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1. Full Text In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture
by Miyoshi, Hiroyuki and Stappenbeck, Thaddeus S
Nature Protocols, ISSN 1754-2189, 2013, Volume 8, Issue 12, pp. 2471 - 2482
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2. Full Text Thaddeus Stappenbeck and Hiroshi Kiyono
by Stappenbeck, T and Kiyono, H
CURRENT OPINION IN IMMUNOLOGY, ISSN 0952-7915, 08/2011, Volume 23, Issue 4, pp. 445 - 447
IMMUNOLOGY
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3. Full Text In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture
by Miyoshi, H and Stappenbeck, TS
NATURE PROTOCOLS, ISSN 1754-2189, 12/2013, Volume 8, Issue 12, pp. 2471 - 2482
It is useful to be able to grow enriched populations of stem cells in vitro. Growth of stem cells as tissue spheroids is a key methodology permitting... 
COLON | INTESTINE | EPITHELIUM | LGR5 | BIOCHEMICAL RESEARCH METHODS | Cell Line | Animals | Humans | Mice, Inbred C57BL | HEK293 Cells | Female | Male | Gastrointestinal Tract - cytology | Mice | Stem Cells - cytology | Cell Culture Techniques | Spheroids, Cellular | Gastrointestinal system | Stem cells | Physiological aspects | Genetic research | Genetic aspects | Genetic engineering | Research | Index Medicus
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4. Full Text Accounting for reciprocal host-microbiome interactions in experimental science
by Stappenbeck, Thaddeus S and Virgin, Herbert W
Nature, ISSN 0028-0836, 06/2016, Volume 534, Issue 7606, pp. 191 - 199
Mammals are defined by their metagenome, a combination of host and microbiome genes. This knowledge presents opportunities to further basic biology with... 
METABOLITES | VIROME | INTESTINAL MICROBIOTA | MULTIDISCIPLINARY SCIENCES | BACTERIAL MICROBIOME | MOUSE MODEL | DISEASE | INFECTION | GUT MICROBIOTA | ENTERIC VIRUS | IMMUNODEFICIENCY | Reproducibility of Results | Humans | Male | Sequence Analysis, DNA | Fecal Microbiota Transplantation | Metagenome - genetics | Phenotype | Reference Standards | Animals | Microbiota - genetics | Biomedical Research - methods | Female | Models, Animal | Mice | Research Design | Biomedical Research - standards | Microbiota (Symbiotic organisms) | Physiological research | Research | Microorganisms | Biology | Physiology | Genomes | Mammals | Gene expression | Experiments | Chromosomes | Index Medicus
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5. Full Text IgG “Detoxes” the Intestinal Mucosa
by Eckmann, Lars and Stappenbeck, Thaddeus S
Cell Host & Microbe, ISSN 1931-3128, 05/2015, Volume 17, Issue 5, pp. 538 - 539
Secretory IgA is important in mucosal defense, but other, incompletely understood effectors exist. In this issue of , show that IgG antibodies are produced... 
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6. Full Text In vitro expansion and genetic modification of gastrointestinal stem cells as organoids
by Miyoshi, Hiroyuki and Stappenbeck, Thaddeus S
Nature protocols, ISSN 1754-2189, 12/2013, Volume 8, Issue 12, pp. 2471 - 2482
A key issue for sustainable culture of adult epithelial cells is enrichment for stem cell populations in tissue organoids. Gastrointestinal stem cells can be... 
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7. Full Text Paneth Cell Alterations in the Development and Phenotype of Crohn's Disease
by Stappenbeck, Thaddeus S and McGovern, Dermot P.B
Gastroenterology, ISSN 0016-5085, 02/2017, Volume 152, Issue 2, pp. 322 - 326
Pathogenesis of Crohn's disease (CD) involves immune and microbial dysregulation, induced by environmental factors in genetically susceptible individuals.... 
Paneth Cell | Crohn's Disease | Autophagy | Subtype | SUSCEPTIBILITY | DEFENSINS | NOD2 | VARIANT | ATG16L1 GENE | INTESTINAL INFLAMMATION | PATHOGENESIS | INFLAMMATORY-BOWEL-DISEASE | INHERITANCE | GASTROENTEROLOGY & HEPATOLOGY | Paneth Cells - metabolism | Crohn Disease - genetics | Genetic Predisposition to Disease | Intestinal Mucosa - metabolism | Humans | Crohn Disease - metabolism | Crohn Disease - immunology | Gene-Environment Interaction | Dysbiosis - metabolism | Autophagy - immunology | Carrier Proteins - genetics | Dysbiosis - immunology | Phenotype | Animals | Dysbiosis - genetics | Paneth Cells - immunology | Intestinal Mucosa - immunology | Mice | Autophagy - genetics | Autophagy-Related Proteins - genetics | Disease susceptibility | Genetic aspects | Gastrointestinal diseases | Index Medicus | Abridged Index Medicus
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8. Full Text Wnt5a Potentiates TGF-β Signaling to Promote Colonic Crypt Regeneration After Tissue Injury
by Hiroyuki Miyoshi and Rieko Ajima and Christine T. Luo and Terry P. Yamaguchi and Thaddeus S. Stappenbeck
Science, ISSN 0036-8075, 10/2012, Volume 338, Issue 6103, pp. 108 - 113
Reestablishing homeostasis after tissue damage depends on the proper organization of stem cells and their progeny, though the repair mechanisms are unclear.... 
Regeneration | Messenger RNA | Organoids | Epithelial cells | Crypts | Stromal cells | REPORTS | Stem cells | Homeostasis | Ligands | Endothelial cells | STEM-CELLS | IN-VITRO | GENE | EPITHELIUM | WNT/BETA-CATENIN | MULTIDISCIPLINARY SCIENCES | MOUSE | NICHE | SMALL-INTESTINE | CELL-CYCLE ARREST | WOUND REPAIR | Wnt Proteins - pharmacology | Colon - physiology | Colon - embryology | Culture Media, Conditioned - pharmacology | Colon - injuries | Stem Cells - cytology | Mesoderm - cytology | Wnt-5a Protein | Cell Movement - physiology | Wnt Proteins - genetics | Intestinal Mucosa - embryology | Homeostasis - drug effects | Wound Healing - drug effects | Mesoderm - embryology | Signal Transduction | Receptor Tyrosine Kinase-like Orphan Receptors - metabolism | Cells, Cultured | Recombinant Proteins - pharmacology | Mice, Knockout | Intestinal Mucosa - physiology | Cell Movement - drug effects | Animals | Homeostasis - physiology | Tamoxifen - pharmacology | Stem Cells - drug effects | Stem Cells - physiology | Cell Proliferation - drug effects | Intestinal Mucosa - injuries | Mice | Wnt Proteins - physiology | Wound Healing - physiology | Transforming Growth Factor beta - metabolism | Index Medicus | Pathogens | Repairing | Maintenance | Injuries
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9. Full Text Paneth Cell Alterations in the Development and Phenotype of Crohn’s Disease
by Stappenbeck, Thaddeus S and McGovern, Dermot P.B
Gastroenterology, ISSN 0016-5085, 2017, Volume 152, Issue 2, pp. 322 - 326
Pathogenesis of Crohn’s disease (CD) involves immune and microbial dysregulation, induced by environmental factors in genetically susceptible individuals.... 
Gastroenterology and Hepatology | Paneth Cell | Crohn's Disease | Autophagy | Subtype | Paneth cell | autophagy | subtype | Crohn’s disease
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10. Full Text Peripheral education of the immune system by colonic commensal microbiota
by Lathrop, Stephanie K and Bloom, Seth M and Rao, Sindhuja M and Nutsch, Katherine and Lio, Chan-Wang and Santacruz, Nicole and Peterson, Daniel A and Stappenbeck, Thaddeus S and Hsieh, Chyi-Song
Nature, ISSN 0028-0836, 10/2011, Volume 478, Issue 7368, pp. 250 - 254
The instruction of the immune system to be tolerant of self, thereby preventing autoimmunity, is facilitated by the education of T cells in a specialized... 
MAINTENANCE | INTESTINAL MICROBIOTA | INFLAMMATION | MULTIDISCIPLINARY SCIENCES | RETINOIC-ACID | REGULATORY T-CELLS | SELF | MICE | DIFFERENTIATION | FOXP3 | REPERTOIRES | Colon - cytology | Immunity, Mucosal - immunology | T-Lymphocytes, Regulatory - metabolism | Receptors, Antigen, T-Cell - metabolism | Mice, Inbred C57BL | Thymus Gland - cytology | Colon - immunology | Mice, Transgenic | Immune System - cytology | T-Lymphocytes, Regulatory - immunology | Animals | Immune Tolerance - immunology | Immune System - immunology | Receptors, Antigen, T-Cell - immunology | Thymus Gland - immunology | Colon - microbiology | Mice | Colitis - immunology | Metagenome - immunology | Colitis - prevention & control | Flow cytometry | Bacteria | Immunology | Bacterial proteins | Rodents | Index Medicus
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11. Full Text IL-6 stimulates intestinal epithelial proliferation and repair after injury
by Kuhn, Kristine A and Manieri, Nicholas A and Liu, Ta-Chiang and Stappenbeck, Thaddeus S
PLoS ONE, ISSN 1932-6203, 12/2014, Volume 9, Issue 12, pp. e114195 - e114195
IL-6 is a pleiotropic cytokine often associated with inflammation. Inhibition of this pathway has led to successful treatment of rheumatoid arthritis, but one... 
RHEUMATOID-ARTHRITIS | COLON-CANCER | INTERLEUKIN-6 RECEPTOR | CELLS | INFLAMMATORY-BOWEL-DISEASE | CROHNS-DISEASE | MULTIDISCIPLINARY SCIENCES | MOUSE MODEL | RANDOMIZED-TRIAL | NECROSIS-FACTOR-ALPHA | CLINICAL-RELEVANCE | Inflammation - pathology | Intestinal Mucosa - metabolism | Epithelial Cells - metabolism | Humans | Apoptosis - genetics | Colitis - pathology | Intestines - metabolism | Inflammatory Bowel Diseases - metabolism | Intestinal Mucosa - growth & development | Inflammation - metabolism | T-Lymphocytes - metabolism | Inflammatory Bowel Diseases - pathology | T-Lymphocytes - pathology | Wound Healing - genetics | Disease Models, Animal | Cell Proliferation - genetics | Interleukin-6 - genetics | Colon - pathology | Intestines - growth & development | Intestines - injuries | Epithelial Cells - pathology | Inflammation - immunology | Colon - metabolism | Animals | Biopsy | Colitis - metabolism | T-Lymphocytes - immunology | Intestinal Mucosa - injuries | Mice | Rheumatoid factor | Inflammation | Colitis | Cytokines | Analysis | Apoptosis | Animal models | Wound healing | Perforation | Arthritis | Interleukin 6 | Lymphocytes | Intestine | Rheumatoid arthritis | Surgery | Colon | Inhibition | Repair | Injuries | Index Medicus
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12. Full Text Su1832 – Inhibition of Intestinal Epithelial Cell Pyroptosis and Associated Mucosal Barrier Defects is a Potential Therapeutic Mechanism of Action for Mesalamine in Ibd
by Davis, Elisabeth M and Zhang, Di and Glover, Sarah C and Stappenbeck, Thaddeus S and Wang, Shanzi and Liu, Julia J
Gastroenterology, ISSN 0016-5085, 05/2019, Volume 156, Issue 6, pp. S-627 - S-627
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13. Full Text Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays
by VanDussen, Kelli L and Marinshaw, Jeffrey M and Shaikh, Nurmohammad and Miyoshi, Hiroyuki and Moon, Clara and Tarr, Phillip I and Ciorba, Matthew A and Stappenbeck, Thaddeus S
Gut, ISSN 0017-5749, 06/2015, Volume 64, Issue 6, pp. 911 - 920
Objective The technology for the growth of human intestinal epithelial cells is rapidly progressing. An exciting possibility is that this system could serve as... 
DIARRHEA | CROHNS-DISEASE | INTESTINAL STEM-CELLS | PEYERS-PATCHES | CELL BIOLOGY | MUCUS LAYERS | EPITHELIAL CELLS | INTESTINAL EPITHELIUM | ESCHERICHIA-COLI STRAINS | INFLAMMATORY-BOWEL-DISEASE | COLI | IN-VITRO EXPANSION | ILEAL MUCOSA | EXPLANT CULTURE | DIFFERENTIATION | GASTROENTEROLOGY & HEPATOLOGY | Cell Line | Reproducibility of Results | Humans | Cells, Cultured | RNA, Messenger - analysis | Biological Assay - methods | Genetic Markers | Intestinal Mucosa - microbiology | Cell Culture Techniques - methods | Bacterial Adhesion | Intestinal Mucosa - cytology | Culture Media, Conditioned | Animals | Analysis of Variance | Rectum - cytology | Biopsy | Epithelial Cells - microbiology | Cell Differentiation | Mice | Epithelial Cells - cytology | Ileum - cytology | Spheroids, Cellular | Host-bacteria relationships | Research | Epithelial cells | Analysis | Cell culture | E coli | Stem cells | Bacteria | Infections | Endoscopy | Small intestine | Patients | Methods | Index Medicus | Abridged Index Medicus | pathogen | infection | mucus layer | diarrhea | inflammatory bowel disease | organoid
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14. Full Text A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility
by Desai, Mahesh S and Seekatz, Anna M and Koropatkin, Nicole M and Kamada, Nobuhiko and Hickey, Christina A and Wolter, Mathis and Pudlo, Nicholas A and Kitamoto, Sho and Terrapon, Nicolas and Muller, Arnaud and Young, Vincent B and Henrissat, Bernard and Wilmes, Paul and Stappenbeck, Thaddeus S and Núñez, Gabriel and Martens, Eric C
Cell, ISSN 0092-8674, 11/2016, Volume 167, Issue 5, pp. 1339 - 1353.e21
Despite the accepted health benefits of consuming dietary fiber, little is known about the mechanisms by which fiber deprivation impacts the gut microbiota and... 
microbiota | polysaccharides | gylcans | bacteroides | mucus layer | mucin | Akkermansia | Citrobacter rodentium | dietary fiber | microbiome | CELLS | MUCIN | COLITIS | BIOCHEMISTRY & MOLECULAR BIOLOGY | BACTEROIDES-THETAIOTAOMICRON | MODEL | LAYER | SULFATE-REDUCING BACTERIA | CELL BIOLOGY | Mucin-2 - genetics | Citrobacter rodentium - physiology | Disease Susceptibility | Enterobacteriaceae Infections - microbiology | Escherichia coli | Humans | Dietary Fiber - administration & dosage | Gastrointestinal Microbiome | Male | Intestinal Mucosa - microbiology | Animals | Colitis - microbiology | Germ-Free Life | Female | Colon - microbiology | Mice | Medical colleges | Microbiota (Symbiotic organisms) | Analysis | Bacteria | Glycoproteins | Colitis | Fiber in human nutrition | Polysaccharides | Index Medicus | Life Sciences | Biomolecules | Quantitative Methods | Biochemistry, Molecular Biology
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15. Full Text Developmental Regulation of Intestinal Angiogenesis by Indigenous Microbes Via Paneth Cells
by Thaddeus S. Stappenbeck and Lora V. Hooper and Jeffrey I. Gordon
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 11/2002, Volume 99, Issue 24, pp. 15451 - 15455
The adult mouse intestine contains an intricate vascular network. The factors that control development of this network are poorly understood. Quantitative... 
Angiogenesis | Biological Sciences | Microbiota | Microorganisms | Germ free animals | Epithelial cells | Crypts | Germ free state | Microvessels | Mice | Capillaries | Symbiosis | Gnotobiotics | Ecology | Small intestine | HUMAN COLON | MULTIDISCIPLINARY SCIENCES | MOUSE SMALL-INTESTINE | DEFENSINS | RENEWAL | ecology | EPITHELIUM | PLANT POLYSACCHARIDES | symbiosis | gnotobiotics | FERMENTATION | small intestine | BACTEROIDES-THETAIOTAOMICRON | DIFFERENTIATION | TRANSGENIC MICE | Intestine, Small - ultrastructure | Diphtheria Toxin - pharmacology | Peptide Fragments - pharmacology | Intestinal Mucosa - growth & development | Intestinal Mucosa - cytology | Proteins - secretion | Intestine, Small - growth & development | Cell Differentiation | Imaging, Three-Dimensional | Specific Pathogen-Free Organisms | Intestine, Small - microbiology | Paneth Cells - cytology | Bacteroides - physiology | Mice, Transgenic | Intestine, Small - blood supply | Microvilli | Proteins - genetics | alpha-Defensins - secretion | Cell Lineage | Neovascularization, Physiologic - physiology | Animals | Paneth Cells - secretion | Paneth Cells - drug effects | Germ-Free Life | Genetically modified mice | Anaerobic bacteria | Intestines | Usage | Intestine, Small | Developmental biology | Environmental aspects | Research | Physiological aspects | Neovascularization | Biology | Rodents | Cells | Index Medicus
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16. Full Text Vertically transmitted faecal IgA levels determine extra-chromosomal phenotypic variation
by Moon, Clara and Baldridge, Megan T and Wallace, Meghan A and Burnham, Carey-Ann D and Virgin, Herbert W and Stappenbeck, Thaddeus S
Nature, ISSN 0028-0836, 05/2015, Volume 521, Issue 7550, pp. 90 - 93
The proliferation of genetically modified mouse models has exposed phenotypic variation between investigators and institutions that has been challenging to... 
DEFENSE | TRANSPORT | BACTERIA | T-CELL RESPONSES | PROTEOLYTIC DEGRADATION | IMMUNOGLOBULIN-A | INTESTINAL MICROBIOTA | SECRETORY COMPONENT | MULTIDISCIPLINARY SCIENCES | RECEPTOR | DEFICIENT MICE | Anaerobiosis | Reproducibility of Results | Immunoglobulin A - metabolism | Microbiota - immunology | Chromosomes, Mammalian - genetics | Biomarkers - analysis | Microbiota - drug effects | Male | Secretory Component - metabolism | Immunoglobulin A, Secretory - metabolism | Secretory Component - immunology | Feces - microbiology | Phenotype | Animals | Immunoglobulin A - immunology | Female | Ampicillin - pharmacology | Mice | Mutation | Immunoglobulin A - analysis | Immunoglobulins | Genetic variation | Genetically modified organisms | Physiological aspects | Health aspects | Identification and classification | Medical research | Genotype & phenotype | Bacteria | Rodents | Index Medicus
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