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Ma Q, Meng M, Zhou X, Guo W, Feng K, Huang T, Cai YD. Identification of Key Genes in Fetal Gut Development at Single-Cell Level by Exploiting Machine Learning Techniques. Proteomics 2024:e202400104. [PMID: 39324223 DOI: 10.1002/pmic.202400104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 08/29/2024] [Accepted: 09/11/2024] [Indexed: 09/27/2024]
Abstract
The study of fetal gut development is critical due to its substantial influence on immediate neonatal and long-term adult health. Current research largely focuses on microbiome colonization, gut immunity, and barrier function, alongside the impact of external factors on these phenomena. Limited research has been dedicated to the categorization of developing fetal gut cells. Our study aimed to enhance our understanding of fetal gut development by employing advanced machine-learning techniques on single-cell sequencing data. This dataset consisted of 62,849 samples, each characterized by 33,694 distinct gene features. Four feature ranking algorithms were utilized to sort features according to their significance, resulting in four feature lists. Then, these lists were fed into an incremental feature selection method to extract essential genes, classification rules, and build efficient classifiers. Several important genes were recognized by multiple feature ranking algorithms, such as FGG, MDK, RBP1, RBP2, IGFBP7, and SPON2. These features were key in differentiating specific developing intestinal cells, including epithelial, immune, mesenchymal, and vasculature cells of the colon, duo jejunum, and ileum cells. The classification rules showed special gene expression patterns on some intestinal cell types and the efficient classifiers can be useful tools for identifying intestinal cells.
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Affiliation(s)
- QingLan Ma
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Mei Meng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - XianChao Zhou
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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2
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Moulder R, Bhosale SD, Viiri K, Lahesmaa R. Comparative proteomics analysis of the mouse mini-gut organoid: insights into markers of gluten challenge from celiac disease intestinal biopsies. Front Mol Biosci 2024; 11:1446822. [PMID: 39263374 PMCID: PMC11387180 DOI: 10.3389/fmolb.2024.1446822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/05/2024] [Indexed: 09/13/2024] Open
Abstract
Introduction Organoid models enable three-dimensional representation of cellular systems, providing flexible and accessible research tools, and can highlight key biomolecules. Such models of the intestinal epithelium can provide significant knowledge for the study of celiac disease and provide an additional context for the nature of markers observed from patient biopsy data. Methods Using LC-MS/MS, the proteomes of the crypt and enterocyte-like states of a mouse mini-gut organoid model were measured. The data were further compared with published biopsy data by comparing the changes induced by gluten challenge after a gluten-free diet. Results and discussion These analyses identified 4,850 protein groups and revealed how 400 putative biomarkers of dietary challenge were differentially expressed in the organoid model. In addition to the extensive changes within the differentiated cells, the data reiterated the disruption of the crypt-villus axis after gluten challenge. The mass spectrometry data are available via ProteomeXchange with the identifier PXD025690.
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Affiliation(s)
- Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Santosh D Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Keijo Viiri
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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3
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Swisa A, Kieckhaefer J, Daniel SG, El-Mekkoussi H, Kolev HM, Tigue M, Jin C, Assenmacher CA, Dohnalová L, Thaiss CA, Karlsson NG, Bittinger K, Kaestner KH. The evolutionarily ancient FOXA transcription factors shape the murine gut microbiome via control of epithelial glycosylation. Dev Cell 2024; 59:2069-2084.e8. [PMID: 38821056 PMCID: PMC11338728 DOI: 10.1016/j.devcel.2024.05.006] [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: 11/16/2022] [Revised: 12/19/2023] [Accepted: 05/09/2024] [Indexed: 06/02/2024]
Abstract
Evolutionary adaptation of multicellular organisms to a closed gut created an internal microbiome differing from that of the environment. Although the composition of the gut microbiome is impacted by diet and disease state, we hypothesized that vertebrates promote colonization by commensal bacteria through shaping of the apical surface of the intestinal epithelium. Here, we determine that the evolutionarily ancient FOXA transcription factors control the composition of the gut microbiome by establishing favorable glycosylation on the colonic epithelial surface. FOXA proteins bind to regulatory elements of a network of glycosylation enzymes, which become deregulated when Foxa1 and Foxa2 are deleted from the intestinal epithelium. As a direct consequence, microbial composition shifts dramatically, and spontaneous inflammatory bowel disease ensues. Microbiome dysbiosis was quickly reversed upon fecal transplant into wild-type mice, establishing a dominant role for the host epithelium, in part mediated by FOXA factors, in controlling symbiosis in the vertebrate holobiont.
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Affiliation(s)
- Avital Swisa
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA
| | - Julia Kieckhaefer
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hilana El-Mekkoussi
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA
| | - Hannah M Kolev
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA
| | - Mark Tigue
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA
| | - Chunsheng Jin
- Department of Medical Biochemistry, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Charles-Antoine Assenmacher
- Comparative Pathology Core, Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Lenka Dohnalová
- Microbiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christoph A Thaiss
- Microbiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Niclas G Karlsson
- Department of Medical Biochemistry, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, 0130 Oslo, Norway
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Department of Genetics and Center for Molecular Studies in Liver and Digestive Diseases, Perelman School of Medicine, University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5156, USA.
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4
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Sekiguchi R, Martin D, Doyle A, Wang S, Yamada K. Salivary Gland Tissue Recombination Can Modify Cell Fate. J Dent Res 2024; 103:755-764. [PMID: 38715201 PMCID: PMC11191754 DOI: 10.1177/00220345241247484] [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] [Indexed: 06/21/2024] Open
Abstract
Although mesenchyme is essential for inducing the epithelium of ectodermal organs, its precise role in organ-specific epithelial fate determination remains poorly understood. To elucidate the roles of tissue interactions in cellular differentiation, we performed single-cell RNA sequencing and imaging analyses on recombined tissues, where mesenchyme and epithelium were switched ex vivo between two types of embryonic mouse salivary glands: the parotid gland (a serous gland) and the submandibular gland (a predominantly mucous gland). We found partial induction of molecules that define gland-specific acinar and myoepithelial cells in recombined salivary epithelium. The parotid epithelium recombined with submandibular mesenchyme began to express mucous acinar genes not intrinsic to the parotid gland. While myoepithelial cells do not normally line parotid acini, newly induced myoepithelial cells densely populated recombined parotid acini. However, mucous acinar and myoepithelial markers continued to be expressed in submandibular epithelial cells recombined with parotid mesenchyme. Consequently, some epithelial cells appeared to be plastic, such that their fate could still be modified in response to mesenchymal signaling, whereas other epithelial cells appeared to be already committed to a specific fate. We also discovered evidence for bidirectional induction: transcriptional changes were observed not only in the epithelium but also in the mesenchyme after heterotypic tissue recombination. For example, parotid epithelium induced the expression of muscle-related genes in submandibular fibroblasts that began to mimic parotid fibroblast gene expression. These studies provide the first comprehensive unbiased molecular characterization of tissue recombination approaches exploring the regulation of cell fate.
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Affiliation(s)
- R. Sekiguchi
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - D. Martin
- Genomics and Computational Biology Core, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - A.D. Doyle
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
- Imaging Core, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - S. Wang
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - K.M. Yamada
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
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5
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Xu C, Fang X, Song Y, Xiang Z, Xu X, Wei X. Transcriptional Control: A Directional Sign at the Crossroads of Adult Hepatic Progenitor Cells' Fates. Int J Biol Sci 2024; 20:3544-3556. [PMID: 38993564 PMCID: PMC11234216 DOI: 10.7150/ijbs.93739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 05/31/2024] [Indexed: 07/13/2024] Open
Abstract
Hepatic progenitor cells (HPCs) have a bidirectional potential to differentiate into hepatocytes and bile duct epithelial cells and constitute a second barrier to liver regeneration in the adult liver. They are usually located in the Hering duct in the portal vein region where various cells, extracellular matrix, cytokines, and communication signals together constitute the niche of HPCs in homeostasis to maintain cellular plasticity. In various types of liver injury, different cellular signaling streams crosstalk with each other and point to the inducible transcription factor set, including FoxA1/2/3, YB-1, Foxl1, Sox9, HNF4α, HNF1α, and HNF1β. These transcription factors exert different functions by binding to specific target genes, and their products often interact with each other, with diverse cascades of regulation in different molecular events that are essential for homeostatic regulation, self-renewal, proliferation, and selective differentiation of HPCs. Furthermore, the tumor predisposition of adult HPCs is found to be significantly increased under transcriptional factor dysregulation in transcriptional analysis, and the altered initial commitment of the differentiation pathway of HPCs may be one of the sources of intrahepatic tumors. Related transcription factors such as HNF4α and HNF1 are expected to be future targets for tumor treatment.
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Affiliation(s)
- Chenhao Xu
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou 310006, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou 310006, China
| | - Xixi Fang
- Hangzhou Normal University, Hangzhou 310006, China
| | - Yisu Song
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou 310006, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou 310006, China
| | - Ze Xiang
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou 310006, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou 310006, China
| | - Xiao Xu
- Zhejiang University School of Medicine, Hangzhou 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou 310006, China
| | - Xuyong Wei
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou 310006, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou 310006, China
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6
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Akinsuyi OS, Xhumari J, Ojeda A, Roesch LFW. Gut permeability among Astronauts during Space missions. LIFE SCIENCES IN SPACE RESEARCH 2024; 41:171-180. [PMID: 38670644 DOI: 10.1016/j.lssr.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/02/2024] [Accepted: 03/13/2024] [Indexed: 04/28/2024]
Abstract
The space environment poses substantial challenges to human physiology, including potential disruptions in gastrointestinal health. Gut permeability has only recently become widely acknowledged for its potential to cause adverse effects on a systemic level, rendering it a critical factor to investigate in the context of spaceflight. Here, we propose that astronauts experience the onset of leaky gut during space missions supported by transcriptomic and metagenomic analysis of human and murine samples. A genetic map contributing to intestinal permeability was constructed from a systematic review of current literature. This was referenced against our re-analysis of three independent transcriptomic datasets which revealed significant changes in gene expression patterns associated with the gut barrier. Specifically, in astronauts during flight, we observed a substantial reduction in the expression genes that are crucial for intestinal barrier function, goblet cell development, gut microbiota modulation, and immune responses. Among rodent spaceflight studies, differential expression of cytokines, chemokines, and genes which regulate mucin production and post-translational modifications suggest a similar dysfunction of intestinal permeability. Metagenomic analysis of feces from two murine studies revealed a notable reduction probiotic, short chain fatty acid-producing bacteria and an increase in the Gram-negative pathogens, including Citrobacter rodentium, Enterobacter cloacea, Klebsiella aerogenes, and Proteus hauseri which promote LPS circulation, a recipe for barrier disruption and systemic inflammatory activation. These findings emphasize the critical need to understand the underlying mechanisms and develop interventions to maintain gastrointestinal health in space.
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Affiliation(s)
- Oluwamayowa S Akinsuyi
- Institute of Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville 32611, FL, USA
| | - Jessica Xhumari
- Institute of Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville 32611, FL, USA
| | - Amanda Ojeda
- Institute of Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville 32611, FL, USA
| | - Luiz F W Roesch
- Institute of Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville 32611, FL, USA.
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7
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Pope HF, Pilmane M, Junga A, Pētersons A. The Assessment of CDX1, IHH, SHH, GATA4, FOXA2, FOXF1 in Congenital Intra-Abdominal Adhesions. Acta Med Litu 2024; 31:109-121. [PMID: 38978864 PMCID: PMC11227690 DOI: 10.15388/amed.2024.31.1.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/17/2024] [Accepted: 03/25/2024] [Indexed: 07/10/2024] Open
Abstract
Congenital abdominal adhesions are a rare condition that can result in a small bowel obstruction at any age, more frequently in pediatric populations. The cause remains unknown, and the importance of aberrant congenital bands is related to the difficulty of diagnosis, and cases of death with late detection have been documented. This research examines the expression of Caudal Type Homeobox 1 (CDX1), Indian Hedgehog (IHH), Sonic Hedgehog (SHH), GATA Binding Protein 4 (GATA4), Forkhead Box A2 (FOXA2) and Forkhead Box F1 (FOXF1) gene expression in human abdominal congenital adhesion fibroblast and endothelium cells by chromogenic in situ hybridization, with the aim of elucidating their potential association with the etiology of congenital intra-abdominal adhesion band development. The potential genes' signals were examined using a semi-quantitative approach. Significant correlations were observed between the expression of CDX1 (p <.001) and SHH (p=0.032) genes in fibroblasts from congenital intra-abdominal adhesions compared to fibroblasts from control peritoneal tissue. Statistically significant very strong correlations were found between the CDX1 and IHH comparing endothelium and fibroblast cells in congenital abdominal adhesion bands. There was no statistically significant difference found in the distribution of IHH, FOXA2, GATA4, and FOXF1 between the fibroblasts and endothelium of the patients compared to the control group. The presence of notable distinctions and diverse associations suggests the potential involvement of numerous morpho-pathogenetic processes in the development of intraabdominal adhesions.
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Affiliation(s)
| | - Māra Pilmane
- Institute of Anatomy and Anthropology, Riga Stradiņš University, Riga, Latvia
| | - Anna Junga
- Institute of Anatomy and Anthropology, Riga Stradiņš University, Riga, Latvia
| | - Aigars Pētersons
- Children’s Clinical University Hospital, Riga Stradiņš University, Riga, Latvia
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8
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Hoffman SE, Dowrey TW, Villacorta Martin C, Bi K, Titchen B, Johri S, DelloStritto L, Patel M, Mackichan C, Inga S, Chen J, Grimaldi G, Napolitano S, Wakiro I, Wu J, Yeung J, Rotem A, Sicinska E, Shannon E, Clancy T, Wang J, Denning S, Brais L, Besson NR, Pfaff KL, Huang Y, Kao KZ, Rodig S, Hornick JL, Vigneau S, Park J, Kulke MH, Chan J, Van Allen EM, Murphy GJ. Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors. SCIENCE ADVANCES 2023; 9:eadd9668. [PMID: 37756410 PMCID: PMC10530100 DOI: 10.1126/sciadv.add9668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/24/2023] [Indexed: 09/29/2023]
Abstract
Neuroendocrine tumors (NETs) are rare cancers that most often arise in the gastrointestinal tract and pancreas. The fundamental mechanisms driving gastroenteropancreatic (GEP)-NET growth remain incompletely elucidated; however, the heterogeneous clinical behavior of GEP-NETs suggests that both cellular lineage dynamics and tumor microenvironment influence tumor pathophysiology. Here, we investigated the single-cell transcriptomes of tumor and immune cells from patients with gastroenteropancreatic NETs. Malignant GEP-NET cells expressed genes and regulons associated with normal, gastrointestinal endocrine cell differentiation, and fate determination stages. Tumor and lymphoid compartments sparsely expressed immunosuppressive targets commonly investigated in clinical trials, such as the programmed cell death protein-1/programmed death ligand-1 axis. However, infiltrating myeloid cell types within both primary and metastatic GEP-NETs were enriched for genes encoding other immune checkpoints, including VSIR (VISTA), HAVCR2 (TIM3), LGALS9 (Gal-9), and SIGLEC10. Our findings highlight the transcriptomic heterogeneity that distinguishes the cellular landscapes of GEP-NET anatomic subtypes and reveal potential avenues for future precision medicine therapeutics.
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Affiliation(s)
- Samantha E. Hoffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Harvard-MIT MD-PhD Program, Harvard Medical School, Boston, MA 02115, USA
- PhD Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Todd W. Dowrey
- Section of Hematology and Medical Oncology, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Carlos Villacorta Martin
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Kevin Bi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Breanna Titchen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- PhD Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Shreya Johri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- PhD Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | | | - Miraj Patel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Colin Mackichan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Stephanie Inga
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Judy Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Grace Grimaldi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sara Napolitano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Isaac Wakiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jingyi Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jason Yeung
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Asaf Rotem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Ewa Sicinska
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Erin Shannon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Thomas Clancy
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jiping Wang
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Denning
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lauren Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Naomi R. Besson
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kathleen L. Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Ying Huang
- Molecular Pathology Core Laboratory, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Katrina Z. Kao
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jason L. Hornick
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sebastien Vigneau
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jihye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthew H. Kulke
- Section of Hematology and Medical Oncology, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
| | - Jennifer Chan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - George J. Murphy
- Section of Hematology and Medical Oncology, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
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9
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Fu X, Pereira R, Liu CC, De Angelis C, Shea MJ, Nanda S, Qin L, Mitchell T, Cataldo ML, Veeraraghavan J, Sethunath V, Giuliano M, Gutierrez C, Győrffy B, Trivedi MV, Cohen O, Wagle N, Nardone A, Jeselsohn R, Rimawi MF, Osborne CK, Schiff R. High FOXA1 levels induce ER transcriptional reprogramming, a pro-metastatic secretome, and metastasis in endocrine-resistant breast cancer. Cell Rep 2023; 42:112821. [PMID: 37467106 DOI: 10.1016/j.celrep.2023.112821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/03/2022] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, the key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estrogen receptor-positive (ER+) breast cancer (BC) metastasis in a xenograft mouse model. Mechanistically, H-FOXA1 reprograms ER-chromatin binding to elicit a core gene signature (CGS) enriched in ER+ endocrine-resistant (EndoR) cells. We identify Secretome14, a CGS subset encoding ER-dependent cancer secretory proteins, as a strong predictor for poor outcomes of ER+ BC. It is elevated in ER+ metastases vs. primary tumors, irrespective of ESR1 mutations. Genomic ER binding near Secretome14 genes is also increased in mutant ER-expressing or mitogen-treated ER+ BC cells and in ER+ metastatic vs. primary tumors, suggesting a convergent pathway including high growth factor receptor signaling in activating pro-metastatic secretome genes. Our findings uncover H-FOXA1-induced ER reprogramming that drives EndoR and metastasis partly via an H-FOXA1/ER-dependent secretome.
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Affiliation(s)
- Xiaoyong Fu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Resel Pereira
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chia-Chia Liu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carmine De Angelis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Martin J Shea
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarmistha Nanda
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lanfang Qin
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tamika Mitchell
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Maria L Cataldo
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Jamunarani Veeraraghavan
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vidyalakshmi Sethunath
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mario Giuliano
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Carolina Gutierrez
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, 1085 Budapest, Hungary; RCNS Cancer Biomarker Research Group, Institute of Enzymology, Magyar Tudósok körútja 2, 1117 Budapest, Hungary
| | - Meghana V Trivedi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacy Practice and Translational Research, University of Houston, Houston, TX 77204, USA; Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, USA
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Agostina Nardone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA
| | - Mothaffar F Rimawi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - C Kent Osborne
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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10
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Zheng Y, Ziman B, Ho AS, Sinha UK, Xu LY, Li EM, Koeffler HP, Berman BP, Lin DC. Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation. Genome Biol 2023; 24:193. [PMID: 37620896 PMCID: PMC10463844 DOI: 10.1186/s13059-023-03035-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND As one of the most common malignancies, esophageal cancer has two subtypes, squamous cell carcinoma and adenocarcinoma, arising from distinct cells-of-origin. Distinguishing cell-type-specific molecular features from cancer-specific characteristics is challenging. RESULTS We analyze whole-genome bisulfite sequencing data on 45 esophageal tumor and nonmalignant samples from both subtypes. We develop a novel sequence-aware method to identify large partially methylated domains (PMDs), revealing profound heterogeneity at both methylation level and genomic distribution of PMDs across tumor samples. We identify subtype-specific PMDs that are associated with repressive transcription, chromatin B compartments and high somatic mutation rate. While genomic locations of these PMDs are pre-established in normal cells, the degree of loss is significantly higher in tumors. We find that cell-type-specific deposition of H3K36me2 may underlie genomic distribution of PMDs. At a smaller genomic scale, both cell-type- and cancer-specific differentially methylated regions (DMRs) are identified for each subtype. Using binding motif analysis within these DMRs, we show that a cell-type-specific transcription factor HNF4A maintains the binding sites that it generates in normal cells, while establishing new binding sites cooperatively with novel partners such as FOSL1 in esophageal adenocarcinoma. Finally, leveraging pan-tissue single-cell and pan-cancer epigenomic datasets, we demonstrate that a substantial fraction of cell-type-specific PMDs and DMRs identified here in esophageal cancer are actually markers that co-occur in other cancers originating from related cell types. CONCLUSIONS These findings advance our understanding of DNA methylation dynamics at various genomic scales in normal and malignant states, providing novel mechanistic insights into cell-type- and cancer-specific epigenetic regulations.
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Affiliation(s)
- Yueyuan Zheng
- Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Benjamin Ziman
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, 2250 Alcazar Street - CSA 207D, Los Angeles, CA, 90033, USA
| | - Allen S Ho
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Uttam K Sinha
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Guangdong, China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Guangdong, China
| | - H Phillip Koeffler
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Benjamin P Berman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - De-Chen Lin
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, USA.
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, 2250 Alcazar Street - CSA 207D, Los Angeles, CA, 90033, USA.
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11
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Miura M, Igarashi M, Isotani R, Nakagawa-Nagahama Y, Kuranami S, Naruse K, Kadowaki T, Yamauchi T. SIRT1 Controls Enteroendocrine Progenitor Cell Proliferation in High-Fat Diet-Fed Mice. Cell Mol Gastroenterol Hepatol 2023; 16:1040-1057. [PMID: 37598893 PMCID: PMC10685171 DOI: 10.1016/j.jcmgh.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
BACKGROUND & AIMS We aimed to investigate how sirtuin 1 (SIRT1), a conserved mammalian Nicotinamide adenine dinucleotide+-dependent protein deacetylase, regulates the number of enteroendocrine cells (EECs). EECs benefit metabolism, and their increase potentially could treat type 2 diabetes and obesity. METHODS We used mice with specific Sirt1 disruption in the intestinal epithelium (VilKO, villin-Cre+, and Sirt1flox/flox mice) or enteroendocrine progenitor cells (EEPCs) (NgnKO, neurogenin 3-Cre+, Sirt1flox/flox mice) and mice with increased SIRT1 activity owing to overexpression (Sir2d mice) or 24-hour fasting. Mice were fed a high-fat diet (HFD), and blood glucagon-like peptide 1 (GLP-1) and glucose levels were measured. Intestinal tissues, EECs, and formed organoids were analyzed using quantitative polymerase chain reaction, immunoblotting, and immunohistochemistry. RESULTS In HFD-fed VilKO and NgnKO mice, an increase in EECs (42.3% and 37.2%), GLP-1- or GLP-2-producing L cells (93.0% and 61.4%), and GLP-1 (85.7% and 109.6%) was observed after glucose loading, explaining the improved metabolic phenotype of HFD-VilKO mice. These increases were associated with up-regulated expression of neurogenin 3 (EEPC marker) in crypts of HFD-VilKO and HFD-NgnKO mice, respectively. Conversely, Sir2d or 24-hour fasted mice showed a decrease in EECs (21.6%), L cells (41.6%), and proliferative progenitor cells. SIRT1 overexpression- or knockdown-mediated change in the progenitor cell proliferation was associated with Wnt/β-catenin activity changes. Notably, Wnt/β-catenin inhibitor completely suppressed EEC and L-cell increases in HFD-VilKO mice or organoids from HFD-VilKO and HFD-NgnKO mice. CONCLUSIONS Intestinal SIRT1 in EECs modulates the EEPC cycle by regulating β-catenin activity and can control the number of EECs in HFD-fed mice, which is a previously unknown role.
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Affiliation(s)
- Masaomi Miura
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaki Igarashi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Biology, Koch Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts.
| | - Ryosuke Isotani
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshiko Nakagawa-Nagahama
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoshi Kuranami
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kyoko Naruse
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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12
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Kolev HM, Kaestner KH. Mammalian Intestinal Development and Differentiation-The State of the Art. Cell Mol Gastroenterol Hepatol 2023; 16:809-821. [PMID: 37507088 PMCID: PMC10520362 DOI: 10.1016/j.jcmgh.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
The development of the mammalian intestine, from its earliest origins as a morphologically uniform sheet of endoderm cells during gastrulation into the complex organ system that is essential for the life of the organism, is a truly fascinating process. During midgestation development, reciprocal interactions between endoderm-derived epithelium and mesoderm-derived mesenchyme enable villification, or the conversion of a radially symmetric pseudostratified epithelium into the functional subdivision of crypts and villi. Once a mature crypt-villus axis is established, proliferation and differentiation of new epithelial cells continue throughout life. Spatially localized signals including the wingless and Int-1, fibroblast growth factor, and Hippo systems, among others, ensure that new cells are being born continuously in the crypt. As cells exit the crypt compartment, a gradient of bone morphogenetic protein signaling limits proliferation to allow for the specification of multiple mature cell types. The first major differentiation decision is dependent on Notch signaling, which specifies epithelial cells into absorptive and secretory lineages. The secretory lineage is subdivided further into Paneth, goblet, tuft, and enteroendocrine cells via a complex network of transcription factors. Although some of the signaling molecules are produced by epithelial cells, critical components are derived from specialized crypt-adjacent mesenchymal cells termed telocytes, which are marked by Forkhead box l1, GLI Family Zinc Finger 1, and platelet-derived growth factor receptor α. The crucial nature of these processes is evidenced by the multitude of intestinal disorders such as colorectal cancer, short-bowel syndrome, and inflammatory bowel disease, which all reflect perturbations of the development and/or differentiation of the intestine.
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Affiliation(s)
- Hannah M Kolev
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Klaus H Kaestner
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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13
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Ansari I, Solé-Boldo L, Ridnik M, Gutekunst J, Gilliam O, Korshko M, Liwinski T, Jickeli B, Weinberg-Corem N, Shoshkes-Carmel M, Pikarsky E, Elinav E, Lyko F, Bergman Y. TET2 and TET3 loss disrupts small intestine differentiation and homeostasis. Nat Commun 2023; 14:4005. [PMID: 37414790 PMCID: PMC10326054 DOI: 10.1038/s41467-023-39512-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
TET2/3 play a well-known role in epigenetic regulation and mouse development. However, their function in cellular differentiation and tissue homeostasis remains poorly understood. Here we show that ablation of TET2/3 in intestinal epithelial cells results in a murine phenotype characterized by a severe homeostasis imbalance in the small intestine. Tet2/3-deleted mice show a pronounced loss of mature Paneth cells as well as fewer Tuft and more Enteroendocrine cells. Further results show major changes in DNA methylation at putative enhancers, which are associated with cell fate-determining transcription factors and functional effector genes. Notably, pharmacological inhibition of DNA methylation partially rescues the methylation and cellular defects. TET2/3 loss also alters the microbiome, predisposing the intestine to inflammation under homeostatic conditions and acute inflammation-induced death. Together, our results uncover previously unrecognized critical roles for DNA demethylation, possibly occurring subsequently to chromatin opening during intestinal development, culminating in the establishment of normal intestinal crypts.
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Affiliation(s)
- Ihab Ansari
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Llorenç Solé-Boldo
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Meshi Ridnik
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Oliver Gilliam
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Maria Korshko
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Timur Liwinski
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- University Psychiatric Clinics Basel, Clinic for Adults, University of Basel, Basel, Switzerland
| | - Birgit Jickeli
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Noa Weinberg-Corem
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Michal Shoshkes-Carmel
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eli Pikarsky
- The Lautenberg Center for Immunology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eran Elinav
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
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14
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Zinina VV, Sauer M, Nigmatullina L, Kreim N, Soshnikova N. TCF7L1 Controls the Differentiation of Tuft Cells in Mouse Small Intestine. Cells 2023; 12:1452. [PMID: 37296573 PMCID: PMC10253002 DOI: 10.3390/cells12111452] [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: 04/27/2023] [Revised: 05/10/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Continuous and rapid renewal of the intestinal epithelium depends on intestinal stem cells (ISCs). A large repertoire of transcription factors mediates the correct maintenance and differentiation of ISCs along either absorptive or secretory lineages. In the present study, we addressed the role of TCF7L1, a negative regulator of WNT signalling, in embryonic and adult intestinal epithelium using conditional mouse mutants. We found that TCF7L1 prevents precocious differentiation of the embryonic intestinal epithelial progenitors towards enterocytes and ISCs. We show that Tcf7l1 deficiency leads to upregulation of the Notch effector Rbp-J, resulting in a subsequent loss of embryonic secretory progenitors. In the adult small intestine, TCF7L1 is required for the differentiation of secretory epithelial progenitors along the tuft cell lineage. Furthermore, we show that Tcf7l1 promotes the differentiation of enteroendocrine D- and L-cells in the anterior small intestine. We conclude that TCF7L1-mediated repression of both Notch and WNT pathways is essential for the correct differentiation of intestinal secretory progenitors.
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Affiliation(s)
- Valeriya V. Zinina
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University, 55131 Mainz, Germany; (V.V.Z.); (M.S.)
| | - Melanie Sauer
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University, 55131 Mainz, Germany; (V.V.Z.); (M.S.)
| | | | - Nastasja Kreim
- Institute of Molecular Biology gGmbH, 55128 Mainz, Germany (N.K.)
| | - Natalia Soshnikova
- Institute for Molecular Medicine and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University, 55131 Mainz, Germany
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15
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Tomoshige K, Stuart WD, Fink-Baldauf IM, Ito M, Tsuchiya T, Nagayasu T, Yamatsuji T, Okada M, Fukazawa T, Guo M, Maeda Y. FOXA2 Cooperates with Mutant KRAS to Drive Invasive Mucinous Adenocarcinoma of the Lung. Cancer Res 2023; 83:1443-1458. [PMID: 37067057 PMCID: PMC10160002 DOI: 10.1158/0008-5472.can-22-2805] [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: 09/04/2022] [Revised: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 04/18/2023]
Abstract
The endoderm-lineage transcription factor FOXA2 has been shown to inhibit lung tumorigenesis in in vitro and xenograft studies using lung cancer cell lines. However, FOXA2 expression in primary lung tumors does not correlate with an improved patient survival rate, and the functional role of FOXA2 in primary lung tumors remains elusive. To understand the role of FOXA2 in primary lung tumors in vivo, here, we conditionally induced the expression of FOXA2 along with either of the two major lung cancer oncogenes, EGFRL858R or KRASG12D, in the lung epithelium of transgenic mice. Notably, FOXA2 suppressed autochthonous lung tumor development driven by EGFRL858R, whereas FOXA2 promoted tumor growth driven by KRASG12D. Importantly, FOXA2 expression along with KRASG12D produced invasive mucinous adenocarcinoma (IMA) of the lung, a fatal mucus-producing lung cancer comprising approximately 5% of human lung cancer cases. In the mouse model in vivo and human lung cancer cells in vitro, FOXA2 activated a gene regulatory network involved in the key mucous transcription factor SPDEF and upregulated MUC5AC, whose expression is critical for inducing IMA. Coexpression of FOXA2 with mutant KRAS synergistically induced MUC5AC expression compared with that induced by FOXA2 alone. ChIP-seq combined with CRISPR interference indicated that FOXA2 bound directly to the enhancer region of MUC5AC and induced the H3K27ac enhancer mark. Furthermore, FOXA2 was found to be highly expressed in primary tumors of human IMA. Collectively, this study reveals that FOXA2 is not only a biomarker but also a driver for IMA in the presence of a KRAS mutation. SIGNIFICANCE FOXA2 expression combined with mutant KRAS drives invasive mucinous adenocarcinoma of the lung by synergistically promoting a mucous transcriptional program, suggesting strategies for targeting this lung cancer type that lacks effective therapies.
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Affiliation(s)
- Koichi Tomoshige
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - William D. Stuart
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Iris M. Fink-Baldauf
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Masaoki Ito
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Tomoshi Tsuchiya
- Department of Surgical Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takeshi Nagayasu
- Department of Surgical Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomoki Yamatsuji
- Department of General Surgery, Kawasaki Medical School, Okayama, Japan
| | - Morihito Okada
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takuya Fukazawa
- Department of General Surgery, Kawasaki Medical School, Okayama, Japan
| | - Minzhe Guo
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yutaka Maeda
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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16
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Liu Y, Yu Z, Zhu L, Ma S, Luo Y, Liang H, Liu Q, Chen J, Guli S, Chen X. Orchestration of MUC2 - The key regulatory target of gut barrier and homeostasis: A review. Int J Biol Macromol 2023; 236:123862. [PMID: 36870625 DOI: 10.1016/j.ijbiomac.2023.123862] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023]
Abstract
The gut mucosa of human is covered by mucus, functioning as a crucial defense line for the intestine against external stimuli and pathogens. Mucin2 (MUC2) is a subtype of secretory mucins generated by goblet cells and is the major macromolecular component of mucus. Currently, there is an increasing interest on the investigations of MUC2, noting that its function is far beyond a maintainer of the mucus barrier. Moreover, numerous gut diseases are associated with dysregulated MUC2 production. Appropriate production level of MUC2 and mucus contributes to gut barrier function and homeostasis. The production of MUC2 is regulated by a series of physiological processes, which are orchestrated by various bioactive molecules, signaling pathways and gut microbiota, etc., forming a complex regulatory network. Incorporating the latest findings, this review provided a comprehensive summary of MUC2, including its structure, significance and secretory process. Furthermore, we also summarized the molecular mechanisms of the regulation of MUC2 production aiming to provide developmental directions for future researches on MUC2, which can act as a potential prognostic indicator and targeted therapeutic manipulation for diseases. Collectively, we elucidated the micro-level mechanisms underlying MUC2-related phenotypes, hoping to offer some constructive guidance for intestinal and overall health of mankind.
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Affiliation(s)
- Yaxin Liu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Zihan Yu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Lanping Zhu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Shuang Ma
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Yang Luo
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Huixi Liang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Qinlingfei Liu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Jihua Chen
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Sitan Guli
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China
| | - Xin Chen
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China; Tianjin Institute of Digestive Disease, Tianjin Medical University General Hospital, Anshan Road 154, Heping District, Tianjin 300052, China.
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17
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Xing Y, Liu Z, Ma X, Zhou C, Wang Y, Yao B, Fu J, Qi Y, Zhao P. Targeted metabolomics analysis identified the role of FOXA1 in the change in glutamate-glutamine metabolic pattern of BaP malignantly transformed 16HBE cells. Toxicol Appl Pharmacol 2023; 461:116402. [PMID: 36702312 DOI: 10.1016/j.taap.2023.116402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023]
Abstract
The carcinogenic mechanism of benzo[a]pyrene (BaP) is far from being elucidated. FOXA1 has been confirmed to play an oncogenic role in BaP-transformed cell THBEc1. To explore the changes in amino acid metabolic patterns, especially glutamate-glutamine (Glu-Gln) metabolic pattern caused by BaP-induced transformation and the possible role FOXA1 might play in it, we compared amino acid metabolic characteristics between THBEc1 cells and control 16HBE cells using a targeted metabolomics method and determined the effects of FOXA1 knockout on the amino acid metabolic pattern using FOXA1 knockout cell THBEc1-ΔFOXA1-c34. The amino acid metabolic patterns of THBEc1 and 16HBE cells were different, which was manifested by the differential consumption of 18 amino acids and the difference in the intracellular content of 21 amino acids. The consumption and intracellular content of Glu and Gln are different between the two types of cells, accompanied by upregulation of FOXA1, GLUL, SLC1A3, SLC1A4, SLC1A5 and SLC6A14, and downregulation of FOXA2 and GPT2 in THBEc1 cells. FOXA1 knockout changed the consumption of 19 amino acids and the intracellular content of 21 amino acids and reversed the metabolic pattern of Glu and the changes in FOXA2, GLUL, SLC1A3 and SLC6A14 in THBEc1 cells. Additionally, FOXA1 knockout inhibited cell proliferation and further increased the dependence of THBEc1 cells on Glu. In conclusion, FOXA1 knockout partially reversed the change in Glu-Gln metabolism caused by BaP-induced transformation by upregulating the expression of GLUL and SLC1A3. Our findings provide a clue for the possible role of FOXA1 in amino acid metabolism regulation.
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Affiliation(s)
- Yunkun Xing
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China
| | - Zhiyu Liu
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China
| | - Xue Ma
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China; Zhejiang Province Center for Disease Control and Prevention, Hangzhou 310051, People's Republic of China
| | - Chuan Zhou
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China
| | - Yu Wang
- National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 10021, People's Republic of China
| | - Biyun Yao
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China
| | - Juanling Fu
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China
| | - Yanmin Qi
- Civil Aviation Medicine Center, Civil Aviation Administration of China, Beijing 10123, People's Republic of China
| | - Peng Zhao
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University Health Science Center, Beijing 100191, People's Republic of China.
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18
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Yu C, Li X, Zhao Y, Hu Y. The role of FOXA family transcription factors in glucolipid metabolism and NAFLD. Front Endocrinol (Lausanne) 2023; 14:1081500. [PMID: 36798663 PMCID: PMC9927216 DOI: 10.3389/fendo.2023.1081500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Abnormal glucose metabolism and lipid metabolism are common pathological processes in many metabolic diseases, such as nonalcoholic fatty liver disease (NAFLD). Many studies have shown that the forkhead box (FOX) protein subfamily FOXA has a role in regulating glucolipid metabolism and is closely related to hepatic steatosis and NAFLD. FOXA exhibits a wide range of functions ranging from the initiation steps of metabolism such as the development of the corresponding metabolic organs and the differentiation of cells, to multiple pathways of glucolipid metabolism, to end-of-life problems of metabolism such as age-related obesity. The purpose of this article is to review and discuss the currently known targets and signal transduction pathways of FOXA in glucolipid metabolism. To provide more experimental evidence and basis for further research and clinical application of FOXA in the regulation of glucolipid metabolism and the prevention and treatment of NAFLD.
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Affiliation(s)
- Chuchu Yu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Institute of Liver Diseases, Shuguang Hospital Affifiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaojing Li
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Institute of Liver Diseases, Shuguang Hospital Affifiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yu Zhao
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Institute of Liver Diseases, Shuguang Hospital Affifiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Yu Zhao, ; Yiyang Hu,
| | - Yiyang Hu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Institute of Liver Diseases, Shuguang Hospital Affifiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Clinical Pharmacology, Shuguang Hospital Affifiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Yu Zhao, ; Yiyang Hu,
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19
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Warren I, Moeller MM, Guiggey D, Chiang A, Maloy M, Ogoke O, Groth T, Mon T, Meamardoost S, Liu X, Thompson S, Szeglowski A, Thompson R, Chen P, Paulmurugan R, Yarmush ML, Kidambi S, Parashurama N. FOXA1/2 depletion drives global reprogramming of differentiation state and metabolism in a human liver cell line and inhibits differentiation of human stem cell-derived hepatic progenitor cells. FASEB J 2023; 37:e22652. [PMID: 36515690 DOI: 10.1096/fj.202101506rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 12/15/2022]
Abstract
FOXA factors are critical members of the developmental gene regulatory network (GRN) composed of master transcription factors (TF) which regulate murine cell fate and metabolism in the gut and liver. How FOXA factors dictate human liver cell fate, differentiation, and simultaneously regulate metabolic pathways is poorly understood. Here, we aimed to determine the role of FOXA2 (and FOXA1 which is believed to compensate for FOXA2) in controlling hepatic differentiation and cell metabolism in a human hepatic cell line (HepG2). siRNA mediated knockdown of FOXA1/2 in HepG2 cells significantly downregulated albumin (p < .05) and GRN TF gene expression (HNF4α, HEX, HNF1ß, TBX3) (p < .05) and significantly upregulated endoderm/gut/hepatic endoderm markers (goosecoid [GSC], FOXA3, and GATA4), gut TF (CDX2), pluripotent TF (NANOG), and neuroectodermal TF (PAX6) (p < .05), all consistent with partial/transient reprograming. shFOXA1/2 targeting resulted in similar findings and demonstrated evidence of reversibility of phenotype. RNA-seq followed by bioinformatic analysis of shFOXA1/2 knockdown HepG2 cells demonstrated 235 significant downregulated genes and 448 upregulated genes, including upregulation of markers for alternate germ layers lineages (cardiac, endothelial, muscle) and neurectoderm (eye, neural). We found widespread downregulation of glycolysis, citric acid cycle, mitochondrial genes, and alterations in lipid metabolism, pentose phosphate pathway, and ketogenesis. Functional metabolic analysis agreed with these findings, demonstrating significantly diminished glycolysis and mitochondrial respiration, with concomitant accumulation of lipid droplets. We hypothesized that FOXA1/2 inhibit the initiation of human liver differentiation in vitro. During human pluripotent stem cells (hPSC)-hepatic differentiation, siRNA knockdown demonstrated de-differentiation and unexpectedly, activation of pluripotency factors and neuroectoderm. shRNA knockdown demonstrated similar results and activation of SOX9 (hepatobiliary). These results demonstrate that FOXA1/2 controls hepatic and developmental GRN, and their knockdown leads to reprogramming of both differentiation and metabolism, with applications in studies of cancer, differentiation, and organogenesis.
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Affiliation(s)
- Iyan Warren
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Michael M Moeller
- Department of Chemical and Biomolecular Engineering, University of Nebraska- Lincoln, Lincoln, Nebraska, USA
| | - Daniel Guiggey
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Alexander Chiang
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Mitchell Maloy
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ogechi Ogoke
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Theodore Groth
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Tala Mon
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Saber Meamardoost
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Xiaojun Liu
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Sarah Thompson
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Antoni Szeglowski
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ryan Thompson
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Peter Chen
- Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ramasamy Paulmurugan
- Department of Radiology, Canary Center for Early Cancer Detection and the Molecular Imaging Program at Stanford, Stanford University, Palo Alto, California, USA
| | - Martin L Yarmush
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Srivatsan Kidambi
- Department of Chemical and Biomolecular Engineering, University of Nebraska- Lincoln, Lincoln, Nebraska, USA
| | - Natesh Parashurama
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Clinical and Translation Research Center (CTRC), University at Buffalo (State University of New York), Buffalo, New York, USA
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20
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Kalhori MR, Soleimani M, Yari K, Moradi M, Kalhori AA. MiR-1290: a potential therapeutic target for regenerative medicine or diagnosis and treatment of non-malignant diseases. Clin Exp Med 2022:10.1007/s10238-022-00854-9. [PMID: 35802264 DOI: 10.1007/s10238-022-00854-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/20/2022] [Indexed: 11/03/2022]
Abstract
MicroRNAs are a set of small non-coding RNAs that could change gene expression with post-transcriptional regulation. MiRNAs have a significant role in regulating molecular signaling pathways and innate and adaptive immune system activity. Moreover, miRNAs can be utilized as a powerful instrument for tissue engineers and regenerative medicine by altering the expression of genes and growth factors. MiR-1290, which was first discovered in human embryonic stem cells, is one of those miRNAs that play an essential role in developing the fetal nervous system. This review aims to discuss current findings on miR-1290 in different human pathologies and determine whether manipulation of miR-1290 could be considered a possible therapeutic strategy to treat different non-malignant diseases. The results of these studies suggest that the regulation of miR-1290 may be helpful in the treatment of some bacterial (leprosy) and viral infections (HIV, influenza A, and Borna disease virus). Also, adjusting the expression of miR-1290 in non-infectious diseases such as celiac disease, necrotizing enterocolitis, polycystic ovary syndrome, pulmonary fibrosis, ankylosing spondylitis, muscle atrophy, sarcopenia, and ischemic heart disease can help to treat these diseases better. In addition to acting as a biomarker for the diagnosis of non-malignant diseases (such as NAFLD, fetal growth, preeclampsia, down syndrome, chronic rhinosinusitis, and oral lichen planus), the miR-1290 can also be used as a valuable instrument in tissue engineering and reconstructive medicine. Consequently, it is suggested that the regulation of miR-1290 could be considered a possible therapeutic target in the treatment of non-malignant diseases in the future.
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Affiliation(s)
- Mohammad Reza Kalhori
- Regenerative Medicine Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Kheirollah Yari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mahmoudreza Moradi
- Regenerative Medicine Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amir Ali Kalhori
- Regenerative Medicine Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
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21
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Enteroendocrine System and Gut Barrier in Metabolic Disorders. Int J Mol Sci 2022; 23:ijms23073732. [PMID: 35409092 PMCID: PMC8998765 DOI: 10.3390/ijms23073732] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 02/06/2023] Open
Abstract
With the continuous rise in the worldwide prevalence of obesity and type 2 diabetes, developing therapies regulating body weight and glycemia has become a matter of great concern. Among the current treatments, evidence now shows that the use of intestinal hormone analogs (e.g., GLP1 analogs and others) helps to control glycemia and reduces body weight. Indeed, intestinal endocrine cells produce a large variety of hormones regulating metabolism, including appetite, digestion, and glucose homeostasis. Herein, we discuss how the enteroendocrine system is affected by local environmental and metabolic signals. These signals include those arising from unbalanced diet, gut microbiota, and the host metabolic organs and their complex cross-talk with the intestinal barrier integrity.
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22
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Tian F, Huang S, Xu W, Chen L, Su J, Ni H, Feng X, Chen J, Wang X, Huang Q. Compound K attenuates hyperglycemia by enhancing glucagon-like peptide-1 secretion through activating TGR5 via the remodeling of gut microbiota and bile acid metabolism. J Ginseng Res 2022; 46:780-789. [PMID: 36312739 PMCID: PMC9597441 DOI: 10.1016/j.jgr.2022.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/25/2022] [Accepted: 03/29/2022] [Indexed: 01/06/2023] Open
Abstract
Background Incretin impairment, characterized by insufficient secretion of L-cell-derived glucagon-like peptide-1 (GLP-1), is a defining step of type 2 diabetes mellitus (T2DM). Ginsenoside compound K (CK) can stimulate GLP-1 secretion; however, the potential mechanism underlying this effect has not been established. Methods CK (40 mg/kg) was administered orally to male db/db mice for 4 weeks. The body weight, oral glucose tolerance, GLP-1 secretion, gut microbiota sequencing, bile acid (BA) profiles, and BA synthesis markers of each subject were then analyzed. Moreover, TGR5 expression was evaluated by immunoblotting and immunofluorescence, and L-cell lineage markers involved in L-cell abundance were analyzed. Results CK ameliorated obesity and impaired glucose tolerance in db/db mice by altering the gut microbiota, especially Ruminococcaceae family, and this changed microbe was positively correlated with secondary BA synthesis. Additionally, CK treatment resulted in the up-regulation of CYP7B1 and CYP27A1 and the down-regulation of CYP8B1, thereby shifting BA biosynthesis from the classical pathway to the alternative pathway. CK altered the BA pool by mainly increasing LCA and DCA. Furthermore, CK induced L-cell number expansion leading to enhanced GLP-1 release through TGR5 activation. These increases were supported by the upregulation of genes governing GLP-1 secretion and L-cell differentiation. Conclusions The results indicate that CK improves glucose homeostasis by increasing L-cell numbers, which enhances GLP-1 release through a mechanism partially mediated by the gut microbiota-BA-TGR5 pathway. Therefore, that therapeutic attempts with CK might be useful for patients with T2DM.
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Affiliation(s)
- Fengyuan Tian
- First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Shuo Huang
- First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Wangda Xu
- First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Lan Chen
- First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jianming Su
- Department of Emergency, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Haixiang Ni
- Department of Endocrinology, First Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, China
| | - Xiaohong Feng
- Department of Endocrinology, First Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, China
| | - Jie Chen
- Department of Endocrinology, First Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, China
| | - Xi Wang
- Central Laboratory, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
- Corresponding author. Central Laboratory, First Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, 310006, China.
| | - Qi Huang
- Department of Endocrinology, First Affiliated Hospital of Zhejiang Chinese Medicine University, Hangzhou, China
- Corresponding author. Department of Endocrinology, First Affiliated Hospital of Zhejiang, Chinese Medicine University. Hangzhou, 310006, China.
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23
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Verma P, Mohanty N, Pruseth B, Sahoo S, Katiyar A, Singh H, Jena SK, Das RR, Som TK, Sahoo SK, Nanda P, Ghosh A. Identification of Candidate Immune System MicroRNAs Differentially Found in Colostrum and Milk Exosomes. Microrna 2022; 11:216-226. [PMID: 35786199 DOI: 10.2174/2211536611666220630102316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/01/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The fetus grows in a sterile womb environment. After birth, the newborn immune system has two immediate hurdles to clear. First immediate suppression of the womb compatible immune system and turn on the immune system of the newborn that can counter the antigenic world. The underlying mechanism of immune fluctuation by milk microRNAs (miRNAs) can be crucial for the treatment of critical or premature newborn. METHODS We collected fourteen samples of each colostrum and mature milk from lactating mothers, four samples of each were used for microarray analysis, and the other ten were used for miRNA expression profiling by real-time PCR. RESULTS From the microarray, 154 differentially expressed miRNAs were identified, whereas 49 miRNAs were revealed as immune-related miRNAs based on a literature study. Among the 49 miRNAs, 33 were already shown as strongly validated immune-related miRNAs (validated by qPCR, Western Blot, and Luciferase assay) and were considered for further analysis. Twenty-two miRNA expressions were analysed by real-time PCR as their Ct values were within considerable limits. Twelve numbers of miRNAs were significantly downregulated in mature milk compared to colostrum, which were again subjected to bioinformatics analysis to predict the biological mechanisms behind the differentially expressed miRNAs. CONCLUSION This study shed light on the human milk exosome miRNA expression dynamics during lactation and their possible role in the gradual skewing of the newborns' immune system. The information is crucial for the development and onset of sepsis in premature newborns in the NICU.
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Affiliation(s)
- Poonam Verma
- Department of Physiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
| | - Niharika Mohanty
- Department of Physiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
| | - Babita Pruseth
- Department of Physiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
| | - Sonali Sahoo
- Department of Physiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
| | - Amit Katiyar
- ICMR-AIIMS Computational Genomics Centre, Division of Biomedical Informatics, Indian Council of Medical Research, Ansari Nagar, New Delhi-110029, India
| | - Harpreet Singh
- ICMR-AIIMS Computational Genomics Centre, Division of Biomedical Informatics, Indian Council of Medical Research, Ansari Nagar, New Delhi-110029, India
| | - Saubhagya Kumar Jena
- Department of Obstetrics & Gynaecology, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
| | - Rashmi Ranjan Das
- Department of Paediatrics, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
| | - Tapas Kumar Som
- Department of Neonatology, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
| | | | - Pranati Nanda
- Department of Physiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
| | - Amit Ghosh
- Department of Physiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
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24
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Ali M, Ribeiro MM, Del Sol A. Computational Methods to Identify Cell-Fate Determinants, Identity Transcription Factors, and Niche-Induced Signaling Pathways for Stem Cell Research. Methods Mol Biol 2022; 2471:83-109. [PMID: 35175592 DOI: 10.1007/978-1-0716-2193-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The large-scale development of high-throughput sequencing technologies has not only allowed the generation of reliable omics data related to various regulatory layers but also the development of novel computational models in the field of stem cell research. These computational approaches have enabled the disentangling of a complex interplay between these interrelated layers of regulation by interpreting large quantities of biomedical data in a systematic way. In the context of stem cell research, network modeling of complex gene-gene interactions has been successfully used for understanding the mechanisms underlying stem cell differentiation and cellular conversion. Notably, it has proven helpful for predicting cell-fate determinants and signaling molecules controlling such processes. This chapter will provide an overview of various computational approaches that rely on single-cell and/or bulk RNA sequencing data for elucidating the molecular underpinnings of cell subpopulation identities, lineage specification, and the process of cell-fate decisions. Furthermore, we discuss how these computational methods provide the right framework for computational modeling of biological systems in order to address long-standing challenges in the stem cell field by guiding experimental efforts in stem cell research and regenerative medicine.
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Affiliation(s)
- Muhammad Ali
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Mariana Messias Ribeiro
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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25
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MLL1 is required for maintenance of intestinal stem cells. PLoS Genet 2021; 17:e1009250. [PMID: 34860830 PMCID: PMC8641872 DOI: 10.1371/journal.pgen.1009250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/30/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic mechanisms are gatekeepers for the gene expression patterns that establish and maintain cellular identity in mammalian development, stem cells and adult homeostasis. Amongst many epigenetic marks, methylation of histone 3 lysine 4 (H3K4) is one of the most widely conserved and occupies a central position in gene expression. Mixed lineage leukemia 1 (MLL1/KMT2A) is the founding mammalian H3K4 methyltransferase. It was discovered as the causative mutation in early onset leukemia and subsequently found to be required for the establishment of definitive hematopoiesis and the maintenance of adult hematopoietic stem cells. Despite wide expression, the roles of MLL1 in non-hematopoietic tissues remain largely unexplored. To bypass hematopoietic lethality, we used bone marrow transplantation and conditional mutagenesis to discover that the most overt phenotype in adult Mll1-mutant mice is intestinal failure. MLL1 is expressed in intestinal stem cells (ISCs) and transit amplifying (TA) cells but not in the villus. Loss of MLL1 is accompanied by loss of ISCs and a differentiation bias towards the secretory lineage with increased numbers and enlargement of goblet cells. Expression profiling of sorted ISCs revealed that MLL1 is required to promote expression of several definitive intestinal transcription factors including Pitx1, Pitx2, Foxa1, Gata4, Zfp503 and Onecut2, as well as the H3K27me3 binder, Bahcc1. These results were recapitulated using conditional mutagenesis in intestinal organoids. The stem cell niche in the crypt includes ISCs in close association with Paneth cells. Loss of MLL1 from ISCs promoted transcriptional changes in Paneth cells involving metabolic and stress responses. Here we add ISCs to the MLL1 repertoire and observe that all known functions of MLL1 relate to the properties of somatic stem cells, thereby highlighting the suggestion that MLL1 is a master somatic stem cell regulator.
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26
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Long Non-coding RNAs: Potential Players in Cardiotoxicity Induced by Chemotherapy Drugs. Cardiovasc Toxicol 2021; 22:191-206. [PMID: 34417760 DOI: 10.1007/s12012-021-09681-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/24/2021] [Indexed: 10/20/2022]
Abstract
One of the most important side effects of chemotherapy is cardiovascular complications, such as cardiotoxicity. Many factors are involved in the pathogenesis of cardiotoxicity; one of the most important of which is long non-coding RNAs (lncRNAs). lncRNA has 200-1000 nucleotides. It is involved in important processes such as cell proliferation, regeneration and apoptosis; today it is used as a prognostic and diagnostic factor. A, various drugs by acting on lncRNAs can affect cells. Therefore, by accurately identifying IncRNAs function, we can play an effective role in preventing the development of cardiotoxicity-induced chemotherapy drugs, and use them as a therapeutic strategy to improve clinical symptoms and increase patient survival.
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27
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A 'tad' of hope in the fight against airway disease. Biochem Soc Trans 2021; 48:2347-2357. [PMID: 33079166 PMCID: PMC7614538 DOI: 10.1042/bst20200745] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 11/17/2022]
Abstract
Xenopus tadpoles have emerged as a powerful in vivo model system to study mucociliary epithelia such as those found in the human airways. The tadpole skin has mucin-secreting cells, motile multi-ciliated cells, ionocytes (control local ionic homeostasis) and basal stem cells. This cellular architecture is very similar to the large airways of the human lungs and represents an easily accessible and experimentally tractable model system to explore the molecular details of mucociliary epithelia. Each of the cell types in the tadpole skin has a human equivalent and a conserved network of genes and signalling pathways for their differentiation has been discovered. Great insight into the function of each of the cell types has been achieved using the Xenopus model and this has enhanced our understanding of airway disease. This simple model has already had a profound impact on the field but, as molecular technologies (e.g. gene editing and live imaging) continue to develop apace, its use for understanding individual cell types and their interactions will likely increase. For example, its small size and genetic tractability make it an ideal model for live imaging of a mucociliary surface especially during environmental challenges such as infection. Further potential exists for the mimicking of human genetic mutations that directly cause airway disease and for the pre-screening of drugs against novel therapeutic targets.
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28
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High Glucose Exposure Impairs L-Cell Differentiation in Intestinal Organoids: Molecular Mechanisms and Clinical Implications. Int J Mol Sci 2021; 22:ijms22136660. [PMID: 34206340 PMCID: PMC8268781 DOI: 10.3390/ijms22136660] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Intestinal organoids are used to analyze the differentiation of enteroendocrine cells (EECs) and to manipulate their density for treating type 2 diabetes. EEC differentiation is a continuous process tightly regulated in the gut by a complex regulatory network. However, the effect of chronic hyperglycemia, in the modulation of regulatory networks controlling identity and differentiation of EECs, has not been analyzed. This study aimed to investigate the effect of glucotoxicity on EEC differentiation in small intestinal organoid platforms. Mouse intestinal organoids were cultured in the presence/absence of high glucose concentrations (35 mM) for 48 h to mimic glucotoxicity. Chronic hyperglycemia impaired the expression of markers related to the differentiation of EEC progenitors (Ngn3) and L-cells (NeuroD1), and it also reduced the expression of Gcg and GLP-1 positive cell number. In addition, the expression of intestinal stem cell markers was reduced in organoids exposed to high glucose concentrations. Our data indicate that glucotoxicity impairs L-cell differentiation, which could be associated with decreased intestinal stem cell proliferative capacity. This study provides the identification of new targets involved in new molecular signaling mechanisms impaired by glucotoxicity that could be a useful tool for the treatment of type 2 diabetes.
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29
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Guo X, Lv J, Xi R. The specification and function of enteroendocrine cells in Drosophila and mammals: a comparative review. FEBS J 2021; 289:4773-4796. [PMID: 34115929 DOI: 10.1111/febs.16067] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022]
Abstract
Enteroendocrine cells (EECs) in both invertebrates and vertebrates derive from intestinal stem cells (ISCs) and are scattered along the digestive tract, where they function in sensing various environmental stimuli and subsequently secrete neurotransmitters or neuropeptides to regulate diverse biological and physiological processes. To fulfill these functions, EECs are specified into multiple subtypes that occupy specific gut regions. With advances in single-cell technology, organoid culture experimental systems, and CRISPR/Cas9-mediated genomic editing, rapid progress has been made toward characterization of EEC subtypes in mammals. Additionally, studies of genetic model organisms-especially Drosophila melanogaster-have also provided insights about the molecular processes underlying EEC specification from ISCs and about the establishment of diverse EEC subtypes. In this review, we compare the regulation of EEC specification and function in mammals and Drosophila, with a focus on EEC subtype characterization, on how internal and external regulators mediate EEC subtype specification, and on how EEC-mediated intra- and interorgan communications affect gastrointestinal physiology and pathology.
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Affiliation(s)
- Xingting Guo
- National Institute of Biological Sciences, Beijing, China
| | - Jiaying Lv
- National Institute of Biological Sciences, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Rongwen Xi
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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30
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Južnić L, Peuker K, Strigli A, Brosch M, Herrmann A, Häsler R, Koch M, Matthiesen L, Zeissig Y, Löscher BS, Nuber A, Schotta G, Neumeister V, Chavakis T, Kurth T, Lesche M, Dahl A, von Mässenhausen A, Linkermann A, Schreiber S, Aden K, Rosenstiel PC, Franke A, Hampe J, Zeissig S. SETDB1 is required for intestinal epithelial differentiation and the prevention of intestinal inflammation. Gut 2021; 70:485-498. [PMID: 32503845 PMCID: PMC7873423 DOI: 10.1136/gutjnl-2020-321339] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/05/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The intestinal epithelium is a rapidly renewing tissue which plays central roles in nutrient uptake, barrier function and the prevention of intestinal inflammation. Control of epithelial differentiation is essential to these processes and is dependent on cell type-specific activity of transcription factors which bind to accessible chromatin. Here, we studied the role of SET Domain Bifurcated Histone Lysine Methyltransferase 1, also known as ESET (SETDB1), a histone H3K9 methyltransferase, in intestinal epithelial homeostasis and IBD. DESIGN We investigated mice with constitutive and inducible intestinal epithelial deletion of Setdb1, studied the expression of SETDB1 in patients with IBD and mouse models of IBD, and investigated the abundance of SETDB1 variants in healthy individuals and patients with IBD. RESULTS Deletion of intestinal epithelial Setdb1 in mice was associated with defects in intestinal epithelial differentiation, barrier disruption, inflammation and mortality. Mechanistic studies showed that loss of SETDB1 leads to de-silencing of endogenous retroviruses, DNA damage and intestinal epithelial cell death. Predicted loss-of-function variants in human SETDB1 were considerably less frequently observed than expected, consistent with a critical role of SETDB1 in human biology. While the vast majority of patients with IBD showed unimpaired mucosal SETDB1 expression, comparison of IBD and non-IBD exomes revealed over-representation of individual rare missense variants in SETDB1 in IBD, some of which are predicted to be associated with loss of function and may contribute to the pathogenesis of intestinal inflammation. CONCLUSION SETDB1 plays an essential role in intestinal epithelial homeostasis. Future work is required to investigate whether rare variants in SETDB1 contribute to the pathogenesis of IBD.
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Affiliation(s)
- Lea Južnić
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany,Center for Regenerative Therapies (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Kenneth Peuker
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany,Center for Regenerative Therapies (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Anne Strigli
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany,Center for Regenerative Therapies (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Mario Brosch
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany,Center for Regenerative Therapies (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Alexander Herrmann
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany,Center for Regenerative Therapies (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael Koch
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany,Center for Regenerative Therapies (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Liz Matthiesen
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany,Center for Regenerative Therapies (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Yvonne Zeissig
- Department of General Pediatrics, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Britt-Sabina Löscher
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alexander Nuber
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig Maximilians University Munich, Munich, Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig Maximilians University Munich, Munich, Germany
| | - Volker Neumeister
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Thomas Kurth
- Center for Molecular and Cellular Bioengineering (CMBC), Technology Platform, Technische Universität (TU) Dresden, Dresden, Germany
| | - Mathias Lesche
- DRESDEN-concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität (TU) Dresden, Dresden, Germany
| | - Andreas Dahl
- DRESDEN-concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität (TU) Dresden, Dresden, Germany
| | - Anne von Mässenhausen
- BIOTEChnology Center, Technische Universität (TU) Dresden, Dresden, Germany,Division of Nephrology, Department of Medicine III, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Andreas Linkermann
- BIOTEChnology Center, Technische Universität (TU) Dresden, Dresden, Germany,Division of Nephrology, Department of Medicine III, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian-Albrechts-University of Kiel, Kiel, Germany,Department of Internal Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian-Albrechts-University of Kiel, Kiel, Germany,Department of Internal Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philip C Rosenstiel
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Jochen Hampe
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany,Center for Regenerative Therapies (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Sebastian Zeissig
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany .,Center for Regenerative Therapies (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
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31
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Hung YH, Huang S, Dame MK, Yu Q, Yu QC, Zeng YA, Camp JG, Spence JR, Sethupathy P. Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model. Nucleic Acids Res 2021; 49:726-744. [PMID: 33406262 PMCID: PMC7826262 DOI: 10.1093/nar/gkaa1204] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/20/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
The establishment of the small intestinal (SI) lineage during human embryogenesis ensures functional integrity of the intestine after birth. The chromatin dynamics that drive SI lineage formation and regional patterning in humans are essentially unknown. To fill this knowledge void, we apply a cutting-edge genomic technology to a state-of-the-art human model of early SI development. Specifically, we leverage chromatin run-on sequencing (ChRO-seq) to define the landscape of active promoters, enhancers and gene bodies across distinct stages of directed differentiation of human pluripotent stem cells into SI spheroids with regional specification. Through comprehensive ChRO-seq analysis we identify candidate stage-specific chromatin activity states, novel markers and enhancer hotspots during the directed differentiation. Moreover, we propose a detailed transcriptional network associated with SI lineage formation or regional patterning. Our ChRO-seq analyses uncover a previously undescribed pattern of enhancer activity and transcription at HOX gene loci underlying SI regional patterning. We also validated this unique HOX dynamics by the analysis of single cell RNA-seq data from human fetal SI. Overall, the results lead to a new proposed working model for the regulatory underpinnings of human SI development, thereby adding a novel dimension to the literature that has relied almost exclusively on non-human models.
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Affiliation(s)
- Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael K Dame
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basal, Basel 4056, Switzerland
| | - Qing C Yu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yi A Zeng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basal, Basel 4056, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4001, Switzerland
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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32
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MicroRNA-194: a novel regulator of glucagon-like peptide-1 synthesis in intestinal L cells. Cell Death Dis 2021; 12:113. [PMID: 33479193 PMCID: PMC7820456 DOI: 10.1038/s41419-020-03366-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/18/2020] [Accepted: 10/09/2020] [Indexed: 12/24/2022]
Abstract
In the status of obesity, the glucagon-like peptide-1 (GLP-1) level usually declines and results in metabolic syndrome. This study aimed to investigate the intracellular mechanism of GLP-1 synthesis in L cells from the perspective of microRNA (miRNA). In the present study, we found that GLP-1 level was down-regulated in the plasma and ileum tissues of obese mice, while the ileac miR-194 expression was up-regulated. In vitro experiments indicated that miR-194 overexpression down-regulated GLP-1 level, mRNA levels of proglucagon gene (gcg) and prohormone convertase 1/3 gene (pcsk1), and the nuclear protein level of beta-catenin (β-catenin). Further investigation confirmed that β-catenin could promote gcg transcription through binding to transcription factor 7-like 2 (TCF7L2). miR-194 suppressed gcg mRNA level via negatively regulating TCF7L2 expression. What’s more, forkhead box a1 (Foxa1) could bind to the promoter of pcsk1 and enhanced its transcription. miR-194 suppressed pcsk1 transcription through targeting Foxa1. Besides, the interference of miR-194 reduced palmitate (PA)-induced cell apoptosis and the anti-apoptosis effect of miR-194 inhibitor was abolished by TCF7L2 knockdown. Finally, in HFD-induced obese mice, the silence of miR-194 significantly elevated GLP-1 level and improved the metabolic symptoms caused by GLP-1 deficiency. To sum up, our study found that miR-194 suppressed GLP-1 synthesis in L cells via inhibiting TCF7L2-mediated gcg transcription and Foxa1-mediated pcsk1 transcription. Meanwhile, miR-194 took part in the PA-induced apoptosis of L cells.
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33
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Fawkner-Corbett D, Antanaviciute A, Parikh K, Jagielowicz M, Gerós AS, Gupta T, Ashley N, Khamis D, Fowler D, Morrissey E, Cunningham C, Johnson PRV, Koohy H, Simmons A. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell 2021; 184:810-826.e23. [PMID: 33406409 PMCID: PMC7864098 DOI: 10.1016/j.cell.2020.12.016] [Citation(s) in RCA: 248] [Impact Index Per Article: 82.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/10/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022]
Abstract
Development of the human intestine is not well understood. Here, we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis, and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe diverse functions for these including as vascular niche cells. We pinpoint the origins of Peyer’s patches and gut-associated lymphoid tissue (GALT) and describe location-specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders. We compile a publicly available online resource, spatio-temporal analysis resource of fetal intestinal development (STAR-FINDer), to facilitate further work. Multimodal atlas of human intestinal development maps 101 cell types onto tissue Charts developmental origins of diverse cellular compartments and their progenitors Functional diversity of fibroblasts in stem cell, vasculature, and GALT formation Resource applied to interrogate pathology of in utero intestinal diseases
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Affiliation(s)
- David Fawkner-Corbett
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK; Academic Paediatric Surgery Unit (APSU), Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Agne Antanaviciute
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Kaushal Parikh
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Marta Jagielowicz
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ana Sousa Gerós
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Tarun Gupta
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Neil Ashley
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Doran Khamis
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Darren Fowler
- Paediatric Pathology, Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Edward Morrissey
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Chris Cunningham
- Colorectal Surgery Department, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Paul R V Johnson
- Academic Paediatric Surgery Unit (APSU), Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Hashem Koohy
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
| | - Alison Simmons
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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34
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Saitou M, Gaylord EA, Xu E, May AJ, Neznanova L, Nathan S, Grawe A, Chang J, Ryan W, Ruhl S, Knox SM, Gokcumen O. Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. Cell Rep 2020; 33:108402. [PMID: 33207190 PMCID: PMC7703872 DOI: 10.1016/j.celrep.2020.108402] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/31/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022] Open
Abstract
Salivary proteins are essential for maintaining health in the oral cavity and proximal digestive tract, and they serve as potential diagnostic markers for monitoring human health and disease. However, their precise organ origins remain unclear. Through transcriptomic analysis of major adult and fetal salivary glands and integration with the saliva proteome, the blood plasma proteome, and transcriptomes of 28+ organs, we link human saliva proteins to their source, identify salivary-gland-specific genes, and uncover fetal- and adult-specific gene repertoires. Our results also provide insights into the degree of gene retention during gland maturation and suggest that functional diversity among adult gland types is driven by specific dosage combinations of hundreds of transcriptional regulators rather than by a few gland-specific factors. Finally, we demonstrate the heterogeneity of the human acinar cell lineage. Our results pave the way for future investigations into glandular biology and pathology, as well as saliva's use as a diagnostic fluid.
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Affiliation(s)
- Marie Saitou
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY, U.S.A; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, U.S.A; Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Viken, Norway
| | - Eliza A Gaylord
- Program in Craniofacial Biology, Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, CA, U.S.A
| | - Erica Xu
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY, U.S.A
| | - Alison J May
- Program in Craniofacial Biology, Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, CA, U.S.A
| | - Lubov Neznanova
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY, U.S.A
| | - Sara Nathan
- Program in Craniofacial Biology, Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, CA, U.S.A
| | - Anissa Grawe
- Program in Craniofacial Biology, Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, CA, U.S.A
| | - Jolie Chang
- Department of Otolaryngology, School of Medicine, University of California, San Francisco, CA, U.S.A
| | - William Ryan
- Department of Otolaryngology, School of Medicine, University of California, San Francisco, CA, U.S.A
| | - Stefan Ruhl
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY, U.S.A.
| | - Sarah M Knox
- Program in Craniofacial Biology, Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, CA, U.S.A.
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY, U.S.A.
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Lazar SB, Pongor L, Li XL, Grammatikakis I, Muys BR, Dangelmaier EA, Redon CE, Jang SM, Walker RL, Tang W, Ambs S, Harris CC, Meltzer PS, Aladjem MI, Lal A. Genome-Wide Analysis of the FOXA1 Transcriptional Network Identifies Novel Protein-Coding and Long Noncoding RNA Targets in Colorectal Cancer Cells. Mol Cell Biol 2020; 40:e00224-20. [PMID: 32839292 PMCID: PMC7556848 DOI: 10.1128/mcb.00224-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/12/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023] Open
Abstract
Differentiation status of tumors is correlated with metastatic potential and malignancy. FOXA1 (forkhead box A1) is a transcription factor known to regulate differentiation in certain tissues. Here, we investigate FOXA1 function in human colorectal cancer (CRC). We found that FOXA1 is robustly expressed in the normal human colon but significantly downregulated in colon adenocarcinoma. Applying FOXA1 chromatin immunoprecipitation coupled with deep sequencing and transcriptome analysis upon FOXA1 knockdown in well-differentiated CRC cells and FOXA1 overexpression in poorly differentiated CRC cells, we identified novel protein-coding and lncRNA genes regulated by FOXA1. Among the numerous novel FOXA1 targets we identified, we focused on CEACAM5, a tumor marker and facilitator of cell adhesion. We show that FOXA1 binds to a distal enhancer downstream of CEACAM5 and strongly activates its expression. Consistent with these data, we show that FOXA1 inhibits anoikis in CRC cells. Collectively, our results uncover novel protein-coding and noncoding targets of FOXA1 and suggest a vital role of FOXA1 in enhancing CEACAM5 expression and anoikis resistance in CRC cells.
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Affiliation(s)
- Sarah B Lazar
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Lorinc Pongor
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Ioannis Grammatikakis
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Bruna R Muys
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Emily A Dangelmaier
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Sang-Min Jang
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Robert L Walker
- Molecular Genetics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Wei Tang
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Stefan Ambs
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Curtis C Harris
- Molecular Genetics and Carcinogenesis Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Paul S Meltzer
- Molecular Genetics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
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36
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Osinski C, Le Gléau L, Poitou C, de Toro-Martin J, Genser L, Fradet M, Soula HA, Leturque A, Blugeon C, Jourdren L, Hubert EL, Clément K, Serradas P, Ribeiro A. Type 2 diabetes is associated with impaired jejunal enteroendocrine GLP-1 cell lineage in human obesity. Int J Obes (Lond) 2020; 45:170-183. [PMID: 33037328 PMCID: PMC7752761 DOI: 10.1038/s41366-020-00694-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/07/2020] [Accepted: 09/26/2020] [Indexed: 12/15/2022]
Abstract
Objectives Altered enteroendocrine cell (EEC) function in obesity and type 2 diabetes is not fully understood. Understanding the transcriptional program that controls EEC differentiation is important because some EEC types harbor significant therapeutic potential for type 2 diabetes. Methods EEC isolation from jejunum of obese individuals with (ObD) or without (Ob) type 2 diabetes was obtained with a new method of cell sorting. EEC transcriptional profiles were established by RNA-sequencing in a first group of 14 Ob and 13 ObD individuals. EEC lineage and densities were studied in the jejunum of a second independent group of 37 Ob, 21 ObD and 22 non obese (NOb) individuals. Results The RNA seq analysis revealed a distinctive transcriptomic signature and a decreased differentiation program in isolated EEC from ObD compared to Ob individuals. In the second independent group of ObD, Ob and NOb individuals a decreased GLP-1 cell lineage and GLP-1 maturation from proglucagon, were observed in ObD compared to Ob individuals. Furthermore, jejunal density of GLP-1-positive cells was significantly reduced in ObD compared to Ob individuals. Conclusions These results highlight that the transcriptomic signature of EEC discriminate obese subjects according to their diabetic status. Furthermore, type 2 diabetes is associated with reduced GLP-1 cell differentiation and proglucagon maturation leading to low GLP-1-cell density in human obesity. These mechanisms could account for the decrease plasma GLP-1 observed in metabolic diseases.
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Affiliation(s)
- Céline Osinski
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approaches, F-75013, Paris, France
| | - Léa Le Gléau
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approaches, F-75013, Paris, France
| | - Christine Poitou
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approaches, F-75013, Paris, France.,Nutrition Department, Pitié-Salpêtrière hospital, Assistance Publique/Hôpitaux de Paris, F-75013, Paris, France
| | - Juan de Toro-Martin
- Sorbonne Université, Université de Paris, INSERM, Cordeliers Research Center, F-75006, Paris, France.,Institute of Nutrition and Functional Foods (INAF), School of Nutrition, Université Laval, Quebec, QC, Canada
| | - Laurent Genser
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approaches, F-75013, Paris, France.,Hepato-Biliary-Pancreatic Gastrointestinal Surgery and Liver Transplantation, Pitié-Salpêtrière Hospital, Assistance Publique/Hôpitaux de Paris, F-75013, Paris, France
| | - Magali Fradet
- Cytometry platform, Institut Cardiometabolism and Nutrition, F-75013, Paris, France.,Institut de Biologie, CIRB, Collège de France, F-75005, Paris, France
| | - Hédi Antoine Soula
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approaches, F-75013, Paris, France
| | - Armelle Leturque
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approaches, F-75013, Paris, France
| | - Corinne Blugeon
- Genomics core facility, Département de biologie, Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Laurent Jourdren
- Genomics core facility, Département de biologie, Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Edwige Ludiwyne Hubert
- Sorbonne Université, Université de Paris, INSERM, Cordeliers Research Center, F-75006, Paris, France.,SERVIER, ADIR, F-92284, Suresnes, cedex, France
| | - Karine Clément
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approaches, F-75013, Paris, France.,Nutrition Department, Pitié-Salpêtrière hospital, Assistance Publique/Hôpitaux de Paris, F-75013, Paris, France
| | - Patricia Serradas
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approaches, F-75013, Paris, France.
| | - Agnès Ribeiro
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approaches, F-75013, Paris, France.
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Kumar V, Mahajan N, Khare P, Kondepudi KK, Bishnoi M. Role of TRPV1 in colonic mucin production and gut microbiota profile. Eur J Pharmacol 2020; 888:173567. [PMID: 32946867 DOI: 10.1016/j.ejphar.2020.173567] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/12/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022]
Abstract
This study focuses on exploring the role of sensory cation channel Transient Receptor Potential channel subfamily Vanilloid 1 (TRPV1) in gut health, specifically mucus production and microflora profile in gut. We employed resiniferatoxin (ultrapotent TRPV1 agonist) induced chemo-denervation model in rats and studied the effects of TRPV1 ablation on colonic mucus secretion patterns. Histological and transcriptional analysis showed substantial decrease in mucus production as well as in expression of genes involved in goblet cell differentiation, mucin production and glycosylation. 16S metagenome analysis revealed changes in abundance of various gut bacteria, including decrease in beneficial bacteria like Lactobacillus spp and Clostridia spp. Also, TRPV1 ablation significantly decreased the levels of short chain fatty acids, i.e. acetate and butyrate. The present study provides first evidence that systemic TRPV1 ablation leads to impairment in mucus production and causes dysbiosis in gut. Further, it suggests to address mucin production and gut microbiota related adverse effects during the development of TRPV1 antagonism/ablation-based therapeutic and preventive strategies.
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Affiliation(s)
- Vijay Kumar
- National Agri-Food Biotechnology Institute (NABI), Knowledge City-Sector 81, SAS Nagar, Punjab, 140306, India; Department of Biotechnology, Panjab University, Sector-25, Chandigarh, 160014, India
| | - Neha Mahajan
- National Agri-Food Biotechnology Institute (NABI), Knowledge City-Sector 81, SAS Nagar, Punjab, 140306, India; Regional Centre for Biotechnology, Faridabad-Gurgaon expressway, Faridabad, Haryana, 121001, India
| | - Pragyanshu Khare
- National Agri-Food Biotechnology Institute (NABI), Knowledge City-Sector 81, SAS Nagar, Punjab, 140306, India
| | - Kanthi Kiran Kondepudi
- National Agri-Food Biotechnology Institute (NABI), Knowledge City-Sector 81, SAS Nagar, Punjab, 140306, India
| | - Mahendra Bishnoi
- National Agri-Food Biotechnology Institute (NABI), Knowledge City-Sector 81, SAS Nagar, Punjab, 140306, India.
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Reizel Y, Morgan A, Gao L, Lan Y, Manduchi E, Waite EL, Wang AW, Wells A, Kaestner KH. Collapse of the hepatic gene regulatory network in the absence of FoxA factors. Genes Dev 2020; 34:1039-1050. [PMID: 32561546 PMCID: PMC7397852 DOI: 10.1101/gad.337691.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/14/2020] [Indexed: 12/18/2022]
Abstract
Here, Reizel et al. investigated the FoxA factor's role in maintaining the regulatory network needed for liver development, and ablated all FoxA genes in the adult mouse liver. They found that loss of FoxA caused rapid and massive reduction in the expression of critical liver genes, and that FoxA proteins are be required for maintaining enhancer activity, chromatin accessibility, nucleosome positioning, and binding of HNF4α. The FoxA transcription factors are critical for liver development through their pioneering activity, which initiates a highly complex regulatory network thought to become progressively resistant to the loss of any individual hepatic transcription factor via mutual redundancy. To investigate the dispensability of FoxA factors for maintaining this regulatory network, we ablated all FoxA genes in the adult mouse liver. Remarkably, loss of FoxA caused rapid and massive reduction in the expression of critical liver genes. Activity of these genes was reduced back to the low levels of the fetal prehepatic endoderm stage, leading to necrosis and lethality within days. Mechanistically, we found FoxA proteins to be required for maintaining enhancer activity, chromatin accessibility, nucleosome positioning, and binding of HNF4α. Thus, the FoxA factors act continuously, guarding hepatic enhancer activity throughout adult life.
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Affiliation(s)
- Yitzhak Reizel
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ashleigh Morgan
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Long Gao
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yemin Lan
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Elisabetta Manduchi
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Eric L Waite
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Amber W Wang
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew Wells
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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39
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Ramos Caetano BF, Baptista Tablas M, Ribeiro Romualdo G, Marchesan Rodrigues MA, Barbisan LF. Early molecular events associated with liver and colon sub-acute responses to 1,2-dimethylhydrazine: Potential implications on preneoplastic and neoplastic lesion development. Toxicol Lett 2020; 329:67-79. [PMID: 32387197 DOI: 10.1016/j.toxlet.2020.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023]
Abstract
This study unveiled the early cellular and molecular events induced by 1,2-dimethylhydrazine (DMH) in the colon and liver and their implications on pre- and neoplastic lesion burden in a late timepoint. Male Wistar rats received four DMH injections (40 mg/kg body weight) for 2 weeks and were sacrificed 24 h (short-term study) or 22 (medium-term study) weeks after the last DMH administration. In the short-term study, DMH led to increased leukocyte (comet assay) and colon (H2AX) genotoxicity, enhanced proliferation (Ki-67) and apoptosis (caspase-3) indexes in both liver and colon. Furthermore, the expression of mRNA (Cat, Gsta1, Gsta2, Gpx1, Gstm1, Sod1, Sod2 and Sod3) and the activity of antioxidant agents were diminished in the colon and liver of DMH-induced rats, eliciting an environment of oxidative stress featuring elevated lipid hydroperoxide levels. Apoptosis effectors were upregulated in the liver (Bax, Casp3 and Fas), and developmental genes were downregulated in both colon and liver (Foxa1, Foxa2, Smad2 and Smad4). In the medium-term study, DMH led to a high number of preneoplastic colonic aberrant crypt foci and tumors (adenomas and invasive adenocarcinomas) but few preneoplastic hepatic glutathione S-transferase (GST-P)-positive foci. Our novel gene expression data highlights overlooked mechanisms in the liver (main metabolizing organ) and colon (main target organ) on toxicity and carcinogenesis induced by repeated doses of DMH, as both organs should be considered in further interventions on the initiation stage of colon carcinogenesis.
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Affiliation(s)
| | - Mariana Baptista Tablas
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Guilherme Ribeiro Romualdo
- Department of Pathology, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | | | - Luís Fernando Barbisan
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil.
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40
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Lund ML, Sorrentino G, Egerod KL, Kroone C, Mortensen B, Knop FK, Reimann F, Gribble FM, Drucker DJ, de Koning EJP, Schoonjans K, Bäckhed F, Schwartz TW, Petersen N. L-Cell Differentiation Is Induced by Bile Acids Through GPBAR1 and Paracrine GLP-1 and Serotonin Signaling. Diabetes 2020; 69:614-623. [PMID: 32041793 PMCID: PMC7224989 DOI: 10.2337/db19-0764] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/22/2020] [Indexed: 12/20/2022]
Abstract
Glucagon-like peptide 1 (GLP-1) mimetics are effective drugs for treatment of type 2 diabetes, and there is consequently extensive interest in increasing endogenous GLP-1 secretion and L-cell abundance. Here we identify G-protein-coupled bile acid receptor 1 (GPBAR1) as a selective regulator of intestinal L-cell differentiation. Lithocholic acid and the synthetic GPBAR1 agonist, L3740, selectively increased L-cell density in mouse and human intestinal organoids and elevated GLP-1 secretory capacity. L3740 induced expression of Gcg and transcription factors Ngn3 and NeuroD1 L3740 also increased the L-cell number and GLP-1 levels and improved glucose tolerance in vivo. Further mechanistic examination revealed that the effect of L3740 on L cells required intact GLP-1 receptor and serotonin 5-hydroxytryptamine receptor 4 (5-HT4) signaling. Importantly, serotonin signaling through 5-HT4 mimicked the effects of L3740, acting downstream of GLP-1. Thus, GPBAR1 agonists and other powerful GLP-1 secretagogues facilitate L-cell differentiation through a paracrine GLP-1-dependent and serotonin-mediated mechanism.
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Affiliation(s)
- Mari Lilith Lund
- Novo Nordisk Foundation Center for Basic Metabolic Research Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Giovanni Sorrentino
- Laboratory of Metabolic Signaling, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kristoffer Lihme Egerod
- Novo Nordisk Foundation Center for Basic Metabolic Research Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chantal Kroone
- Department of Thrombosis and Hemostasis, Leiden University Medical Centre, Leiden, the Netherlands
| | - Brynjulf Mortensen
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Filip Krag Knop
- Novo Nordisk Foundation Center for Basic Metabolic Research Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Frank Reimann
- Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Addenbrooke's Hospital, Cambridge, U.K
| | - Fiona M Gribble
- Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Addenbrooke's Hospital, Cambridge, U.K
| | - Daniel J Drucker
- Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Eelco J P de Koning
- Department of Medicine, Leiden University Medical Centre, Leiden, the Netherlands
- Hubrecht Institute/Koninklijke Nederlandse Akademie van Wetenschappen (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kristina Schoonjans
- Laboratory of Metabolic Signaling, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Fredrik Bäckhed
- Novo Nordisk Foundation Center for Basic Metabolic Research Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Molecular and Clinical Medicine at Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Thue W Schwartz
- Novo Nordisk Foundation Center for Basic Metabolic Research Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Natalia Petersen
- Novo Nordisk Foundation Center for Basic Metabolic Research Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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41
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Tsakmaki A, Fonseca Pedro P, Pavlidis P, Hayee B, Bewick GA. ISX-9 manipulates endocrine progenitor fate revealing conserved intestinal lineages in mouse and human organoids. Mol Metab 2020; 34:157-173. [PMID: 32180555 PMCID: PMC7036449 DOI: 10.1016/j.molmet.2020.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/08/2020] [Accepted: 01/21/2020] [Indexed: 01/17/2023] Open
Abstract
Objective Enteroendocrine cells (EECs) survey the gut luminal environment and coordinate hormonal, immune and neuronal responses to it. They exhibit well-characterised physiological roles ranging from the control of local gut function to whole body metabolism, but little is known regarding the regulatory networks controlling their differentiation, especially in the human gut. The small molecule isoxazole-9 (ISX-9) has been shown to stimulate neuronal and pancreatic beta-cell differentiation, both closely related to EEC differentiation. Our aim was to use ISX-9 as a tool to explore EEC differentiation. Methods We investigated the effects of ISX-9 on EEC differentiation in mouse and human intestinal organoids, using real-time quantitative polymerase chain reaction (RT-qPCR), fluorescent-activated cell sorting, immunostaining and single-cell RNA sequencing. Results ISX-9 increased the number of neurogenin3-RFP (Ngn3)-positive endocrine progenitor cells and upregulated NeuroD1 and Pax4, transcription factors that play roles in mouse EEC specification. Single-cell analysis showed induction of Pax4 expression in a developmentally late Ngn3+ population of cells and potentiation of genes associated with progenitors biased toward serotonin-producing enterochromaffin (EC) cells. Further, we observed enrichment of organoids with functional EC cells that was partly dependent on stimulation of calcium signalling in a population of cells residing outside the crypt base. Inducible Pax4 overexpression, in ileal organoids, uncovered its importance as a component of early human endocrine specification and highlighted the potential existence of two major endocrine lineages, the early appearing enterochromaffin lineage and the later developing peptidergic lineage which contains classical gut hormone cell types. Conclusion Our data provide proof-of-concept for the controlled manipulation of specific endocrine lineages with small molecules, whilst also shedding new light on human EEC differentiation and its similarity to the mouse. Given their diverse roles, understanding endocrine lineage plasticity and its control could have multiple therapeutic implications. ISX-9 promotes flux through the Ngn3 lineage and enriches it with enterochromaffin cells. ISX-9 engages an enterochromaffin biased transcriptional programme in endocrine fated cells. Enterochromaffin bias is partly dependent on calcium signalling in progenitor cells. ISX-9 reveals conserved gut endocrine specification between mouse and human. Pax4 overexpression in human ileum organoids mimics the effects of ISX-9 on EC bias.
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Affiliation(s)
- Anastasia Tsakmaki
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Patricia Fonseca Pedro
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Polychronis Pavlidis
- Centre for Inflammation Biology and Cancer Immunology, King's College London, London, UK
| | - Bu'Hussain Hayee
- Department of Gastroenterology, King's College Hospital NHS Foundation Trust, London, UK
| | - Gavin A Bewick
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK.
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42
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The microbiota programs DNA methylation to control intestinal homeostasis and inflammation. Nat Microbiol 2020; 5:610-619. [PMID: 32015497 DOI: 10.1038/s41564-019-0659-3] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/11/2019] [Indexed: 12/12/2022]
Abstract
Although much research has been done on the diversity of the gut microbiome, little is known about how it influences intestinal homeostasis under normal and pathogenic conditions. Epigenetic mechanisms have recently been suggested to operate at the interface between the microbiota and the intestinal epithelium. We performed whole-genome bisulfite sequencing on conventionally raised and germ-free mice, and discovered that exposure to commensal microbiota induced localized DNA methylation changes at regulatory elements, which are TET2/3-dependent. This culminated in the activation of a set of 'early sentinel' response genes to maintain intestinal homeostasis. Furthermore, we demonstrated that exposure to the microbiota in dextran sodium sulfate-induced acute inflammation results in profound DNA methylation and chromatin accessibility changes at regulatory elements, leading to alterations in gene expression programs enriched in colitis- and colon-cancer-associated functions. Finally, by employing genetic interventions, we show that microbiota-induced epigenetic programming is necessary for proper intestinal homeostasis in vivo.
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43
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Raab JR, Tulasi DY, Wager KE, Morowitz JM, Magness ST, Gracz AD. Quantitative classification of chromatin dynamics reveals regulators of intestinal stem cell differentiation. Development 2020; 147:dev.181966. [PMID: 31862843 DOI: 10.1242/dev.181966] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/27/2019] [Indexed: 12/26/2022]
Abstract
Intestinal stem cell (ISC) plasticity is thought to be regulated by broadly permissive chromatin shared between ISCs and their progeny. Here, we have used a Sox9EGFP reporter to examine chromatin across ISC differentiation. We find that open chromatin regions (OCRs) can be defined as broadly permissive or dynamic in a locus-specific manner, with dynamic OCRs found primarily in loci consistent with distal enhancers. By integrating gene expression with chromatin accessibility at transcription factor (TF) motifs in the context of Sox9EGFP populations, we classify broadly permissive and dynamic chromatin relative to TF usage. These analyses identify known and potential regulators of ISC differentiation via association with dynamic changes in chromatin. Consistent with computational predictions, Id3-null mice exhibit increased numbers of cells expressing the ISC-specific biomarker OLFM4. Finally, we examine the relationship between gene expression and 5-hydroxymethylcytosine (5hmC) in Sox9EGFP populations, which reveals 5hmC enrichment in absorptive lineage-specific genes. Our data demonstrate that intestinal chromatin dynamics can be quantitatively defined in a locus-specific manner, identify novel potential regulators of ISC differentiation and provide a chromatin roadmap for further dissecting cis regulation of cell fate in the intestine.
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Affiliation(s)
- Jesse R Raab
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Deepthi Y Tulasi
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Kortney E Wager
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Jeremy M Morowitz
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Scott T Magness
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, NC 27599, USA.,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, NC 27599, USA.,Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, NC 27599, USA
| | - Adam D Gracz
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599, USA .,Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, NC 27599, USA
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Seiglie MP, Huang L, Cottone P, Sabino V. Role of the PACAP system of the extended amygdala in the acoustic startle response in rats. Neuropharmacology 2019; 160:107761. [PMID: 31493466 PMCID: PMC6842120 DOI: 10.1016/j.neuropharm.2019.107761] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 08/27/2019] [Accepted: 09/03/2019] [Indexed: 11/19/2022]
Abstract
Anxiety-related disorders are the most prevalent mental disorders in the world and they are characterized by abnormal responses to stressors. Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide highly expressed in the extended amygdala, a brain macrostructure involved in the response to threat that includes the central nucleus of the amygdala (CeA) and the bed nucleus of the stria terminalis (BNST). The aim of this series of experiments was to systematically elucidate the role of the PACAP system of the CeA and BNST under both control, unstressed conditions and after the presentation of a stressor in rats. For this purpose, we used the acoustic startle response (ASR), an unconscious response to sudden acoustic stimuli sensitive to changes in stress which can be used as an operationalization of the hypervigilance present in anxiety- and trauma-related disorders. We found that infusion of PACAP, but not the related peptide vasoactive intestinal peptide (VIP), into either the CeA or the BNST causes a dose-dependent increase in ASR. In addition, while infusion of the antagonist PACAP(6-38) into either the CeA or the BNST does not affect ASR in non-stressed conditions, it prevents the sensitization of ASR induced by an acute footshock stress. Finally, we found that footshock stress induces a significant increase in PACAP, but not VIP, levels in both of these brain areas. Altogether, these data show that the PACAP system of the extended amygdala contributes to stress-induced hyperarousal and suggest it as a potential novel target for the treatment of stress-related disorders.
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Affiliation(s)
- Mariel P Seiglie
- Laboratory of Addictive Disorders, Departments of Pharmacology and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Lillian Huang
- Laboratory of Addictive Disorders, Departments of Pharmacology and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Pietro Cottone
- Laboratory of Addictive Disorders, Departments of Pharmacology and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Valentina Sabino
- Laboratory of Addictive Disorders, Departments of Pharmacology and Psychiatry, Boston University School of Medicine, Boston, MA, USA.
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Kurrle Y, Kunesch K, Bogusch S, Schweickert A. Serotonin and MucXS release by small secretory cells depend on
Xpod
, a SSC specific marker gene. Genesis 2019; 58:e23344. [DOI: 10.1002/dvg.23344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Yvonne Kurrle
- Institute of ZoologyUniversity of Hohenheim Stuttgart Germany
| | | | - Susanne Bogusch
- Institute of ZoologyUniversity of Hohenheim Stuttgart Germany
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Zhou X, Zhang K, Qi W, Zhou Y, Hong T, Xiong T, Xie M, Nie S. Exopolysaccharides from Lactobacillus plantarum NCU116 Enhances Colonic Mucosal Homeostasis by Controlling Epithelial Cell Differentiation and c-Jun/Muc2 Signaling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9831-9839. [PMID: 31407897 DOI: 10.1021/acs.jafc.9b03939] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Probiotic lactobacilli and their exopolysaccharides (EPS) are thought to modulate mucosal homeostasis; however, their mechanisms remain elusive. Thus, we tried to clarify the role of exopolysaccharides from Lactobacillus plantarum NCU116 (EPS116) in the intestinal mucosal homeostasis. Our results indicated that EPS116 regulated the colon mucosal healing and homeostasis, enhanced the goblet cell differentiation, and promoted the expression of Muc2 gene in vivo and in vitro. Further experiments showed that EPS116 promoted the expression and phosphorylation of transcription factor c-Jun and facilitated its binding to the promoter of Muc2. Moreover, knocking down c-Jun or inhibiting its function in LS 174T cells treated with EPS116 led to decreased expression of Muc2, implying that EPS116 promoted the colonic mucosal homeostasis and Muc2 expression via c-Jun. Therefore, our study uncovered a novel model where EPS116 enhanced colon mucosal homeostasis by controlling the epithelial cell differentiation and c-Jun/Muc2 signaling.
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Affiliation(s)
- Xingtao Zhou
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Ke Zhang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Wucheng Qi
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - YuJia Zhou
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Tao Hong
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Tao Xiong
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Mingyong Xie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
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Piccand J, Vagne C, Blot F, Meunier A, Beucher A, Strasser P, Lund ML, Ghimire S, Nivlet L, Lapp C, Petersen N, Engelstoft MS, Thibault-Carpentier C, Keime C, Correa SJ, Schreiber V, Molina N, Schwartz TW, De Arcangelis A, Gradwohl G. Rfx6 promotes the differentiation of peptide-secreting enteroendocrine cells while repressing genetic programs controlling serotonin production. Mol Metab 2019; 29:24-39. [PMID: 31668390 PMCID: PMC6728766 DOI: 10.1016/j.molmet.2019.08.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/01/2019] [Accepted: 08/10/2019] [Indexed: 12/16/2022] Open
Abstract
Objective Enteroendocrine cells (EECs) of the gastro-intestinal tract sense gut luminal factors and release peptide hormones or serotonin (5-HT) to coordinate energy uptake and storage. Our goal is to decipher the gene regulatory networks controlling EECs specification from enteroendocrine progenitors. In this context, we studied the role of the transcription factor Rfx6 which had been identified as the cause of Mitchell–Riley syndrome, characterized by neonatal diabetes and congenital malabsorptive diarrhea. We previously reported that Rfx6 was essential for pancreatic beta cell development and function; however, the role of Rfx6 in EECs differentiation remained to be elucidated. Methods We examined the molecular, cellular, and metabolic consequences of constitutive and conditional deletion of Rfx6 in the embryonic and adult mouse intestine. We performed single cell and bulk RNA-Seq to characterize EECs diversity and identify Rfx6-regulated genes. Results Rfx6 is expressed in the gut endoderm; later, it is turned on in, and restricted to, enteroendocrine progenitors and persists in hormone-positive EECs. In the embryonic intestine, the constitutive lack of Rfx6 leads to gastric heterotopia, suggesting a role in the maintenance of intestinal identity. In the absence of intestinal Rfx6, EECs differentiation is severely impaired both in the embryo and adult. However, the number of serotonin-producing enterochromaffin cells and mucosal 5-HT content are increased. Concomitantly, Neurog3-positive enteroendocrine progenitors accumulate. Combined analysis of single-cell and bulk RNA-Seq data revealed that enteroendocrine progenitors differentiate in two main cell trajectories, the enterochromaffin (EC) cells and the Peptidergic Enteroendocrine (PE) cells, the differentiation programs of which are differentially regulated by Rfx6. Rfx6 operates upstream of Arx, Pax6 and Isl1 to trigger the differentiation of peptidergic EECs such as GIP-, GLP-1-, or CCK-secreting cells. On the contrary, Rfx6 represses Lmx1a and Tph1, two genes essential for serotonin biosynthesis. Finally, we identified transcriptional changes uncovering adaptive responses to the prolonged lack of enteroendocrine hormones and leading to malabsorption and lower food efficiency ratio in Rfx6-deficient mouse intestine. Conclusion These studies identify Rfx6 as an essential transcriptional regulator of EECs specification and shed light on the molecular mechanisms of intestinal failures in human RFX6-deficiencies such as Mitchell–Riley syndrome. The lack of Rfx6 impairs the differentiation of peptide-producing enteroendocrine cells. The number of 5-HT-expressing-cells is increased in Rfx6-deficient intestine. Intestinal inactivation of Rfx6 leads to lipid malabsorption and decreased food efficiency.
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Affiliation(s)
- Julie Piccand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Constance Vagne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Florence Blot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Aline Meunier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Anthony Beucher
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Perrine Strasser
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Mari L Lund
- Centre for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Science, University of Copenhagen, Denmark
| | - Sabitri Ghimire
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Laure Nivlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Céline Lapp
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Natalia Petersen
- Centre for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Science, University of Copenhagen, Denmark
| | - Maja S Engelstoft
- Centre for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Science, University of Copenhagen, Denmark
| | - Christelle Thibault-Carpentier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Céline Keime
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Sara Jimenez Correa
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Valérie Schreiber
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Nacho Molina
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Thue W Schwartz
- Centre for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Science, University of Copenhagen, Denmark
| | - Adèle De Arcangelis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France.
| | - Gérard Gradwohl
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR7104, Illkirch, France; Université de Strasbourg, Illkirch, France.
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Funakoshi A, Tatsuno K, Shimauchi T, Fujiyama T, Ito T, Tokura Y. Cholecystokinin Downregulates Psoriatic Inflammation by Its Possible Self-Regulatory Effect on Epidermal Keratinocytes. THE JOURNAL OF IMMUNOLOGY 2019; 202:2609-2615. [PMID: 30902899 DOI: 10.4049/jimmunol.1801426] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/27/2019] [Indexed: 12/21/2022]
Abstract
Cholecystokinin (CCK) is a peptide hormone that functions in digestive organs and the CNS. We previously showed that CCK downregulates peripheral pruritus by suppressing degranulation of mast cells. In this study, we demonstrated that CCK octapeptide (CCK8) was constitutively expressed in the epidermis of normal skin, whereas its expression was lost in acanthotic lesions of psoriasis. In contrast, CCKA receptor (CCKAR), a high-affinity receptor for CCK, was constitutively expressed in the epidermis of psoriatic skin lesions. Expression of CCK was also reduced in skin lesions of an imiquimod (IMQ)-induced psoriatic mouse model. Notably, the expression level of CCK inversely correlated with the severity of epidermal inflammation, raising the possibility that CCK from epidermal keratinocytes suppresses the psoriatic inflammation. To verify this hypothesis, we investigated the effects of sulfated CCK octapeptide (CCK8S) on the development of IMQ-induced psoriatic inflammation. i.p. injection of CCK8S suppressed the IMQ-induced psoriatic inflammation accompanied by reduced mRNA expression of IL-17, IL-22, and IL-6 but not of IL-23. The suppressive effect of CCK8S was completely restored by administration of CCKAR antagonist. In vitro studies showed that exogenous CCK8S suppressed IL-6 production in CCKAR-expressing cultured human keratinocytes, and blocking the endogenous CCK signaling with CCKAR antagonist markedly enhanced IL-6 production. When keratinocytes were stimulated with IL-17, the expression of endogenous CCK was significantly decreased. These findings suggest that CCK physiologically functions as a negative regulator of keratinocyte-based inflammation in an autocrine or paracrine manner, although decreased CCK may pathologically contribute to continuous and aggravated skin lesions such as psoriasis.
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Affiliation(s)
- Atsuko Funakoshi
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Kazuki Tatsuno
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Takatoshi Shimauchi
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Toshiharu Fujiyama
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Taisuke Ito
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Yoshiki Tokura
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
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Wu YZ, Chan KYY, Leung KT, Lam HS, Tam YH, Lee KH, Li K, Ng PC. Dysregulation of miR-431 and target gene FOXA1 in intestinal tissues of infants with necrotizing enterocolitis. FASEB J 2019; 33:5143-5152. [PMID: 30624964 DOI: 10.1096/fj.201801470r] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The level of microRNA (miR)-431 was found to be markedly up-regulated in intestinal tissue of necrotizing enterocolitis (NEC). The objective of this study was to identify the target gene of miR-431 and to investigate the role of the miR-431-FOXA1 axis in the pathophysiology of NEC. The target gene of miR-431 was identified by in silico target prediction bioinformatics, luciferase assay, and Western blotting. Effects of miR-431 on downstream expression signals, cell proliferation, and apoptosis were investigated by overexpression in Caco-2 cells upon stimulation by LPS or lipoteichoic acid (LTA). FOXA1 was identified as the target gene of miR-431. Overexpression of miR-431 in Caco-2 cells significantly inhibited FOXA1, ESRRG, and HNF4A and activated IL-6, LGR5, NFKB2, PLA2G2A, PRKCZ, and TNF. IL-8 and - 10 were enhanced when costimulated with LPS or LTA. These potential downstream genes were also significantly dysregulated in primary NEC tissues compared with surgical-control tissues. Overexpression of miR-431 significantly decreased proliferation and increased apoptosis of Caco-2 cells. A proposed network of miR-431-FOXA1 interaction with LPS and LTA receptors demonstrates dysregulation of transcription factors, inflammatory mediators, epithelium tight junction regulators, and cell proliferation and apoptosis signals. The miR-431-FOXA1 axis could in part be responsible for the intensification of the inflammatory response in NEC tissues and contribute to the proinflammatory pathophysiology.-Wu, Y. Z., Chan, K. Y. Y., Leung, K. T., Lam, H. S., Tam, Y. H., Lee, K. H., Li, K., Ng, P. C. Dysregulation of miR-431 and target gene FOXA1 in intestinal tissues of infants with necrotizing enterocolitis.
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Affiliation(s)
- Yu Zheng Wu
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
| | - Kathy Yuen Yee Chan
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
| | - Kam Tong Leung
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
| | - Hugh Simon Lam
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
| | - Yuk Him Tam
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kim Hung Lee
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Karen Li
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
| | - Pak Cheung Ng
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong; and
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50
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Gracz AD, Samsa LA, Fordham MJ, Trotier DC, Zwarycz B, Lo YH, Bao K, Starmer J, Raab JR, Shroyer NF, Reinhardt RL, Magness ST. Sox4 Promotes Atoh1-Independent Intestinal Secretory Differentiation Toward Tuft and Enteroendocrine Fates. Gastroenterology 2018; 155:1508-1523.e10. [PMID: 30055169 PMCID: PMC6232678 DOI: 10.1053/j.gastro.2018.07.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/10/2018] [Accepted: 07/16/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS The intestinal epithelium is maintained by intestinal stem cells (ISCs), which produce postmitotic absorptive and secretory epithelial cells. Initial fate specification toward enteroendocrine, goblet, and Paneth cell lineages requires the transcription factor Atoh1, which regulates differentiation of the secretory cell lineage. However, less is known about the origin of tuft cells, which participate in type II immune responses to parasite infections and appear to differentiate independently of Atoh1. We investigated the role of Sox4 in ISC differentiation. METHODS We performed experiments in mice with intestinal epithelial-specific disruption of Sox4 (Sox4fl/fl:vilCre; SOX4 conditional knockout [cKO]) and mice without disruption of Sox4 (control mice). Crypt- and single-cell-derived organoids were used in assays to measure proliferation and ISC potency. Lineage allocation and gene expression changes were studied by immunofluorescence, real-time quantitative polymerase chain reaction, and RNA-seq analyses. Intestinal organoids were incubated with the type 2 cytokine interleukin 13 and gene expression was analyzed. Mice were infected with the helminth Nippostrongylus brasiliensis and intestinal tissues were collected 7 days later for analysis. Intestinal tissues collected from mice that express green fluorescent protein regulated by the Atoh1 promoter (Atoh1GFP mice) and single-cell RNA-seq analysis were used to identify cells that coexpress Sox4 and Atoh1. We generated SOX4-inducible intestinal organoids derived from Atoh1fl/fl:vilCreER (ATOH1 inducible knockout) mice and assessed differentiation. RESULTS Sox4cKO mice had impaired ISC function and secretory differentiation, resulting in decreased numbers of tuft and enteroendocrine cells. In control mice, numbers of SOX4+ cells increased significantly after helminth infection, coincident with tuft cell hyperplasia. Sox4 was activated by interleukin 13 in control organoids; SOX4cKO mice had impaired tuft cell hyperplasia and parasite clearance after infection with helminths. In single-cell RNA-seq analysis, Sox4+/Atoh1- cells were enriched for ISC, progenitor, and tuft cell genes; 12.5% of Sox4-expressing cells coexpressed Atoh1 and were enriched for enteroendocrine genes. In organoids, overexpression of Sox4 was sufficient to induce differentiation of tuft and enteroendocrine cells-even in the absence of Atoh1. CONCLUSIONS We found Sox4 promoted tuft and enteroendocrine cell lineage allocation independently of Atoh1. These results challenge the longstanding model in which Atoh1 is the sole regulator of secretory differentiation in the intestine and are relevant for understanding epithelial responses to parasitic infection.
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Affiliation(s)
- Adam D Gracz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| | - Leigh Ann Samsa
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Matthew J Fordham
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Danny C Trotier
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Bailey Zwarycz
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yuan-Hung Lo
- Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas
| | - Katherine Bao
- Department of Immunology, Duke University, Durham, North Carolina
| | - Joshua Starmer
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jesse R Raab
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Noah F Shroyer
- Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas
| | - R Lee Reinhardt
- Department of Immunology, Duke University, Durham, North Carolina
| | - Scott T Magness
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina.
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