis that crypts evolved (at least in part), to separate stem cells at the base of crypts from butyrate produced by commensal bacteria.
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Affiliation(s)
- Mohit S. Verma
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Michael J. Fink
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Gabriel L. Salmon
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Nadine Fornelos
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Takahiro E. Ohara
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Stacy H. Ryu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ramnik J. Xavier
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- The Center for Microbiome Informatics & Therapeutics, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thaddeus S. Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, United States
- Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, United States
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42
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Zhao D, Kim YH, Greenson JK, Chaudhry MS, Hoepting M, Jeong S, Anderson ER, Harris AC, Levine JE, Ozbek U, Hooper LV, Stappenbeck TS, Heul AV, Liu TC, Reddy P, Ferrara J. Regenerating Islet-Derived 3-Alpha (REG3A) Protects the Intestinal Stem Cell Niche to Control Acute Gastrointestinal Graft-Versus-Host Disease. Biol Blood Marrow Transplant 2018. [DOI: 10.1016/j.bbmt.2017.12.614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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43
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Ryu SH, Kaiko GE, Stappenbeck TS. Cellular differentiation: Potential insight into butyrate paradox? Mol Cell Oncol 2018; 5:e1212685. [PMID: 30250879 DOI: 10.1080/23723556.2016.1212685] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 07/09/2016] [Revised: 07/09/2016] [Accepted: 07/10/2016] [Indexed: 02/07/2023]
Abstract
We recently demonstrated that cellular responses to butyrate depend on the differentiation status of the colonic epithelium. Here, we apply the implications of these findings to cancer biology and discuss discrepancies in the effects of butyrate on cancer progression.
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Affiliation(s)
- Stacy H Ryu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gerard E Kaiko
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.,Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
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44
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Steed AL, Christophi GP, Kaiko GE, Sun L, Goodwin VM, Jain U, Esaulova E, Artyomov MN, Morales DJ, Holtzman MJ, Boon ACM, Lenschow DJ, Stappenbeck TS. The microbial metabolite desaminotyrosine protects from influenza through type I interferon. Science 2018; 357:498-502. [PMID: 28774928 DOI: 10.1126/science.aam5336] [Citation(s) in RCA: 328] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/28/2017] [Accepted: 06/15/2017] [Indexed: 12/27/2022]
Abstract
The microbiota is known to modulate the host response to influenza infection through as-yet-unclear mechanisms. We hypothesized that components of the microbiota exert effects through type I interferon (IFN), a hypothesis supported by analysis of influenza in a gain-of-function genetic mouse model. Here we show that a microbially associated metabolite, desaminotyrosine (DAT), protects from influenza through augmentation of type I IFN signaling and diminution of lung immunopathology. A specific human-associated gut microbe, Clostridium orbiscindens, produced DAT and rescued antibiotic-treated influenza-infected mice. DAT protected the host by priming the amplification loop of type I IFN signaling. These findings show that specific components of the enteric microbiota have distal effects on responses to lethal infections through modulation of type I IFN.
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Affiliation(s)
- Ashley L Steed
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - George P Christophi
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gerard E Kaiko
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lulu Sun
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Victoria M Goodwin
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ekaterina Esaulova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Computer Technologies Department, Saint Petersburg National Research University of Information Technologies, Mechanics and Optics, Saint Petersburg 197101, Russia
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David J Morales
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Holtzman
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Adrianus C M Boon
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Deborah J Lenschow
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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45
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Wagner VE, Dey N, Guruge J, Hsiao A, Ahern PP, Semenkovich NP, Blanton LV, Cheng J, Griffin N, Stappenbeck TS, Ilkayeva O, Newgard CB, Petri W, Haque R, Ahmed T, Gordon JI. Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition. Sci Transl Med 2017; 8:366ra164. [PMID: 27881825 DOI: 10.1126/scitranslmed.aah4669] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/04/2016] [Indexed: 12/21/2022]
Abstract
To model how interactions among enteropathogens and gut microbial community members contribute to undernutrition, we colonized gnotobiotic mice fed representative Bangladeshi diets with sequenced bacterial strains cultured from the fecal microbiota of two 24-month-old Bangladeshi children: one healthy and the other underweight. The undernourished donor's bacterial collection contained an enterotoxigenic Bacteroides fragilis strain (ETBF), whereas the healthy donor's bacterial collection contained two nontoxigenic strains of B. fragilis (NTBF). Analyses of mice harboring either the unmanipulated culture collections or systematically manipulated versions revealed that ETBF was causally related to weight loss in the context of its native community but not when introduced into the healthy donor's community. This phenotype was transmissible from the dams to their offspring and was associated with derangements in host energy metabolism manifested by impaired tricarboxylic acid cycle activity and decreased acyl-coenzyme A utilization. NTBF reduced ETBF's expression of its enterotoxin and mitigated the effects of ETBF on the transcriptomes of other healthy donor community members. These results illustrate how intraspecific (ETBF-NTBF) and interspecific interactions influence the effects of harboring B. fragilis.
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Affiliation(s)
- Vitas E Wagner
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Neelendu Dey
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janaki Guruge
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ansel Hsiao
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Philip P Ahern
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas P Semenkovich
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura V Blanton
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiye Cheng
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas Griffin
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710, USA.,Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - William Petri
- Departments of Medicine, Microbiology, and Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA. .,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
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46
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47
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Kim AH, Chung JJ, Akilesh S, Koziell A, Jain S, Hodgin JB, Miller MJ, Stappenbeck TS, Miner JH, Shaw AS. B cell-derived IL-4 acts on podocytes to induce proteinuria and foot process effacement. JCI Insight 2017; 2:81836. [PMID: 29093269 DOI: 10.1172/jci.insight.81836] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 10/05/2017] [Indexed: 12/13/2022] Open
Abstract
The efficacy of B cell depletion therapies in diseases such as nephrotic syndrome and rheumatoid arthritis suggests a broader role in B cells in human disease than previously recognized. In some of these diseases, such as the minimal change disease subtype of nephrotic syndrome, pathogenic antibodies and immune complexes are not involved. We hypothesized that B cells, activated in the kidney, might produce cytokines capable of directly inducing cell injury and proteinuria. To directly test our hypothesis, we targeted a model antigen to the kidney glomerulus and showed that transfer of antigen-specific B cells could induce glomerular injury and proteinuria. This effect was mediated by IL-4, as transfer of IL-4-deficient B cells did not induce proteinuria. Overexpression of IL-4 in mice was sufficient to induce kidney injury and proteinuria and could be attenuated by JAK kinase inhibitors. Since IL-4 is a specific activator of STAT6, we analyzed kidney biopsies and demonstrated STAT6 activation in up to 1 of 3 of minimal change disease patients, suggesting IL-4 or IL-13 exposure in these patients. These data suggest that the role of B cells in nephrotic syndrome could be mediated by cytokines.
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Affiliation(s)
- Alfred Hj Kim
- Division of Rheumatology, Department of Internal Medicine, and
| | - Jun-Jae Chung
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Shreeram Akilesh
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ania Koziell
- Department of Experimental Immunobiology, Division of Transplantation Immunology and Mucosal Biology, King's College London and Department of Paediatric Nephrology, Evelina Children's Hospital, London, United Kingdom
| | - Sanjay Jain
- Renal Division, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Mark J Miller
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Thaddeus S Stappenbeck
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey H Miner
- Renal Division, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrey S Shaw
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.,Howard Hughes Medical Institute, Washington University School of Medicine, St. Louis, Missouri, USA
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48
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Chai JN, Peng Y, Rengarajan S, Solomon BD, Ai TL, Shen Z, Perry JSA, Knoop KA, Tanoue T, Narushima S, Honda K, Elson CO, Newberry RD, Stappenbeck TS, Kau AL, Peterson DA, Fox JG, Hsieh CS. Helicobacter species are potent drivers of colonic T cell responses in homeostasis and inflammation. Sci Immunol 2017; 2:2/13/eaal5068. [PMID: 28733471 DOI: 10.1126/sciimmunol.aal5068] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 06/02/2017] [Indexed: 12/16/2022]
Abstract
Specific gut commensal bacteria improve host health by eliciting mutualistic regulatory T (Treg) cell responses. However, the bacteria that induce effector T (Teff) cells during inflammation are unclear. We addressed this by analyzing bacterial-reactive T cell receptor (TCR) transgenic cells and TCR repertoires in a murine colitis model. Unexpectedly, we found that mucosal-associated Helicobacter species triggered both Treg cell responses during homeostasis and Teff cell responses during colitis, as suggested by an increased overlap between the Teff/Treg TCR repertoires with colitis. Four of six Treg TCRs tested recognized mucosal-associated Helicobacter species in vitro and in vivo. By contrast, the marked expansion of luminal Bacteroides species seen during colitis did not trigger a commensurate Teff cell response. Unlike other Treg cell-inducing bacteria, Helicobacter species are known pathobionts and cause disease in immunodeficient mice. Thus, our study suggests a model in which mucosal bacteria elicit context-dependent Treg or Teff cell responses to facilitate intestinal tolerance or inflammation.
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Affiliation(s)
- Jiani N Chai
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yangqing Peng
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sunaina Rengarajan
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Benjamin D Solomon
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Teresa L Ai
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zeli Shen
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Justin S A Perry
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kathryn A Knoop
- Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Takeshi Tanoue
- RIKEN Center for Integrative Medical Sciences, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Seiko Narushima
- RIKEN Center for Integrative Medical Sciences, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kenya Honda
- RIKEN Center for Integrative Medical Sciences, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Charles O Elson
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Rodney D Newberry
- Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew L Kau
- Center for Women's Infectious Disease Research and Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - James G Fox
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chyi-Song Hsieh
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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49
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Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Núñez G, Martens EC. A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility. Cell 2017; 167:1339-1353.e21. [PMID: 27863247 DOI: 10.1016/j.cell.2016.10.043] [Citation(s) in RCA: 1557] [Impact Index Per Article: 222.4] [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: 05/13/2016] [Revised: 08/13/2016] [Accepted: 10/21/2016] [Indexed: 02/07/2023]
Abstract
Despite the accepted health benefits of consuming dietary fiber, little is known about the mechanisms by which fiber deprivation impacts the gut microbiota and alters disease risk. Using a gnotobiotic mouse model, in which animals were colonized with a synthetic human gut microbiota composed of fully sequenced commensal bacteria, we elucidated the functional interactions between dietary fiber, the gut microbiota, and the colonic mucus barrier, which serves as a primary defense against enteric pathogens. We show that during chronic or intermittent dietary fiber deficiency, the gut microbiota resorts to host-secreted mucus glycoproteins as a nutrient source, leading to erosion of the colonic mucus barrier. Dietary fiber deprivation, together with a fiber-deprived, mucus-eroding microbiota, promotes greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium. Our work reveals intricate pathways linking diet, the gut microbiome, and intestinal barrier dysfunction, which could be exploited to improve health using dietary therapeutics.
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Affiliation(s)
- Mahesh S Desai
- Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette 4362, Luxembourg; University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg.
| | - Anna M Seekatz
- University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Nobuhiko Kamada
- University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette 4354, Luxembourg
| | | | - Sho Kitamoto
- University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Arnaud Muller
- Department of Oncology, Luxembourg Institute of Health, Luxembourg 1526, Luxembourg
| | - Vincent B Young
- University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette 4362, Luxembourg
| | | | - Gabriel Núñez
- University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Eric C Martens
- University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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50
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Liu TC, Naito T, Liu Z, VanDussen KL, Haritunians T, Li D, Endo K, Kawai Y, Nagasaki M, Kinouchi Y, McGovern DP, Shimosegawa T, Kakuta Y, Stappenbeck TS. LRRK2 but not ATG16L1 is associated with Paneth cell defect in Japanese Crohn's disease patients. JCI Insight 2017; 2:e91917. [PMID: 28352666 DOI: 10.1172/jci.insight.91917] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND. Morphological patterns of Paneth cells are a prognostic biomarker in Western Crohn's disease (CD) patients, and are associated with autophagy-associated ATG16L1 and NOD2 variants. We hypothesized that genetic determinants of Paneth cell phenotype in other ethnic CD cohorts are distinct but also involved in autophagy. METHODS. We performed a hypothesis-driven analysis of 56 single nucleotide polymorphisms (SNPs) associated with CD susceptibility or known to affect Paneth cell function in 110 Japanese CD patients who underwent ileal resection. We subsequently performed a genome-wide association analysis. Paneth cell phenotype was determined by defensin-5 immunofluorescence. Selected genotype-Paneth cell defect correlations were compared to a Western CD cohort (n = 164). RESULTS. The average percentage of abnormal Paneth cells in Japanese CD was similar to Western CD (P = 0.87), and abnormal Paneth cell phenotype was also associated with early recurrence (P = 0.013). In contrast to Western CD, ATG16L1 T300A was not associated with Paneth cell defect in Japanese CD (P = 0.20). Among the 56 selected SNPs, only LRRK2 M2397T showed significant association with Paneth cell defect (P = 3.62 × 10-4), whereas in the Western CD cohort it was not (P = 0.76). Pathway analysis of LRRK2 and other candidate genes with P less than 5 × 10-4 showed connections with known CD susceptibility genes and links to autophagy and TNF-α networks. CONCLUSIONS. We found dichotomous effects of ATG16L1 and LRRK2 on Paneth cell defect between Japanese and Western CD. Genes affecting Paneth cell phenotype in Japanese CD were also associated with autophagy. Paneth cell phenotype also predicted prognosis in Japanese CD. FUNDING. Helmsley Charitable Trust, Doris Duke Foundation (grant 2014103), Japan Society for the Promotion of Science (KAKENHI grants JP15H04805 and JP15K15284), Crohn's and Colitis Foundation grant 274415, NIH (grants 1R56DK095820, K01DK109081, and UL1 TR000448).
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Affiliation(s)
- Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Takeo Naito
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Zhenqiu Liu
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Talin Haritunians
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Katsuya Endo
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yosuke Kawai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yoshitaka Kinouchi
- Health Administration Center, Center for the Advancement of Higher Education, Tohoku University, Sendai, Japan
| | - Dermot Pb McGovern
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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