1
|
Moore ML, Ford JL, Schladweiler MC, Dye JA, Jackson TW, Miller CN. Gut metabolic changes during pregnancy reveal the importance of gastrointestinal region in sample collection. Metabolomics 2024; 20:40. [PMID: 38460019 PMCID: PMC11168590 DOI: 10.1007/s11306-024-02099-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/06/2024] [Indexed: 03/11/2024]
Abstract
INTRODUCTION Studies of gastrointestinal physiology and the gut microbiome often consider the influence of intestinal region on experimental endpoints. However, this same consideration is not often applied to the gut metabolome. Understanding the contribution of gut regionality may be critically important to the rapidly changing metabolic environments, such as during pregnancy. OBJECTIVES We sought to characterize the difference in the gut metabolome in pregnant mice stratified by region-comparing the small intestine, cecum, and feces. Pre-pregnancy feces were collected to understand the influence of pregnancy on the fecal metabolome. METHODS Feces were collected from CD-1 female mice before breeding. On gestation day (GD) 18, gut contents were collected from the small intestine, cecum, and descending colon. Metabolites were analyzed with LC-MS/MS using the Biocrates MetaboINDICATOR™ MxP® Quant 500 kit. RESULTS Of the 104 small molecule metabolites meeting analysis criteria, we found that 84 (81%) were differentially abundant based on gut region. The most significant regional comparison observed was between the cecum and small intestines, with 52 (50%) differentially abundant metabolites. Pregnancy itself altered 41 (39.4%) fecal small molecule metabolites. CONCLUSIONS The regional variation observed in the gut metabolome are likely due to the microbial and physiological differences between the different parts of the intestines. Additionally, pregnancy impacts the fecal metabolome, which may be due to evolving needs of both the dam and fetus.
Collapse
Affiliation(s)
- Makala L Moore
- Oak Ridge Institute for Science and Education, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Jermaine L Ford
- Chemical Characterization and Exposure Division, Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Mette C Schladweiler
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Janice A Dye
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Thomas W Jackson
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA.
| | - Colette N Miller
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA.
| |
Collapse
|
2
|
Öling S, Struck E, Noreen-Thorsen M, Zwahlen M, von Feilitzen K, Odeberg J, Pontén F, Lindskog C, Uhlén M, Dusart P, Butler LM. A human stomach cell type transcriptome atlas. BMC Biol 2024; 22:36. [PMID: 38355543 PMCID: PMC10865703 DOI: 10.1186/s12915-024-01812-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND The identification of cell type-specific genes and their modification under different conditions is central to our understanding of human health and disease. The stomach, a hollow organ in the upper gastrointestinal tract, provides an acidic environment that contributes to microbial defence and facilitates the activity of secreted digestive enzymes to process food and nutrients into chyme. In contrast to other sections of the gastrointestinal tract, detailed descriptions of cell type gene enrichment profiles in the stomach are absent from the major single-cell sequencing-based atlases. RESULTS Here, we use an integrative correlation analysis method to predict human stomach cell type transcriptome signatures using unfractionated stomach RNAseq data from 359 individuals. We profile parietal, chief, gastric mucous, gastric enteroendocrine, mitotic, endothelial, fibroblast, macrophage, neutrophil, T-cell, and plasma cells, identifying over 1600 cell type-enriched genes. CONCLUSIONS We uncover the cell type expression profile of several non-coding genes strongly associated with the progression of gastric cancer and, using a sex-based subset analysis, uncover a panel of male-only chief cell-enriched genes. This study provides a roadmap to further understand human stomach biology.
Collapse
Affiliation(s)
- S Öling
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - E Struck
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - M Noreen-Thorsen
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
| | - M Zwahlen
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - K von Feilitzen
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - J Odeberg
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
- The University Hospital of North Norway (UNN), 9019, Tromsø, Norway
- Department of Haematology, Coagulation Unit, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - F Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 752 37, Uppsala, Sweden
| | - C Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 752 37, Uppsala, Sweden
| | - M Uhlén
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
| | - P Dusart
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden
- Clinical Chemistry and Blood Coagulation Research, Department of Molecular Medicine and Surgery, Karolinska Institute, 171 76, Stockholm, Sweden
- Clinical Chemistry, Karolinska University Laboratory, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - L M Butler
- Department of Clinical Medicine, Translational Vascular Research, The Arctic University of Norway, 9019, Tromsø, Norway.
- Science for Life Laboratory, Department of Protein Science, Royal Institute of Technology (KTH), 171 21, Stockholm, Sweden.
- Clinical Chemistry and Blood Coagulation Research, Department of Molecular Medicine and Surgery, Karolinska Institute, 171 76, Stockholm, Sweden.
- Clinical Chemistry, Karolinska University Laboratory, Karolinska University Hospital, 171 76, Stockholm, Sweden.
| |
Collapse
|
3
|
Ito M, Fujii N, Kohara S, Hori S, Tanaka M, Wittwer C, Kikuchi K, Iijima T, Kakimoto Y, Hirabayashi K, Kurotaki D, Jessen HJ, Saiardi A, Nagata E. Inositol pyrophosphate profiling reveals regulatory roles of IP6K2-dependent enhanced IP 7 metabolism in the enteric nervous system. J Biol Chem 2023; 299:102928. [PMID: 36681123 PMCID: PMC9957762 DOI: 10.1016/j.jbc.2023.102928] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/20/2023] Open
Abstract
Inositol pyrophosphates regulate diverse physiological processes; to better understand their functional roles, assessing their tissue-specific distribution is important. Here, we profiled inositol pyrophosphate levels in mammalian organs using an originally designed liquid chromatography-mass spectrometry (LC-MS) protocol and discovered that the gastrointestinal tract (GIT) contained the highest levels of diphosphoinositol pentakisphosphate (IP7) and its precursor inositol hexakisphosphate (IP6). Although their absolute levels in the GIT are diet dependent, elevated IP7 metabolism still exists under dietary regimens devoid of exogenous IP7. Of the major GIT cells, enteric neurons selectively express the IP7-synthesizing enzyme IP6K2. We found that IP6K2-knockout mice exhibited significantly impaired IP7 metabolism in the various organs including the proximal GIT. In addition, our LC-MS analysis displayed that genetic ablation of IP6K2 significantly impaired IP7 metabolism in the gut and duodenal muscularis externa containing myenteric plexus. Whole transcriptome analysis of duodenal muscularis externa further suggested that IP6K2 inhibition significantly altered expression levels of the gene sets associated with mature neurons, neural progenitor/stem cells, and glial cells, as well as of certain genes modulating neuronal differentiation and functioning, implying critical roles of the IP6K2-IP7 axis in developmental and functional regulation of the enteric nervous system. These results collectively reveal an unexpected role of mammalian IP7-a highly active IP6K2-IP7 pathway is conducive to the enteric nervous system.
Collapse
Affiliation(s)
- Masatoshi Ito
- Support Center for Medical Research and Education, Tokai University, Isehara, Japan.
| | - Natsuko Fujii
- Department of Neurology, Tokai University School of Medicine, Isehara, Japan
| | - Saori Kohara
- Department of Neurology, Tokai University School of Medicine, Isehara, Japan
| | - Shuho Hori
- Support Center for Medical Research and Education, Tokai University, Isehara, Japan
| | - Masayuki Tanaka
- Support Center for Medical Research and Education, Tokai University, Isehara, Japan
| | | | - Kenta Kikuchi
- Laboratory of Chromatin Organization in Immune Cell Development, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takatoshi Iijima
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Yu Kakimoto
- Department of Forensic Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Kenichi Hirabayashi
- Department of Pathology, Tokai University School of Medicine, Isehara, Japan
| | - Daisuke Kurotaki
- Laboratory of Chromatin Organization in Immune Cell Development, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Eiichiro Nagata
- Department of Neurology, Tokai University School of Medicine, Isehara, Japan.
| |
Collapse
|
4
|
Matute JD, Duan J, Flak MB, Griebel P, Tascon-Arcila JA, Doms S, Hanley T, Antanaviciute A, Gundrum J, Mark Welch JL, Sit B, Abtahi S, Fuhler GM, Grootjans J, Tran F, Stengel ST, White JR, Krupka N, Haller D, Clare S, Lawley TD, Kaser A, Simmons A, Glickman JN, Bry L, Rosenstiel P, Borisy G, Waldor MK, Baines JF, Turner JR, Blumberg RS. Intelectin-1 binds and alters the localization of the mucus barrier-modifying bacterium Akkermansia muciniphila. J Exp Med 2023; 220:e20211938. [PMID: 36413219 PMCID: PMC9683900 DOI: 10.1084/jem.20211938] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/06/2022] [Accepted: 10/13/2022] [Indexed: 01/25/2023] Open
Abstract
Intelectin-1 (ITLN1) is a lectin secreted by intestinal epithelial cells (IECs) and upregulated in human ulcerative colitis (UC). We investigated how ITLN1 production is regulated in IECs and the biological effects of ITLN1 at the host-microbiota interface using mouse models. Our data show that ITLN1 upregulation in IECs from UC patients is a consequence of activating the unfolded protein response. Analysis of microbes coated by ITLN1 in vivo revealed a restricted subset of microorganisms, including the mucolytic bacterium Akkermansia muciniphila. Mice overexpressing intestinal ITLN1 exhibited decreased inner colonic mucus layer thickness and closer apposition of A. muciniphila to the epithelial cell surface, similar to alterations reported in UC. The changes in the inner mucus layer were microbiota and A. muciniphila dependent and associated with enhanced sensitivity to chemically induced and T cell-mediated colitis. We conclude that by determining the localization of a select group of bacteria to the mucus layer, ITLN1 modifies this critical barrier. Together, these findings may explain the impact of ITLN1 dysregulation on UC pathogenesis.
Collapse
Affiliation(s)
- Juan D. Matute
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Jinzhi Duan
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Magdalena B. Flak
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Paul Griebel
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Jose A. Tascon-Arcila
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Shauni Doms
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Thomas Hanley
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Agne Antanaviciute
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | | | | | - Brandon Sit
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA
- Department of Microbiology, Harvard Medical School, Boston, MA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Shabnam Abtahi
- Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Gwenny M. Fuhler
- Department of Gastroenterology & Hepatology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Joep Grootjans
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology and Metabolism & Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Stephanie T. Stengel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Niklas Krupka
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Dirk Haller
- Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Simon Clare
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Arthur Kaser
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, and Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Alison Simmons
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jonathan N. Glickman
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA
- Department of Microbiology, Harvard Medical School, Boston, MA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
| | - John F. Baines
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Jerrold R. Turner
- Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Richard S. Blumberg
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| |
Collapse
|
5
|
Hindieh P, Yaghi J, Khoury AE, Chokr A, Atoui A, Louka N, Assaf JC. Lactobacillus rhamnosus and Staphylococcus epidermidis in gut microbiota: in vitro antimicrobial resistance. AMB Express 2022; 12:128. [PMID: 36190582 PMCID: PMC9530110 DOI: 10.1186/s13568-022-01468-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
The gastrointestinal tract is one of the most complex microbiological niches containing beneficial and non-pathogenic bacterial strains of which some may evolve into virulent under specific conditions. Lactobacillus rhamnosus GG is of the most known beneficial species with an ability to protect the intestine as opposed to Staphylococcus epidermidis 444 which causes serious health risks due to its high antimicrobial resistance. This study investigates first the survival and coexistence ability of L. rhamnosus GG, and S. epidermidis 444 at different pH levels. Subsequently, lysozyme's antimicrobial and antibiofilm effect on these two strains was elucidated before adding different concentrations of oxytetracycline hydrochloride antibiotic. Results showed that 50% inhibition of L. rhamnosus GG, S. epidermidis 444, and a co-culture of these planktonic strains were obtained respectively at a lysozyme concentration of 30, 18, and 26 mg/mL after the addition of ethylenediamine tetra-acetic acid (EDTA). At a pH of 7.5, mixing lysozyme (at IC50) and EDTA with oxytetracycline hydrochloride (700 μg/mL) showed an additional bactericidal effect as compared to its known bacteriostatic effect. Similarly, the addition of lysozyme to the antibiotic further increased the biofilm eradication of S. epidermidis 444 and L. rhamnosus GG where a maximal eradication of 70% was reached. Therefore, the potential development of new drugs based on adding a lysozyme-EDTA mixture to different types of antibiotics may be highly promising.
Collapse
Affiliation(s)
- Pamela Hindieh
- Centre d'Analyses et de Recherche (CAR), Unité de Recherche TVA/Résistance aux Antibiotiques et Impact Industriel (RAII), Faculté des Sciences, Université Saint-Joseph de Beyrouth, Campus des sciences et technologies, Mar Roukos, Matn, Lebanon.,Laboratoire de Mycologie Et Sécurité Des Aliments (LMSA), Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus des sciences et technologies, Mar Roukos, Matn, Lebanon.,Ecole Doctorale "Sciences Et Santé", Université Saint-Joseph de Beyrouth, Campus des Sciences Médicales et Infirmières, Riad El Solh, Beirut, Lebanon
| | - Joseph Yaghi
- Centre d'Analyses et de Recherche (CAR), Unité de Recherche TVA/Résistance aux Antibiotiques et Impact Industriel (RAII), Faculté des Sciences, Université Saint-Joseph de Beyrouth, Campus des sciences et technologies, Mar Roukos, Matn, Lebanon.,Laboratoire de Mycologie Et Sécurité Des Aliments (LMSA), Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus des sciences et technologies, Mar Roukos, Matn, Lebanon
| | - André El Khoury
- Centre d'Analyses et de Recherche (CAR), Unité de Recherche TVA/Résistance aux Antibiotiques et Impact Industriel (RAII), Faculté des Sciences, Université Saint-Joseph de Beyrouth, Campus des sciences et technologies, Mar Roukos, Matn, Lebanon.,Laboratoire de Mycologie Et Sécurité Des Aliments (LMSA), Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus des sciences et technologies, Mar Roukos, Matn, Lebanon
| | - Ali Chokr
- Research Laboratory of Microbiology (RLM), Department of Life and Earth Sciences, Faculty of Sciences I, Lebanese University, Hadat Campus, Beirut, Lebanon.,Platform of Research and Analysis in Environmental Sciences (PRASE), Doctoral School of Sciences and Technologies, Lebanese University, Hadat Campus, Beirut, Lebanon
| | - Ali Atoui
- Research Laboratory of Microbiology (RLM), Department of Life and Earth Sciences, Faculty of Sciences I, Lebanese University, Hadat Campus, Beirut, Lebanon
| | - Nicolas Louka
- Centre d'Analyses et de Recherche (CAR), Unité de Recherche TVA/Résistance aux Antibiotiques et Impact Industriel (RAII), Faculté des Sciences, Université Saint-Joseph de Beyrouth, Campus des sciences et technologies, Mar Roukos, Matn, Lebanon
| | - Jean Claude Assaf
- Centre d'Analyses et de Recherche (CAR), Unité de Recherche TVA/Résistance aux Antibiotiques et Impact Industriel (RAII), Faculté des Sciences, Université Saint-Joseph de Beyrouth, Campus des sciences et technologies, Mar Roukos, Matn, Lebanon. .,Laboratoire de Mycologie Et Sécurité Des Aliments (LMSA), Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus des sciences et technologies, Mar Roukos, Matn, Lebanon.
| |
Collapse
|
6
|
Koulis A, Di Costanzo N, Mitchell C, Lade S, Goode D, Busuttil RA, Boussioutas A. CD10 and Das1: a biomarker study using immunohistochemistry to subtype gastric intestinal metaplasia. BMC Gastroenterol 2022; 22:197. [PMID: 35448971 PMCID: PMC9026694 DOI: 10.1186/s12876-022-02268-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 03/30/2022] [Indexed: 12/24/2022] Open
Abstract
Background Intestinal metaplasia (IM) is considered a key pivot point in the Correa model of gastric cancer (GC). It is histologically subtyped into the complete and incomplete subtypes, the latter being associated with a greater risk of progression. However, the clinical utility of IM subtyping remains unclear, partially due to the absence of reliable defining biomarkers. Methods Based on gene expression data and existing literature, we selected CD10 and Das1 as candidate biomarkers to distinguish complete and incomplete IM glands in tissues from patients without GC (IM-GC) and patients with GC (IM + GC). Immunohistochemical staining of individually subtyped IM glands was scored after blinding by two researchers using tissue belonging to both IM-GC and IM + GC patients. Whole tissue Das1 staining was further assessed using digital image quantification (cellSens Dimension, Olympus). Results Across both cohorts CD10 stained the IM brush border and was shown to have a high sensitivity (87.5% and 94.9% in IM-GC and IM + GC patients respectively) and specificity (100.0% and 96.7% respectively) with an overall AUROC of 0.944 for complete IM glands. By contrast Das1 stained mainly goblet cells and the apical membrane of epithelial cells, mostly of incomplete IM glands with a low sensitivity (28.6% and 29.3% in IM-GC and IM + GC patients respectively) but high specificity (98.3% and 85.1% respectively) and an overall AUROC of 0.603 for incomplete IM glands. A combined logistic regression model showed a significant increase in AUROC for detecting complete IM glands (0.955 vs 0.970). Whole tissue digital quantification of Das1 staining showed a significant association with incomplete IM compared to complete IM, both in IM-GC and in IM + GC patients (p = 0.016 and p = 0.009 respectively, Mann–Whitney test and unpaired t test used). Additionally, complete IM in IM + GC patients exhibited significantly more Das1 staining than in IM-GC patients (p = 0.019, Mann–Whitney test). Conclusions These findings suggest that CD10 is an outstanding biomarker for complete IM and Das1 may be useful as a secondary biomarker for IM glands at greater risk of progression irrespective of IM subtype. Overall, the clinical use of these biomarkers could lead to improved patient stratification and targeted surveillance. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-022-02268-z.
Collapse
Affiliation(s)
- Athanasios Koulis
- Upper Gastrointestinal Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Natasha Di Costanzo
- Upper Gastrointestinal Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Catherine Mitchell
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Stephen Lade
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - David Goode
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.,Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Rita A Busuttil
- Upper Gastrointestinal Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.,Department of Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | - Alex Boussioutas
- Upper Gastrointestinal Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia. .,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia. .,Department of Medicine, Royal Melbourne Hospital, Melbourne, Australia. .,Upper Gastrointestinal Translational Research Laboratory, Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3050, Australia.
| |
Collapse
|
7
|
Tissue extracellular matrix hydrogels as alternatives to Matrigel for culturing gastrointestinal organoids. Nat Commun 2022; 13:1692. [PMID: 35354790 PMCID: PMC8967832 DOI: 10.1038/s41467-022-29279-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/04/2022] [Indexed: 12/16/2022] Open
Abstract
Matrigel, a mouse tumor extracellular matrix protein mixture, is an indispensable component of most organoid tissue culture. However, it has limited the utility of organoids for drug development and regenerative medicine due to its tumor-derived origin, batch-to-batch variation, high cost, and safety issues. Here, we demonstrate that gastrointestinal tissue-derived extracellular matrix hydrogels are suitable substitutes for Matrigel in gastrointestinal organoid culture. We found that the development and function of gastric or intestinal organoids grown in tissue extracellular matrix hydrogels are comparable or often superior to those in Matrigel. In addition, gastrointestinal extracellular matrix hydrogels enabled long-term subculture and transplantation of organoids by providing gastrointestinal tissue-mimetic microenvironments. Tissue-specific and age-related extracellular matrix profiles that affect organoid development were also elucidated through proteomic analysis. Together, our results suggest that extracellular matrix hydrogels derived from decellularized gastrointestinal tissues are effective alternatives to the current gold standard, Matrigel, and produce organoids suitable for gastrointestinal disease modeling, drug development, and tissue regeneration.
Collapse
|
8
|
Bruland T, Østvik AE, Sandvik AK, Hansen MD. Host-Viral Interactions in the Pathogenesis of Ulcerative Colitis. Int J Mol Sci 2021; 22:ijms221910851. [PMID: 34639191 PMCID: PMC8509287 DOI: 10.3390/ijms221910851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 12/12/2022] Open
Abstract
Ulcerative colitis is characterized by relapsing and remitting colonic mucosal inflammation. During the early stages of viral infection, innate immune defenses are activated, leading to the rapid release of cytokines and the subsequent initiation of downstream responses including inflammation. Previously, intestinal viruses were thought to be either detrimental or neutral to the host. However, persisting viruses may have a role as resident commensals and confer protective immunity during inflammation. On the other hand, the dysregulation of gut mucosal immune responses to viruses can trigger excessive, pathogenic inflammation. The purpose of this review is to discuss virus-induced innate immune responses that are at play in ulcerative colitis.
Collapse
Affiliation(s)
- Torunn Bruland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; (T.B.); (A.E.Ø.); (A.K.S.)
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, 7030 Trondheim, Norway
| | - Ann Elisabet Østvik
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; (T.B.); (A.E.Ø.); (A.K.S.)
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, 7030 Trondheim, Norway
| | - Arne Kristian Sandvik
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; (T.B.); (A.E.Ø.); (A.K.S.)
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, 7030 Trondheim, Norway
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Marianne Doré Hansen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; (T.B.); (A.E.Ø.); (A.K.S.)
- Department of Medical Microbiology, Clinic of Laboratory Medicine, St. Olav’s University Hospital, 7030 Trondheim, Norway
- Correspondence:
| |
Collapse
|
9
|
Tennakoon M, Senarath K, Kankanamge D, Chadee DN, Karunarathne A. A short C-terminal peptide in Gγ regulates Gβγ signaling efficacy. Mol Biol Cell 2021; 32:1446-1458. [PMID: 34106735 PMCID: PMC8351738 DOI: 10.1091/mbc.e20-11-0750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/03/2021] [Accepted: 06/04/2021] [Indexed: 01/03/2023] Open
Abstract
G protein beta-gamma (Gβγ) subunits anchor to the plasma membrane (PM) through the carboxy-terminal (CT) prenyl group in Gγ. This interaction is crucial for the PM localization and functioning of Gβγ, allowing GPCR-G protein signaling to proceed. The diverse Gγ family has 12 members, and we have recently shown that the signaling efficacies of major Gβγ effectors are Gγ-type dependent. This dependency is due to the distinct series of membrane-interacting abilities of Gγ. However, the molecular process allowing for Gβγ subunits to exhibit a discrete and diverse range of Gγ-type-dependent membrane affinities is unclear and cannot be explained using only the type of prenylation. The present work explores the unique designs of membrane-interacting CT residues in Gγ as a major source for this Gγ-type-dependent Gβγ signaling. Despite the type of prenylation, the results show signaling efficacy at the PM, and associated cell behaviors of Gβγ are governed by crucially located specific amino acids in the five to six residue preprenylation region of Gγ. The provided molecular picture of Gγ-membrane interactions may explain how cells gain Gγ-type-dependent G protein-GPCR signaling as well as how Gβγ elicits selective signaling at various subcellular compartments.
Collapse
Affiliation(s)
- Mithila Tennakoon
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606
| | - Kanishka Senarath
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606
| | - Dinesh Kankanamge
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606
| | - Deborah N. Chadee
- Department of Biological Sciences, The University of Toledo, Toledo, OH 43606
| | - Ajith Karunarathne
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606
| |
Collapse
|
10
|
Dave LA, Hayes M, Mora L, Rutherfurd SM, Montoya CA, Moughan PJ. Bioactive Peptides Originating from Gastrointestinal Endogenous Proteins in the Growing Pig: In Vivo Identification. Curr Pharm Des 2021; 27:1382-1395. [PMID: 33292114 DOI: 10.2174/1381612826666201207111209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/17/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent in silico and in vitro studies have shown that gastrointestinal endogenous proteins (GEP) are a source of bioactive peptides. To date, however, the presence of such peptides in the lumen of the digestive tract has not been demonstrated. OBJECTIVE We investigated the generation of GEP-derived bioactive peptides in the growing pig fed a proteinfree diet. METHODS Stomach chyme (SC) and jejunal digesta (JD) fractions from 6 growing pigs (two sampling times) were assessed for their angiotensin-I-converting enzyme (ACE-I; EC 3.4.15.1) inhibition, and antioxidant activity using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) inhibition, ferric reducing antioxidant power (FRAP) and microsomal lipid peroxidation (MLP) inhibition assays. RESULTS Two of the fractions prepared from JD samples inhibited ACE-I and DPPH by 81 (± 2.80)% and 94 (±0.66)%. SC fractions were found to inhibit MLP between 15-39 (±3.52-1.40)%. The study identified over 180 novel peptide sequences that were related to the determined bioactivities, including a porcine serum albuminderived peptide (FAKTCVADESAENCDKS), corresponding to f(7-23) of the human serum albumin peptide LVNEVTEFAKTCVADESAENCDKSLHTLF that was previously identified from the digests of the latter GEP. CONCLUSION This study provides the first in vivo evidence for GEP as a source of bioactive peptides. These new findings help advance our knowledge of the latent bioactive role of GEP-derived peptides in mammalian nutrition and health and their potential pharmaceutical applications.
Collapse
Affiliation(s)
- Lakshmi A Dave
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Maria Hayes
- Teagasc, The Irish Agricultural and Food Development Authority, Food BioSciences Department, Ashtown, Dublin 15, Ireland
| | - Leticia Mora
- Instituto de Agroquıimica y Tecnologıia de Alimentos (CSIC), Avenida Agustín Escardino 7, 46980 Paterna, Valencia, Spain
| | - Shane M Rutherfurd
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Carlos A Montoya
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Paul J Moughan
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| |
Collapse
|
11
|
Liu J, Huang Z, Chen HN, Qin S, Chen Y, Jiang J, Zhang Z, Luo M, Ye Q, Xie N, Zhou ZG, Wei Y, Xie K, Huang C. ZNF37A promotes tumor metastasis through transcriptional control of THSD4/TGF-β axis in colorectal cancer. Oncogene 2021; 40:3394-3407. [PMID: 33875786 DOI: 10.1038/s41388-021-01713-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 02/05/2023]
Abstract
Poorly differentiated colorectal cancer (CRC) is characterized by aggressive invasion and stromal fibroblast activation, which results in rapid progression and poor therapeutic consequences. However, the regulatory mechanism involved remains unclear. Here, we showed that ZNF37A, a member of KRAB-ZFP family, was upregulated in poorly differentiated CRCs and associated with tumor metastasis. ZNF37A enhanced the metastatic potential of multiple CRC cell lines and promoted distant metastasis in an orthotopic CRC model. Further investigation attributed the ZNF37A-exacerbated metastasis to increased extracellular TGF-β and the consequent activation of cancer-associated fibroblasts (CAFs) in tumor microenvironment (TME). Mechanistically, ZNF37A formed a complex with KAP1 and bound to the promoter of THSD4, a TME modulator, to suppress its transcription, which is required for ZNF37A-mediated TGF-β activation and CRC metastasis. Collectively, our study indicates that ZNF37A promotes TGF-β signaling in CRC cells and activates CAFs by transcriptionally repressing THSD4 to drive CRC metastasis, implicating ZNF37A as a potential biomarker for CRC differentiation and progression.
Collapse
Affiliation(s)
- Jiayang Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Hai-Ning Chen
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Siyuan Qin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Yan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Jingwen Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Maochao Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Qin Ye
- Department of Oncology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Na Xie
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Zong-Guang Zhou
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuquan Wei
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China
| | - Ke Xie
- Department of Oncology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, P.R. China. .,School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.
| |
Collapse
|
12
|
Venuprasad K, Theiss AL. NLRP6 in host defense and intestinal inflammation. Cell Rep 2021; 35:109043. [PMID: 33910012 PMCID: PMC8106960 DOI: 10.1016/j.celrep.2021.109043] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/21/2021] [Accepted: 04/06/2021] [Indexed: 02/06/2023] Open
Abstract
NLRP6 is a member of the NLR (nucleotide-oligomerization domain-like receptor) family of proteins that recognize pathogen-derived factors and damage-associated molecular patterns in the cytosol. The function of NLRP6 has been attributed to the maintenance of epithelial integrity and host defense against microbial infections. Under some physiological conditions, NLRP6 forms a complex with ASC and caspase-1 or caspase-11 to form an inflammasome complex cleaving pro-interleukin-1β (IL-1β) and IL-18 into their biologically active forms. Here, we summarize recent advances in the understanding of the mechanisms of activation of the NLRP6 inflammasome and discuss its relevance to human disease.
Collapse
Affiliation(s)
- K Venuprasad
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Arianne L Theiss
- Division of Gastroenterology and Hepatology, School of Medicine at the Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA
| |
Collapse
|
13
|
NLRP6-associated host microbiota composition impacts in the intestinal barrier to systemic dissemination of Brucella abortus. PLoS Negl Trop Dis 2021; 15:e0009171. [PMID: 33617596 PMCID: PMC7932538 DOI: 10.1371/journal.pntd.0009171] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 03/04/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023] Open
Abstract
Brucella abortus is a Gram-negative bacterium responsible for a worldwide zoonotic infection—Brucellosis, which has been associated with high morbidity rate in humans and severe economic losses in infected livestock. The natural route of infection is through oral and nasal mucosa but the invasion process through host gut mucosa is yet to be understood. Studies have examined the role of NLRP6 (NOD-like receptor family pyrin domain-containing-6 protein) in gut homeostasis and defense against pathogens. Here, we investigated the impact of gut microbiota and NLRP6 in a murine model of Ba oral infection. Nlrp6-/- and wild-type (WT) mice were infected by oral gavage with Ba and tissues samples were collected at different time points. Our results suggest that Ba oral infection leads to significant alterations in gut microbiota. Moreover, Nlrp6-/- mice were more resistant to infection, with decreased CFU in the liver and reduction in gut permeability when compared to the control group. Fecal microbiota transplantation from WT and Nlrp6-/- into germ-free mice reflected the gut permeability phenotype from the donors. Additionally, depletion of gut microbiota by broad-spectrum-antibiotic treatment prevented Ba replication in WT while favoring bacterial growth in Nlrp6-/-. Finally, we observed higher eosinophils in the gut and leukocytes in the blood of infected Nlrp6-/- compared to WT-infected mice, which might be associated to the Nlrp6-/- resistance phenotype. Altogether, these results indicated that gut microbiota composition is the major factor involved in the initial stages of pathogen host replication and partially also by the resistance phenotype observed in Nlrp6 -/- mice regulating host inflammation against Ba infection. Brucella abortus (Ba) is an intracellular bacterium that causes zoonotic and clinical problems worldwide. Although the common route of infection is through oral and nasal, the mechanisms toward the gastrointestinal mucosa response is still unexplored. It is well known that microbiota promotes and maintains host intestinal homeostasis during bacterial infections. However, mechanisms by which the gut microbiota affects the Ba infection have not yet been demonstrated. Here, we provide significant insights into the relationship between gut microbiota and B. abortus oral infection and demonstrate the gut microbiota contribution to the gut permeability and dissemination of Ba. Furthermore, we investigated the participation of the gut microbiota from Nlrp6 deficient mice, on the gut permeability and Ba infection. Substantial experiments performed, mostly in vivo, showed that gut microbiota alterations promote gut barrier disruption, as indicated by increased gut permeability after Ba oral infection. Thus, our work highlights the role of gut mucosal environment through gut microbiota and Nlrp6 molecule involved in host innate immune responses to Ba infection.
Collapse
|
14
|
Cortez V, Schultz-Cherry S. The role of goblet cells in viral pathogenesis. FEBS J 2021; 288:7060-7072. [PMID: 33507606 PMCID: PMC8013445 DOI: 10.1111/febs.15731] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 12/19/2022]
Abstract
Goblet cells are specialized epithelial cells that are essential to the formation of the mucus barriers in the airways and intestines. Armed with an arsenal of defenses, goblet cells can rapidly respond to infection but must balance this response with maintaining homeostasis. Whereas goblet cell defenses against bacterial and parasitic infections have been characterized, we are just beginning to understand their responses to viral infections. Here, we outline what is known about the enteric and respiratory viruses that target goblet cells, the direct and bystander effects caused by viral infection and how viral interactions with the mucus barrier can alter the course of infection. Together, these factors can play a significant role in driving viral pathogenesis and disease outcomes.
Collapse
Affiliation(s)
- Valerie Cortez
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| |
Collapse
|
15
|
Digre A, Lindskog C. The Human Protein Atlas-Spatial localization of the human proteome in health and disease. Protein Sci 2021; 30:218-233. [PMID: 33146890 PMCID: PMC7737765 DOI: 10.1002/pro.3987] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022]
Abstract
For a complete understanding of a system's processes and each protein's role in health and disease, it is essential to study protein expression with a spatial resolution, as the exact location of proteins at tissue, cellular, or subcellular levels is tightly linked to protein function. The Human Protein Atlas (HPA) project is a large-scale initiative aiming at mapping the entire human proteome using antibody-based proteomics and integration of various other omics technologies. The publicly available knowledge resource www.proteinatlas.org is one of the world's most visited biological databases and has been extensively updated during the last few years. The current version is divided into six main sections, each focusing on particular aspects of the human proteome: (a) the Tissue Atlas showing the distribution of proteins across all major tissues and organs in the human body; (b) the Cell Atlas showing the subcellular localization of proteins in single cells; (c) the Pathology Atlas showing the impact of protein levels on survival of patients with cancer; (d) the Blood Atlas showing the expression profiles of blood cells and actively secreted proteins; (e) the Brain Atlas showing the distribution of proteins in human, mouse, and pig brain; and (f) the Metabolic Atlas showing the involvement of proteins in human metabolism. The HPA constitutes an important resource for further understanding of human biology, and the publicly available datasets hold much promise for integration with other emerging efforts focusing on single cell analyses, both at transcriptomic and proteomic level.
Collapse
Affiliation(s)
- Andreas Digre
- Department of Immunology, Genetics and PathologyRudbeck Laboratory, Uppsala UniversityUppsalaSweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and PathologyRudbeck Laboratory, Uppsala UniversityUppsalaSweden
| |
Collapse
|
16
|
Bracey NA, Platnich JM, Lau A, Chung H, Hyndman ME, MacDonald JA, Chun J, Beck PL, Girardin SE, Gordon PM, Muruve DA. Tissue-selective alternate promoters guide NLRP6 expression. Life Sci Alliance 2020; 4:4/3/e202000897. [PMID: 33376129 PMCID: PMC7772780 DOI: 10.26508/lsa.202000897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
The NLRP6 innate immune sensor is regulated by tissue-selective alternate promoters that facilitate translational gene silencing outside of the intestinal epithelium in both humans and mice. The pryin domain (PYD) domain is involved in protein interactions that lead to assembly of immune-sensing complexes such as inflammasomes. The repertoire of PYD-containing genes expressed by a cell type arms tissues with responses against a range of stimuli. The transcriptional regulation of the PYD gene family however is incompletely understood. Alternative promoter utilization was identified as a mechanism regulating the tissue distribution of human PYD gene family members, including NLRP6 that is translationally silenced outside of intestinal tissue. Results show that alternative transcriptional promoters mediate NLRP6 silencing in mice and humans, despite no upstream genomic synteny. Human NLRP6 contains an internal alternative promoter within exon 2 of the PYD, resulting in a truncated mRNA in nonintestinal tissue. In mice, a proximal promoter was used that expanded the 5′ leader sequence restricting nuclear export and abolishing translational efficiency. Nlrp6 was dispensable in disease models targeting the kidney, which expresses noncanonical isoforms. Thus, alternative promoter use is a critical mechanism not just for isoform modulation but for determining expression profile and function of PYD family members.
Collapse
Affiliation(s)
- Nathan A Bracey
- Department of Medicine, University of Calgary, Calgary, Canada.,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| | - Jaye M Platnich
- Department of Medicine, University of Alberta, Edmonton, Canada
| | - Arthur Lau
- Department of Medicine, University of Calgary, Calgary, Canada.,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| | - Hyunjae Chung
- Department of Medicine, University of Calgary, Calgary, Canada.,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| | - M Eric Hyndman
- Department of Surgery, University of Calgary, Calgary, Canada
| | - Justin A MacDonald
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Justin Chun
- Department of Medicine, University of Calgary, Calgary, Canada.,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| | - Paul L Beck
- Department of Medicine, University of Calgary, Calgary, Canada.,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| | - Stephen E Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Paul Mk Gordon
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, Canada
| | - Daniel A Muruve
- Department of Medicine, University of Calgary, Calgary, Canada .,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| |
Collapse
|
17
|
Adam RS, van Neerven SM, Pleguezuelos-Manzano C, Simmini S, Léveillé N, de Groot NE, Holding AN, Markowetz F, Vermeulen L. Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development. Cancer Cell Int 2020; 20:578. [PMID: 33292279 PMCID: PMC7713000 DOI: 10.1186/s12935-020-01661-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 11/16/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Cancer results from the accumulation of mutations leading to the acquisition of cancer promoting characteristics such as increased proliferation and resistance to cell death. In colorectal cancer, an early mutation leading to such features usually occurs in the APC or CTNNB1 genes, thereby activating Wnt signalling. However, substantial phenotypic differences between cancers originating within the same organ, such as molecular subtypes, are not fully reflected by differences in mutations. Indeed, the phenotype seems to result from a complex interplay between the cell-intrinsic features and the acquired mutations, which is difficult to disentangle when established tumours are studied. METHODS We use a 3D in vitro organoid model to study the early phase of colorectal cancer development. From three different murine intestinal locations we grow organoids. These are transformed to resemble adenomas after Wnt activation through lentiviral transduction with a stable form of β-Catenin. The gene expression before and after Wnt activation is compared within each intestinal origin and across the three locations using RNA sequencing. To validate and generalize our findings, we use gene expression data from patients. RESULTS In reaction to Wnt activation we observe downregulation of location specific genes and differentiation markers. A similar effect is seen in patient data, where genes with significant differential expression between the normal left and right colon are downregulated in the cancer samples. Furthermore, the signature of Wnt target genes differs between the three intestinal locations in the organoids. The location specific Wnt signatures are dominated by genes which have been lowly expressed in the tissue of origin, and are the targets of transcription factors that are activated following enhanced Wnt signalling. CONCLUSION We observed that the region-specific cell identity has a substantial effect on the reaction to Wnt activation in a simple intestinal adenoma model. These findings provide a way forward in resolving the distinct biology between left- and right-sided human colon cancers with potential clinical relevance.
Collapse
Affiliation(s)
- Ronja S Adam
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Sanne M van Neerven
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Salvatore Simmini
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Research & Development Department at STEMCELL Technologies UK, 7100 Cambridge Research Park, Beach Drive Waterbeach, Cambridge, CB25 9TL, UK
| | - Nicolas Léveillé
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Nina E de Groot
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Andrew N Holding
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- The Alan Turing Institute, 96 Euston Road, Kings Cross, London, NW1 2DB, UK
- University of York, Wentworth Way, York, YO10 5DD, UK
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| |
Collapse
|
18
|
Mutual Interplay of Host Immune System and Gut Microbiota in the Immunopathology of Atherosclerosis. Int J Mol Sci 2020; 21:ijms21228729. [PMID: 33227973 PMCID: PMC7699263 DOI: 10.3390/ijms21228729] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Inflammation is the key for the initiation and progression of atherosclerosis. Accumulating evidence has revealed that an altered gut microbiome (dysbiosis) triggers both local and systemic inflammation to cause chronic inflammatory diseases, including atherosclerosis. There have been some microbiome-relevant pro-inflammatory mechanisms proposed to link the relationships between dysbiosis and atherosclerosis such as gut permeability disruption, trigger of innate immunity from lipopolysaccharide (LPS), and generation of proatherogenic metabolites, such as trimethylamine N-oxide (TMAO). Meanwhile, immune responses, such as inflammasome activation and cytokine production, could reshape both composition and function of the microbiota. In fact, the immune system delicately modulates the interplay between microbiota and atherogenesis. Recent clinical trials have suggested the potential of immunomodulation as a treatment strategy of atherosclerosis. Here in this review, we present current knowledge regarding to the roles of microbiota in contributing atherosclerotic pathogenesis and highlight translational perspectives by discussing the mutual interplay between microbiota and immune system on atherogenesis.
Collapse
|
19
|
Godfrey AK, Naqvi S, Chmátal L, Chick JM, Mitchell RN, Gygi SP, Skaletsky H, Page DC. Quantitative analysis of Y-Chromosome gene expression across 36 human tissues. Genome Res 2020; 30:860-873. [PMID: 32461223 PMCID: PMC7370882 DOI: 10.1101/gr.261248.120] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Little is known about how human Y-Chromosome gene expression directly contributes to differences between XX (female) and XY (male) individuals in nonreproductive tissues. Here, we analyzed quantitative profiles of Y-Chromosome gene expression across 36 human tissues from hundreds of individuals. Although it is often said that Y-Chromosome genes are lowly expressed outside the testis, we report many instances of elevated Y-Chromosome gene expression in a nonreproductive tissue. A notable example is EIF1AY, which encodes eukaryotic translation initiation factor 1A Y-linked, together with its X-linked homolog EIF1AX. Evolutionary loss of a Y-linked microRNA target site enabled up-regulation of EIF1AY, but not of EIF1AX, in the heart. Consequently, this essential translation initiation factor is nearly twice as abundant in male as in female heart tissue at the protein level. Divergence between the X and Y Chromosomes in regulatory sequence can therefore lead to tissue-specific Y-Chromosome-driven sex biases in expression of critical, dosage-sensitive regulatory genes.
Collapse
Affiliation(s)
- Alexander K Godfrey
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sahin Naqvi
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Lukáš Chmátal
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Richard N Mitchell
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| |
Collapse
|
20
|
Abstract
NOD-like receptor family pyrin domain containing 6 (NLRP6) is a novel NLR family member, that shows high expression in the intestine and liver (in contrast to NLRP3 in myeloid cells), to regulate inflammation and host defense against microbes. NLRP6 is reported to involved in inflammasome activation, regulation of nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK) signaling, antiviral interferon (IFN) signaling, mucus secretion, and antimicrobial peptide (AMP) production. Here, we discuss the recent findings as well as debates regarding: how NLRP6 is induced ("signal I″) and activated ("signal II"); its roles in intestinal cells and immune cells; how NLRP6 and NLRP9 coordinate to regulate the anti-viral immune response in the intestine; potential targeting of NLRP6 in human diseases.
Collapse
Affiliation(s)
- Runzhi Li
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Shu Zhu
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; School of Data Science, University of Science and Technology of China, Hefei, 230026, China; CAS Centre for Excellence in Cell and Molecular Biology, University of Science and Technology of China, Hefei, China.
| |
Collapse
|
21
|
Ghimire L, Paudel S, Jin L, Jeyaseelan S. The NLRP6 inflammasome in health and disease. Mucosal Immunol 2020; 13:388-398. [PMID: 31988468 PMCID: PMC7493825 DOI: 10.1038/s41385-020-0256-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 01/05/2020] [Accepted: 01/08/2020] [Indexed: 02/07/2023]
Abstract
NACHT, LRR (leucine-rich repeat), and PYD (pyrin domain) domain-containing 6 (Nlrp6) is a member of the NLR (nucleotide-oligomerization domain-like receptor) family that patrols the cytosolic compartment of cells to detect pathogen- and damage-associated molecular patterns. Because Nlrp6 is a recently discovered inflammasome, details of its signaling mechanism, structural assembly, and roles in host defense have yet to be determined. To date, Nlrp6 has been proposed to perform a multitude of functions ranging from control of microbiota, maintenance of epithelial integrity, and regulation of metabolic diseases to modulation of host defense during microbial infections, cancer protection, and regulation of neuroinflammation. While recent studies have questioned some of the proposed functions of Nlrp6, Nlrp6 has been shown to form an inflammasome complex and cleaves interleukin-1β (IL-1β) and IL-18 during microbial infection, indicating that it is a bonafide inflammasome. In this review, we summarize the recent advancements in knowledge of the signaling mechanisms and structure of the Nlrp6 inflammasome and discuss the relevance of NLRP6 to human disease.
Collapse
Affiliation(s)
- Laxman Ghimire
- Department of Pathobiological Sciences, School of Veterinary Medicine, Center for Lung Biology and Disease, Louisiana State University (LSU), Baton Rouge, LA, 70803, USA
| | - Sagar Paudel
- Department of Pathobiological Sciences, School of Veterinary Medicine, Center for Lung Biology and Disease, Louisiana State University (LSU), Baton Rouge, LA, 70803, USA
| | - Liliang Jin
- Department of Pathobiological Sciences, School of Veterinary Medicine, Center for Lung Biology and Disease, Louisiana State University (LSU), Baton Rouge, LA, 70803, USA
| | - Samithamby Jeyaseelan
- Department of Pathobiological Sciences, School of Veterinary Medicine, Center for Lung Biology and Disease, Louisiana State University (LSU), Baton Rouge, LA, 70803, USA.
- Section of Pulmonary and Critical Care, Department of Medicine, LSU Health Sciences Center, New Orleans, LA, 70112, USA.
| |
Collapse
|
22
|
Gut microbiota as an "invisible organ" that modulates the function of drugs. Biomed Pharmacother 2019; 121:109653. [PMID: 31810138 DOI: 10.1016/j.biopha.2019.109653] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 02/08/2023] Open
Abstract
Gut microbiota plays an important role in the gut and have become a hotspot of recent research interests. Commensal microbiota in gut exert a variety of effects on the host, from shaping the structure and function of the gut and the immune system to the modulation of nutrient status of the host and the treatment outcomes of some drugs. Gut microbiota and its enzyme product and subsequent products, such as short-chain fatty acid and bile acid, play important roles in the biotransformation of drugs via directly or indirectly affecting drug absorption, toxicity, metabolism and bioavailability. Drugs, especially antibiotics, also affect the homeostasis of probiotics and the integrity and function of the intestinal mucosa. These interplaying processes produce a variety of important metabolites of the host and drugs and affect the balance of microbiota and the mucosal barrier then modulate the function of drugs. Gut microbiota imbalance is associated with a broad range of disease mechanisms, and this association denotes a new drug-therapeutic avenue. The present review summarizes how gut microbiota acts as an "invisible organ" to directly or indirectly modulate the function of drugs, on the aspects of probiotic homeostasis, drugs and host nutritional metabolism, AJC, mucus layer and microfold cells.
Collapse
|
23
|
Zhou CB, Fang JY. The role of pyroptosis in gastrointestinal cancer and immune responses to intestinal microbial infection. Biochim Biophys Acta Rev Cancer 2019; 1872:1-10. [DOI: 10.1016/j.bbcan.2019.05.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/18/2019] [Accepted: 05/01/2019] [Indexed: 01/04/2023]
|
24
|
Yin J, Sheng B, Yang K, Sun L, Xiao W, Yang H. The protective roles of NLRP6 in intestinal epithelial cells. Cell Prolif 2018; 52:e12555. [PMID: 30515917 PMCID: PMC6496424 DOI: 10.1111/cpr.12555] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/11/2018] [Accepted: 10/17/2018] [Indexed: 12/12/2022] Open
Abstract
The evolution of chronic inflammatory diseases is thought to be due to a combination of host genetic variations and environmental factors that include the alteration of intestinal flora, termed "dysbiosis." The intestinal mucosal barrier includes a chemical barrier and physical barrier that have important roles in protecting the intestine against inflammatory injury. The chemical barrier includes antimicrobial peptides (AMPs), and the physical barrier includes a mucous layer, a monolayer of intestinal epithelial cells and cell junctions. The intestinal mucosal barrier is not a static barrier, but rather, it strongly interacts with the gut microbiome and cells of the immune system. Correct expression of AMPs, together with mucus and balanced epithelial cell proliferation, prevents the occurrence of disease. NLRP6, a member of the nucleotide-binding domain, leucine-rich repeat-containing (NLR) innate immune receptor family, participates in the progression of intestinal inflammation and enteric pathogen infections. It has become apparent in recent years that NLRP6 is important in disease pathogenesis, as it responds to internal ligands that lead to the release of AMPs and mucus, thus regulating the regeneration of intestinal epithelial cells. This review summarizes the activation of NLRP6 and its protective role in the intestinal epithelial cell.
Collapse
Affiliation(s)
- Jiuheng Yin
- Department of General Surgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Baifa Sheng
- Department of General Surgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Kunqiu Yang
- Department of General Surgery, Navy General Hospital, Beijing, China
| | - Lihua Sun
- Department of General Surgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Weidong Xiao
- Department of General Surgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Hua Yang
- Department of General Surgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| |
Collapse
|
25
|
Wang J, Dong R, Zheng S. Roles of the inflammasome in the gut‑liver axis (Review). Mol Med Rep 2018; 19:3-14. [PMID: 30483776 PMCID: PMC6297761 DOI: 10.3892/mmr.2018.9679] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 10/23/2018] [Indexed: 02/06/2023] Open
Abstract
The gut-liver axis connects the liver with the intestine via bile acid metabolism. Bile acid dysregulation leads to intestinal dysbiosis, that allows enterogenous pathogenic bacteria, including Gram-negative bacteria and their products lipopolysaccharide (LPS), into the liver via the portal vein, triggering inflammation in the liver. The inflammasome serves as an intracellular pattern recognition receptor that detects pathogens or danger signals and mediates innate immunity in the liver or gut. Specifically, the NACHT, LRR and PYD domains-containing protein (NLRP)6 inflammasome maintains intestinal microbial balance, by promoting interleukin (IL)-18-dependent antimicrobial peptide synthesis and mucus secretion from goblet cells. The NLRP3 inflammasome, in contrast, primarily induces IL-1β and aggravates inflammatory liver injury. Furthermore, the NLRP3 inflammasome affects the epithelial integrity of cholangiocytes by inducing the production of pro-inflammatory cytokines. In addition, bile acids, including deoxycholic acid and chenodeoxycholic acid, are able to activate the NLRP3 inflammasome in macrophages; however, bile acids have the potential to exert the opposite role by interacting with the membrane-bound Takeda G-protein receptor 5 or by activating nuclear farnesoid-X receptor. Therefore, further investigation of the molecular mechanisms underlying the inflammasome, involved in the gut-liver axis, may provide important insights into the identification of a potential therapeutic target for the treatment of liver and gut diseases. The present review discusses the roles of the inflammasome in the gut-liver axis, and the emerging associations between the inflammasome and the intestinal microbiota or the bile acids in the gut-liver axis.
Collapse
Affiliation(s)
- Junfeng Wang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai 201102, P.R. China
| | - Rui Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai 201102, P.R. China
| | - Shan Zheng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defect, Shanghai 201102, P.R. China
| |
Collapse
|
26
|
Erdrich J, Schaberg KB, Khodadoust MS, Zhou L, Shelton AA, Visser BC, Ford JM, Alizadeh AA, Quake SR, Kunz PL, Beausang JF. Surgical and molecular characterization of primary and metastatic disease in a neuroendocrine tumor arising in a tailgut cyst. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003004. [PMID: 30087100 PMCID: PMC6169824 DOI: 10.1101/mcs.a003004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/31/2018] [Indexed: 12/11/2022] Open
Abstract
Neuroendocrine tumors (NETs) arising from tailgut cysts are a rare but increasingly reported entity with gene expression profiles that may be indicative of the gastrointestinal cell of origin. We present a case report describing the unique pathological and genomic characteristics of a tailgut cyst NET that metastasized to liver. The histologic and immunohistochemical findings were consistent with a well-differentiated NET. Genomic testing indicates a germline frameshift in BRCA1 and a few somatic mutations of unknown significance. Transcriptomic analysis suggests an enteroendocrine L cell in the tailgut as a putative cell of origin. Genomic profiling of a rare NET and metastasis provides insight into its origin, development, and potential therapeutic options.
Collapse
Affiliation(s)
- Jennifer Erdrich
- Department of Surgery, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kurt B Schaberg
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Michael S Khodadoust
- Department of Medicine/Oncology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Li Zhou
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
| | - Andrew A Shelton
- Department of Surgery, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Brendan C Visser
- Department of Surgery, Stanford University School of Medicine, Stanford, California 94305, USA
| | - James M Ford
- Department of Medicine/Oncology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Genetics; Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ash A Alizadeh
- Department of Medicine/Oncology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Stephen R Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University and Chan Zuckerberg Biohub, Stanford, California 94305, USA
| | - Pamela L Kunz
- Department of Medicine/Oncology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - John F Beausang
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
27
|
Abstract
The intestinal tract is a site of intense immune cell activity that is poised to mount an effective response against a pathogen and yet maintain tolerance toward commensal bacteria and innocuous dietary antigens. The role of cell death in gut pathologies is particularly important as the intestinal epithelium undergoes self-renewal every 4-7 days through a continuous process of cell death and cell division. Cell death is also required for removal of infected, damaged, and cancerous cells. Certain forms of cell death trigger inflammation through release of damage-associated molecular patterns. Further, molecules involved in cell death decisions also moonlight as critical nodes in immune signaling. The manner of cell death is, therefore, highly instructive of the immunological consequences that ensue. Perturbations in cell death pathways can impact the regulation of the immune system with deleterious consequences. In this review, we discuss the various forms of cell death with a special emphasis on lytic cell death pathways of pyroptosis and necroptosis and their implications in inflammation and cancer in the gut. Understanding the implications of distinct cell death pathways will help in the development of therapeutic interventions in intestinal pathologies.
Collapse
Affiliation(s)
- Deepika Sharma
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | |
Collapse
|
28
|
Ranson N, Veldhuis M, Mitchell B, Fanning S, Cook AL, Kunde D, Eri R. Nod-Like Receptor Pyrin-Containing Protein 6 (NLRP6) Is Up-regulated in Ileal Crohn's Disease and Differentially Expressed in Goblet Cells. Cell Mol Gastroenterol Hepatol 2018; 6:110-112.e8. [PMID: 29928676 PMCID: PMC6007817 DOI: 10.1016/j.jcmgh.2018.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/05/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Nicole Ranson
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Mark Veldhuis
- Launceston General Hospital, Launceston, Tasmania, Australia,St Vincent’s Hospital, Calvary Health Care, Launceston, Tasmania, Australia
| | - Brent Mitchell
- Launceston General Hospital, Launceston, Tasmania, Australia,St Vincent’s Hospital, Calvary Health Care, Launceston, Tasmania, Australia
| | - Scott Fanning
- Launceston General Hospital, Launceston, Tasmania, Australia,St Vincent’s Hospital, Calvary Health Care, Launceston, Tasmania, Australia
| | - Anthony L. Cook
- Wicking Dementia Research and Education Centre, Faculty of Health, University of Tasmania, Launceston, Tasmania, Australia
| | - Dale Kunde
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Rajaraman Eri
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia,Corresponding author:
| |
Collapse
|
29
|
Lie KK, Tørresen OK, Solbakken MH, Rønnestad I, Tooming-Klunderud A, Nederbragt AJ, Jentoft S, Sæle Ø. Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish. BMC Genomics 2018; 19:186. [PMID: 29510660 PMCID: PMC5840709 DOI: 10.1186/s12864-018-4570-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/28/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach loss has occurred independently multiple times in the course of evolution. By assembling the ballan wrasse genome and transcriptome we aimed to determine the genetic basis for its digestive system function and appetite regulation. Among other, this knowledge will aid the formulation of aquaculture diets that meet the nutritional needs of agastric species. RESULTS Long and short read sequencing technologies were combined to generate a ballan wrasse genome of 805 Mbp. Analysis of the genome and transcriptome assemblies confirmed the absence of genes that code for proteins involved in gastric function. The gene coding for the appetite stimulating protein ghrelin was also absent in wrasse. Gene synteny mapping identified several appetite-controlling genes and their paralogs previously undescribed in fish. Transcriptome profiling along the length of the intestine found a declining expression gradient from the anterior to the posterior, and a distinct expression profile in the hind gut. CONCLUSIONS We showed gene loss has occurred for all known genes related to stomach function in the ballan wrasse, while the remaining functions of the digestive tract appear intact. The results also show appetite control in ballan wrasse has undergone substantial changes. The loss of ghrelin suggests that other genes, such as motilin, may play a ghrelin like role. The wrasse genome offers novel insight in to the evolutionary traits of this large family. As the stomach plays a major role in protein digestion, the lack of genes related to stomach digestion in wrasse suggests it requires formulated diets with higher levels of readily digestible protein than those for gastric species.
Collapse
Affiliation(s)
- Kai K. Lie
- Institute of Marine Research, P.O. Box. 1870, Nordnes, 5817 Bergen, NO Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, NO Norway
| | - Monica Hongrø Solbakken
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, NO Norway
| | - Ivar Rønnestad
- Department of Biology, University of Bergen, P.O. Box 7803, 5020 Bergen, NO Norway
| | - Ave Tooming-Klunderud
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, NO Norway
| | - Alexander J. Nederbragt
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, NO Norway
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, 0316 Oslo, NO Norway
| | - Øystein Sæle
- Institute of Marine Research, P.O. Box. 1870, Nordnes, 5817 Bergen, NO Norway
| |
Collapse
|
30
|
Wang H, Xu G, Huang Z, Li W, Cai H, Zhang Y, Xiong D, Liu G, Wang S, Xue Z, Luo Q. LRP6 targeting suppresses gastric tumorigenesis via P14 ARF-Mdm2-P53-dependent cellular senescence. Oncotarget 2017; 8:111597-111607. [PMID: 29340077 PMCID: PMC5762345 DOI: 10.18632/oncotarget.22876] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/15/2017] [Indexed: 12/17/2022] Open
Abstract
NLRP6, a member of the Nod-like receptor family, protects against chemically induced intestinal injury and colitis-associated colon cancer. However, the cellular mechanisms involved in this NLRP6-mediated protection remain unclear. Here, we show that NLRP6 was down-regulated in approximately 75% of primary gastric cancer cases and exhibited significant associations with advanced clinical-stage lymph node metastasis and poor overall survival. Functional studies established that ectopic overexpression or down-regulation of NLRP6 inhibited cancer cell proliferation by inducing cell cycle arrest at the G1 phase via P21 and Cyclin D1 both in vitro and in vivo. Activation of the P14ARF-P53 pathway played a crucial role in the observed cellular senescence. We further demonstrated that ectopic overexpression of NLRP6 combined with inactivation of NF-κB(p65) and Mdm2 activates P14ARF-P53 to promote the senescence of gastric cancer cells. These findings indicate that NLRP6 functions as a negative regulator of gastric cancer and offer a potential new option for preventing gastric cancer.
Collapse
Affiliation(s)
- Haibin Wang
- Department of Gastrointestinal Surgery, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China
| | - Guoxing Xu
- Department of Endoscopy Center, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China
| | - Zhengjie Huang
- Department of Gastrointestinal Surgery, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China.,Department of Gastrointestinal Surgery, First Clinical Medical College of Fujian Medical University, Fuzhou 350004, China
| | - Weizheng Li
- Department of Cancer Prevention, Diagnosis and Treatment, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China
| | - Huali Cai
- Department of Gastrointestinal Surgery, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China
| | - Yunda Zhang
- Department of Gastrointestinal Surgery, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China
| | - Disheng Xiong
- Department of Gastrointestinal Surgery, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China
| | - Gang Liu
- Department of Gastrointestinal Surgery, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China
| | - Shengjie Wang
- Department of Gastrointestinal Surgery, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China
| | - Zengfu Xue
- Department of Cancer Prevention, Diagnosis and Treatment, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China
| | - Qi Luo
- Department of Gastrointestinal Surgery, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen 361003, Fujian, China
| |
Collapse
|
31
|
Lemire P, Robertson SJ, Maughan H, Tattoli I, Streutker CJ, Platnich JM, Muruve DA, Philpott DJ, Girardin SE. The NLR Protein NLRP6 Does Not Impact Gut Microbiota Composition. Cell Rep 2017; 21:3653-3661. [DOI: 10.1016/j.celrep.2017.12.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/17/2017] [Accepted: 12/06/2017] [Indexed: 01/17/2023] Open
|
32
|
Kern M, Aschenbach JR, Tedin K, Pieper R, Loss H, Lodemann U. Characterization of Inflammasome Components in Pig Intestine and Analysis of the Influence of Probiotic Enterococcus Faecium during an Escherichia Coli Challenge. Immunol Invest 2017; 46:742-757. [DOI: 10.1080/08820139.2017.1360341] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Martina Kern
- Department of Veterinary Medicine, Institute of Veterinary Physiology, Freie Universitaet Berlin, Berlin, Germany
| | - Jörg R Aschenbach
- Department of Veterinary Medicine, Institute of Veterinary Physiology, Freie Universitaet Berlin, Berlin, Germany
| | - Karsten Tedin
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universitaet Berlin, Berlin, Germany
| | - Robert Pieper
- Department of Veterinary Medicine, Institute of Animal Nutrition, Freie Universitaet Berlin, Berlin, Germany
| | - Henriette Loss
- Department of Veterinary Medicine, Institute of Veterinary Physiology, Freie Universitaet Berlin, Berlin, Germany
| | - Ulrike Lodemann
- Department of Veterinary Medicine, Institute of Veterinary Physiology, Freie Universitaet Berlin, Berlin, Germany
| |
Collapse
|
33
|
Schlieve CR, Fowler KL, Thornton M, Huang S, Hajjali I, Hou X, Grubbs B, Spence JR, Grikscheit TC. Neural Crest Cell Implantation Restores Enteric Nervous System Function and Alters the Gastrointestinal Transcriptome in Human Tissue-Engineered Small Intestine. Stem Cell Reports 2017; 9:883-896. [PMID: 28803915 PMCID: PMC5599241 DOI: 10.1016/j.stemcr.2017.07.017] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 01/20/2023] Open
Abstract
Acquired or congenital disruption in enteric nervous system (ENS) development or function can lead to significant mechanical dysmotility. ENS restoration through cellular transplantation may provide a cure for enteric neuropathies. We have previously generated human pluripotent stem cell (hPSC)-derived tissue-engineered small intestine (TESI) from human intestinal organoids (HIOs). However, HIO-TESI fails to develop an ENS. The purpose of our study is to restore ENS components derived exclusively from hPSCs in HIO-TESI. hPSC-derived enteric neural crest cell (ENCC) supplementation of HIO-TESI establishes submucosal and myenteric ganglia, repopulates various subclasses of neurons, and restores neuroepithelial connections and neuron-dependent contractility and relaxation in ENCC-HIO-TESI. RNA sequencing identified differentially expressed genes involved in neurogenesis, gliogenesis, gastrointestinal tract development, and differentiated epithelial cell types when ENS elements are restored during in vivo development of HIO-TESI. Our findings validate an effective approach to restoring hPSC-derived ENS components in HIO-TESI and may implicate their potential for the treatment of enteric neuropathies.
Collapse
Affiliation(s)
- Christopher R Schlieve
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute at Children's Hospital Los Angeles, 4650 W. Sunset Boulevard, MS#100, Los Angeles, CA 90027, USA; Department of Surgery, Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Kathryn L Fowler
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute at Children's Hospital Los Angeles, 4650 W. Sunset Boulevard, MS#100, Los Angeles, CA 90027, USA
| | - Matthew Thornton
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Sha Huang
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ibrahim Hajjali
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute at Children's Hospital Los Angeles, 4650 W. Sunset Boulevard, MS#100, Los Angeles, CA 90027, USA
| | - Xiaogang Hou
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute at Children's Hospital Los Angeles, 4650 W. Sunset Boulevard, MS#100, Los Angeles, CA 90027, USA
| | - Brendan Grubbs
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Tracy C Grikscheit
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute at Children's Hospital Los Angeles, 4650 W. Sunset Boulevard, MS#100, Los Angeles, CA 90027, USA; Department of Surgery, Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA.
| |
Collapse
|
34
|
Inflammasomes and intestinal inflammation. Mucosal Immunol 2017; 10:865-883. [PMID: 28401932 DOI: 10.1038/mi.2017.19] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/19/2017] [Indexed: 02/04/2023]
Abstract
The inflammasome is a cytosolic multi-protein innate immune rheostat, sensing a variety of endogenous and environmental stimuli, and regulating homeostasis or damage control. In the gastrointestinal tract, inflammasomes orchestrate immune tolerance to microbial and potentially food-related signals or drive the initiation of inflammatory responses to invading pathogens. When inadequately regulated, intestinal inflammasome activation leads to a perpetuated inflammatory response leading to immune pathology and tissue damage. In this review, we present the main features of the predominant types of inflammasomes participating in intestinal homeostasis and inflammation. We then discuss current controversies and open questions related to their functions and implications in disease, highlighting how pathological inflammasome over-activation or impaired function impact gut homeostasis, the microbiome ecosystem, and the propensity to develop gut-associated diseases. Collectively, understanding of the molecular basis of intestinal inflammasome signaling may be translated into clinical manipulation of this fundamental pathway as a potential immune modulatory therapeutic intervention.
Collapse
|
35
|
NLRP6: A Multifaceted Innate Immune Sensor. Trends Immunol 2017; 38:248-260. [PMID: 28214100 DOI: 10.1016/j.it.2017.01.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/31/2016] [Accepted: 01/12/2017] [Indexed: 01/27/2023]
Abstract
NLRP6, a member of the nucleotide-binding domain, leucine-rich repeat-containing (NLR) innate immune receptor family, regulates inflammation and host defense against microorganisms. Similar to other NLRs, NLRP6 not only participates in inflammasome formation, but is also involved in nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK) signaling regulation and facilitation of gastrointestinal antiviral effector functions. Additionally, NLRP6 contributes to the regulation of mucus secretion and antimicrobial peptide production, thereby impacting intestinal microbial colonization and associated microbiome-related infectious, autoinflammatory, metabolic, and neoplastic diseases. However, several of the mechanisms attributed to the functions of NLRP6 remain debatable, leaving open questions as to the relevant molecular mechanisms and interacting partners, and putative human relevance. We herein discuss recent findings related to NLRP6 activity, while highlighting outstanding questions and future perspectives in elucidating its roles in health and disease.
Collapse
|
36
|
Gremel G, Djureinovic D, Niinivirta M, Laird A, Ljungqvist O, Johannesson H, Bergman J, Edqvist PH, Navani S, Khan N, Patil T, Sivertsson Å, Uhlén M, Harrison DJ, Ullenhag GJ, Stewart GD, Pontén F. A systematic search strategy identifies cubilin as independent prognostic marker for renal cell carcinoma. BMC Cancer 2017; 17:9. [PMID: 28052770 PMCID: PMC5215231 DOI: 10.1186/s12885-016-3030-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/23/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND There is an unmet clinical need for better prognostic and diagnostic tools for renal cell carcinoma (RCC). METHODS Human Protein Atlas data resources, including the transcriptomes and proteomes of normal and malignant human tissues, were searched for RCC-specific proteins and cubilin (CUBN) identified as a candidate. Patient tissue representing various cancer types was constructed into a tissue microarray (n = 940) and immunohistochemistry used to investigate the specificity of CUBN expression in RCC as compared to other cancers. Two independent RCC cohorts (n = 181; n = 114) were analyzed to further establish the sensitivity of CUBN as RCC-specific marker and to explore if the fraction of RCCs lacking CUBN expression could predict differences in patient survival. RESULTS CUBN was identified as highly RCC-specific protein with 58% of all primary RCCs staining positive for CUBN using immunohistochemistry. In venous tumor thrombi and metastatic lesions, the frequency of CUBN expression was increasingly lost. Clear cell RCC (ccRCC) patients with CUBN positive tumors had a significantly better prognosis compared to patients with CUBN negative tumors, independent of T-stage, Fuhrman grade and nodal status (HR 0.382, CI 0.203-0.719, P = 0.003). CONCLUSIONS CUBN expression is highly specific to RCC and loss of the protein is significantly and independently associated with poor prognosis. CUBN expression in ccRCC provides a promising positive prognostic indicator for patients with ccRCC. The high specificity of CUBN expression in RCC also suggests a role as a new diagnostic marker in clinical cancer differential diagnostics to confirm or rule out RCC.
Collapse
Affiliation(s)
- Gabriela Gremel
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dijana Djureinovic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marjut Niinivirta
- Department of Oncology, Radiology and Radiation Science, Uppsala University, Uppsala, Sweden
| | - Alexander Laird
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK.,Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | | | - Julia Bergman
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | | | - Åsa Sivertsson
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | | | - Gustav J Ullenhag
- Department of Oncology, Radiology and Radiation Science, Uppsala University, Uppsala, Sweden
| | - Grant D Stewart
- Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Academic Urology Group, University of Cambridge, Box 43, Addenbrooke's Hospital, Cambridge Biomedical Campus, Hill's Road, CB2 0QQ, Cambridge, UK
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds Väg 20, SE-751 85, Uppsala, Sweden.
| |
Collapse
|
37
|
Levy M, Thaiss CA, Zeevi D, Dohnalová L, Zilberman-Schapira G, Mahdi JA, David E, Savidor A, Korem T, Herzig Y, Pevsner-Fischer M, Shapiro H, Christ A, Harmelin A, Halpern Z, Latz E, Flavell RA, Amit I, Segal E, Elinav E. Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling. Cell 2016; 163:1428-43. [PMID: 26638072 DOI: 10.1016/j.cell.2015.10.048] [Citation(s) in RCA: 664] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 10/06/2015] [Accepted: 10/13/2015] [Indexed: 02/06/2023]
Abstract
Host-microbiome co-evolution drives homeostasis and disease susceptibility, yet regulatory principles governing the integrated intestinal host-commensal microenvironment remain obscure. While inflammasome signaling participates in these interactions, its activators and microbiome-modulating mechanisms are unknown. Here, we demonstrate that the microbiota-associated metabolites taurine, histamine, and spermine shape the host-microbiome interface by co-modulating NLRP6 inflammasome signaling, epithelial IL-18 secretion, and downstream anti-microbial peptide (AMP) profiles. Distortion of this balanced AMP landscape by inflammasome deficiency drives dysbiosis development. Upon fecal transfer, colitis-inducing microbiota hijacks this microenvironment-orchestrating machinery through metabolite-mediated inflammasome suppression, leading to distorted AMP balance favoring its preferential colonization. Restoration of the metabolite-inflammasome-AMP axis reinstates a normal microbiota and ameliorates colitis. Together, we identify microbial modulators of the NLRP6 inflammasome and highlight mechanisms by which microbiome-host interactions cooperatively drive microbial community stability through metabolite-mediated innate immune modulation. Therefore, targeted "postbiotic" metabolomic intervention may restore a normal microenvironment as treatment or prevention of dysbiosis-driven diseases.
Collapse
Affiliation(s)
- Maayan Levy
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Christoph A Thaiss
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lenka Dohnalová
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Jemal Ali Mahdi
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel; Ben Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alon Savidor
- The Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tal Korem
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yonatan Herzig
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Hagit Shapiro
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anette Christ
- Institute of Innate Immunity, University of Bonn, Bonn 53127, Germany; Department of Medicine, University of Massachusetts, Worcester, MA 01605, USA
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zamir Halpern
- Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Digestive Center, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel
| | - Eicke Latz
- Institute of Innate Immunity, University of Bonn, Bonn 53127, Germany; Department of Medicine, University of Massachusetts, Worcester, MA 01605, USA
| | - Richard A Flavell
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
38
|
Alipour M, Zaidi D, Valcheva R, Jovel J, Martínez I, Sergi C, Walter J, Mason AL, Wong GKS, Dieleman LA, Carroll MW, Huynh HQ, Wine E. Mucosal Barrier Depletion and Loss of Bacterial Diversity are Primary Abnormalities in Paediatric Ulcerative Colitis. J Crohns Colitis 2016; 10:462-71. [PMID: 26660940 PMCID: PMC4946763 DOI: 10.1093/ecco-jcc/jjv223] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/19/2015] [Accepted: 12/03/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Ulcerative colitis [UC] is associated with colonic mucosa barrier defects and bacterial dysbiosis, but these features may simply be the result of inflammation. Therefore, we sought to assess whether these features are inherently abrogated in the terminal ileum [TI] of UC patients, where inflammation is absent. METHODS TI biopsies from paediatric inflammatory bowel disease [IBD] subsets [Crohn's disease [CD; n = 13] and UC [n = 10]], and non-IBD disease controls [n = 12] were histologically graded, and alcian blue/periodic acid-Schiff stained biopsies were quantified. The mucosal barrier was assessed for mucin [MUC2], immunoglobulin [Ig]A, IgG, and total bacteria (fluorescence in-situ hybridisation [FISH probe EUB338]) by immunofluorescence. The regulation of mucin secretion was investigated by NLRP6 gene expression and immunofluorescence. The composition of the active mucosa-associated microbiota was explored by sequencing the 16S rRNA amplicon generated from total RNA. RESULTS Despite the absence of ileitis, UC patients displayed ileal barrier depletion illustrated by reductions in mucin-containing goblet cells and mucin production and altered epithelial NLRP6 expression. In both CD patients with ileitis and UC patients with normal histology, bacteria coated with IgA and IgG penetrated the TI mucin layer. Biopsy 16S rRNA sequencing revealed a reduction in α-diversity by three methods [Shannon, Simpson, and Equitability indices] between UC and non-IBD paediatric patients. CONCLUSIONS These findings suggest an underlying defect in the UC-afflicted intestinal tract even in the absence of inflammation, implicating barrier and microbial changes as primary abnormalities in UC that may play a causative role in disease development.
Collapse
Affiliation(s)
- Misagh Alipour
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Deenaz Zaidi
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Rosica Valcheva
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Juan Jovel
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Inés Martínez
- Department of Agriculture, Food, and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Consolato Sergi
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Jens Walter
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada Department of Agriculture, Food, and Nutritional Science, University of Alberta, Edmonton, AB, Canada Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Andrew L Mason
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Gane Ka-Shu Wong
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada Department of Medicine, University of Alberta, Edmonton, AB, Canada Department of Biological Sciences, University of Alberta, Edmonton, Canada Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Levinus A Dieleman
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Matthew W Carroll
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Hien Q Huynh
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Eytan Wine
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
39
|
Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. THE PHARMACOGENOMICS JOURNAL 2016; 17:137-145. [PMID: 26856248 PMCID: PMC4980276 DOI: 10.1038/tpj.2015.93] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 11/06/2015] [Accepted: 11/13/2015] [Indexed: 12/15/2022]
Abstract
Variation in the expression level and activity of genes involved in drug disposition and action (‘pharmacogenes') can affect drug response and toxicity, especially when in tissues of pharmacological importance. Previous studies have relied primarily on microarrays to understand gene expression differences, or have focused on a single tissue or small number of samples. The goal of this study was to use RNA-sequencing (RNA-seq) to determine the expression levels and alternative splicing of 389 Pharmacogenomics Research Network pharmacogenes across four tissues (liver, kidney, heart and adipose) and lymphoblastoid cell lines, which are used widely in pharmacogenomics studies. Analysis of RNA-seq data from 139 different individuals across the 5 tissues (20–45 individuals per tissue type) revealed substantial variation in both expression levels and splicing across samples and tissue types. Comparison with GTEx data yielded a consistent picture. This in-depth exploration also revealed 183 splicing events in pharmacogenes that were previously not annotated. Overall, this study serves as a rich resource for the research community to inform biomarker and drug discovery and use.
Collapse
|
40
|
Dave LA, Hayes M, Montoya CA, Rutherfurd SM, Moughan PJ. Human gut endogenous proteins as a potential source of angiotensin-I-converting enzyme (ACE-I)-, renin inhibitory and antioxidant peptides. Peptides 2016; 76:30-44. [PMID: 26617077 DOI: 10.1016/j.peptides.2015.11.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/07/2015] [Accepted: 11/19/2015] [Indexed: 01/17/2023]
Abstract
It is well known that endogenous bioactive proteins and peptides play a substantial role in the body's first line of immunological defence, immune-regulation and normal body functioning. Further, the peptides derived from the luminal digestion of proteins are also important for body function. For example, within the peptide database BIOPEP (http://www.uwm.edu.pl/biochemia/index.php/en/biopep) 12 endogenous antimicrobial and 64 angiotensin-I-converting enzyme (ACE-I) inhibitory peptides derived from human milk and plasma proteins are listed. The antimicrobial peptide database (http://aps.unmc.edu/AP/main.php) lists over 111 human host-defence peptides. Several endogenous proteins are secreted in the gut and are subject to the same gastrointestinal digestion processes as food proteins derived from the diet. The human gut endogenous proteins (GEP) include mucins, serum albumin, digestive enzymes, hormones, and proteins from sloughed off epithelial cells and gut microbiota, and numerous other secreted proteins. To date, much work has been carried out regarding the health altering effects of food-derived bioactive peptides but little attention has been paid to the possibility that GEP may also be a source of bioactive peptides. In this review, we discuss the potential of GEP to constitute a gut cryptome from which bioactive peptides such as ACE-I inhibitory, renin inhibitory and antioxidant peptides may be derived.
Collapse
Affiliation(s)
- Lakshmi A Dave
- Massey Institute of Food Science and Technology, Massey University, Palmerston North, New Zealand; Teagasc, The Irish Agricultural and Food Development Authority, Food BioSciences Department, Ashtown, D 15 Dublin, Ireland
| | - Maria Hayes
- Teagasc, The Irish Agricultural and Food Development Authority, Food BioSciences Department, Ashtown, D 15 Dublin, Ireland
| | - Carlos A Montoya
- Massey Institute of Food Science and Technology, Massey University, Palmerston North, New Zealand
| | - Shane M Rutherfurd
- Massey Institute of Food Science and Technology, Massey University, Palmerston North, New Zealand.
| | - Paul J Moughan
- Massey Institute of Food Science and Technology, Massey University, Palmerston North, New Zealand
| |
Collapse
|
41
|
Yu NYL, Hallström BM, Fagerberg L, Ponten F, Kawaji H, Carninci P, Forrest ARR, Hayashizaki Y, Uhlén M, Daub CO. Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res 2015; 43:6787-98. [PMID: 26117540 PMCID: PMC4538815 DOI: 10.1093/nar/gkv608] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 12/20/2022] Open
Abstract
Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and Heliscope-sequenced CAGE. Here, we report on the first large-scale complex tissue transcriptome comparison between full-length versus 5'-capped mRNA sequencing data. Overall gene expression correlation was high between the 22 corresponding tissues analyzed (R > 0.8). For genes ubiquitously expressed across all tissues, the two data sets showed high genome-wide correlation (91% agreement), with differences observed for a small number of individual genes indicating the need to update their gene models. Among the identified single-tissue enriched genes, up to 75% showed consensus of 7-fold enrichment in the same tissue in both methods, while another 17% exhibited multiple tissue enrichment and/or high expression variety in the other data set, likely dependent on the cell type proportions included in each tissue sample. Our results show that RNA-Seq and CAGE tissue transcriptome data sets are highly complementary for improving gene model annotations and highlight biological complexities within tissue transcriptomes. Furthermore, integration with image-based protein expression data is highly advantageous for understanding expression specificities for many genes.
Collapse
Affiliation(s)
- Nancy Yiu-Lin Yu
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden Science for Life Laboratory, Karolinska Institute, Solna, 17121, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, 751 85, Sweden
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Mathias Uhlén
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden Science for Life Laboratory, Karolinska Institute, Solna, 17121, Sweden RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| |
Collapse
|
42
|
Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI, Deutsch EW. Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. J Proteome Res 2015; 14:3452-60. [PMID: 26155816 DOI: 10.1021/acs.jproteome.5b00499] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Remarkable progress continues on the annotation of the proteins identified in the Human Proteome and on finding credible proteomic evidence for the expression of "missing proteins". Missing proteins are those with no previous protein-level evidence or insufficient evidence to make a confident identification upon reanalysis in PeptideAtlas and curation in neXtProt. Enhanced with several major new data sets published in 2014, the human proteome presented as neXtProt, version 2014-09-19, has 16,491 unique confident proteins (PE level 1), up from 13,664 at 2012-12 and 15,646 at 2013-09. That leaves 2948 missing proteins from genes classified having protein existence level PE 2, 3, or 4, as well as 616 dubious proteins at PE 5. Here, we document the progress of the HPP and discuss the importance of assessing the quality of evidence, confirming automated findings and considering alternative protein matches for spectra and peptides. We provide guidelines for proteomics investigators to apply in reporting newly identified proteins.
Collapse
Affiliation(s)
- Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan , 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Lydie Lane
- CALIPHO Group, Swiss Institute of Bioinformatics , Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Emma K Lundberg
- SciLifeLab Stockholm and School of Biotechnology, KTH , Karolinska Institutet Science Park, Tomtebodavägen 23, SE-171 65 Solna, Sweden
| | - Ronald C Beavis
- Biochemistry & Medical Genetics, University of Manitoba , Winnipeg, MB, Canada R3T 2N2
| | - Alexey I Nesvizhskii
- Pathology Department, University of Michigan , Medical Science Building 1, M4237, Ann Arbor, Michigan 48109-5602, United States
| | - Eric W Deutsch
- Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| |
Collapse
|
43
|
Sellin ME, Maslowski KM, Maloy KJ, Hardt WD. Inflammasomes of the intestinal epithelium. Trends Immunol 2015; 36:442-50. [PMID: 26166583 DOI: 10.1016/j.it.2015.06.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 06/16/2015] [Accepted: 06/16/2015] [Indexed: 02/08/2023]
Abstract
While the functional importance of inflammasomes in blood-derived cell types is well established, it remains poorly understood how inflammasomes in nonhematopoietic cells contribute to mucosal immunity. Recent studies have revealed functional roles of inflammasomes - particularly NAIP/NLRC4, NLRP6, and noncanonical caspase-4 (caspase-11) - within epithelial cells of the gut in mucosal immune defense, inflammation, and tumorigenesis. Here, we review and discuss these findings in the broader context of tissue compartment-specific mucosal immunity. We propose several models whereby activities of the intestinal epithelial inflammasomes converge on mechanisms to remove compromised epithelial cells, maintain host-microbiota mutualism, and communicate with immune cells of the underlying lamina propria.
Collapse
Affiliation(s)
- Mikael E Sellin
- Institute of Microbiology, ETH Zürich, 8093 Zürich, Switzerland.
| | - Kendle M Maslowski
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kevin J Maloy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | | |
Collapse
|
44
|
Sjöstedt E, Fagerberg L, Hallström BM, Häggmark A, Mitsios N, Nilsson P, Pontén F, Hökfelt T, Uhlén M, Mulder J. Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex. PLoS One 2015; 10:e0130028. [PMID: 26076492 PMCID: PMC4468152 DOI: 10.1371/journal.pone.0130028] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/15/2015] [Indexed: 01/25/2023] Open
Abstract
The mammalian brain is a complex organ composed of many specialized cells, harboring sets of both common, widely distributed, as well as specialized and discretely localized proteins. Here we focus on the human brain, utilizing transcriptomics and public available Human Protein Atlas (HPA) data to analyze brain-enriched (frontal cortex) polyadenylated messenger RNA and long non-coding RNA and generate a genome-wide draft of global and cellular expression patterns of the brain. Based on transcriptomics analysis of altogether 27 tissues, we have estimated that approximately 3% (n=571) of all protein coding genes and 13% (n=87) of the long non-coding genes expressed in the human brain are enriched, having at least five times higher expression levels in brain as compared to any of the other analyzed peripheral tissues. Based on gene ontology analysis and detailed annotation using antibody-based tissue micro array analysis of the corresponding proteins, we found the majority of brain-enriched protein coding genes to be expressed in astrocytes, oligodendrocytes or in neurons with molecular properties linked to synaptic transmission and brain development. Detailed analysis of the transcripts and the genetic landscape of brain-enriched coding and non-coding genes revealed brain-enriched splice variants. Several clusters of neighboring brain-enriched genes were also identified, suggesting regulation of gene expression on the chromatin level. This multi-angle approach uncovered the brain-enriched transcriptome and linked genes to cell types and functions, providing novel insights into the molecular foundation of this highly specialized organ.
Collapse
Affiliation(s)
- Evelina Sjöstedt
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden; Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anna Häggmark
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Nicholas Mitsios
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Pontén
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tomas Hökfelt
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jan Mulder
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| |
Collapse
|
45
|
Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CAK, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F. Tissue-based map of the human proteome. Science 2015; 347:1260419. [PMID: 25613900 DOI: 10.1126/science.1260419] [Citation(s) in RCA: 9022] [Impact Index Per Article: 1002.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mathias Uhlén
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.
| | - Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Per Oksvold
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Adil Mardinoglu
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Evelina Sjöstedt
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - IngMarie Olsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) at Dortmund TU, D-44139 Dortmund, Germany
| | - Emma Lundberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | | | | | - Jacob Odeberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Dijana Djureinovic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Jenny Ottosson Takanen
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Sophia Hober
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Tove Alm
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Holger Berling
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Hanna Tegel
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Jan Mulder
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Johan Rockberg
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Marica Hamsten
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Mattias Forsberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Lukas Persson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fredric Johansson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark. Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| |
Collapse
|
46
|
Blazie SM, Babb C, Wilky H, Rawls A, Park JG, Mangone M. Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles. BMC Biol 2015; 13:4. [PMID: 25601023 PMCID: PMC4343181 DOI: 10.1186/s12915-015-0116-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/12/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Tissue-specific RNA plasticity broadly impacts the development, tissue identity and adaptability of all organisms, but changes in composition, expression levels and its impact on gene regulation in different somatic tissues are largely unknown. Here we developed a new method, polyA-tagging and sequencing (PAT-Seq) to isolate high-quality tissue-specific mRNA from Caenorhabditis elegans intestine, pharynx and body muscle tissues and study changes in their tissue-specific transcriptomes and 3'UTRomes. RESULTS We have identified thousands of novel genes and isoforms differentially expressed between these three tissues. The intestine transcriptome is expansive, expressing over 30% of C. elegans mRNAs, while muscle transcriptomes are smaller but contain characteristic unique gene signatures. Active promoter regions in all three tissues reveal both known and novel enriched tissue-specific elements, along with putative transcription factors, suggesting novel tissue-specific modes of transcription initiation. We have precisely mapped approximately 20,000 tissue-specific polyadenylation sites and discovered that about 30% of transcripts in somatic cells use alternative polyadenylation in a tissue-specific manner, with their 3'UTR isoforms significantly enriched with microRNA targets. CONCLUSIONS For the first time, PAT-Seq allowed us to directly study tissue specific gene expression changes in an in vivo setting and compare these changes between three somatic tissues from the same organism at single-base resolution within the same experiment. We pinpoint precise tissue-specific transcriptome rearrangements and for the first time link tissue-specific alternative polyadenylation to miRNA regulation, suggesting novel and unexplored tissue-specific post-transcriptional regulatory networks in somatic cells.
Collapse
Affiliation(s)
- Stephen M Blazie
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA.
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA.
| | - Cody Babb
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA.
| | - Henry Wilky
- Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA.
| | - Alan Rawls
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA.
- Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA.
| | - Jin G Park
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA.
| | - Marco Mangone
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA.
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA.
- Barrett Honors College, Arizona State University, 751 E Lemon Mall, 1282 Tempe, AZ, USA.
| |
Collapse
|