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Wright AP, Harris S, Madden S, Reyes BR, Mulamula E, Gibson A, Rauch I, Constant DA, Nice TJ. Interferon regulatory factor 6 (IRF6) determines intestinal epithelial cell development and immunity. Mucosal Immunol 2024; 17:633-650. [PMID: 38604478 PMCID: PMC11323225 DOI: 10.1016/j.mucimm.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/21/2024] [Accepted: 03/31/2024] [Indexed: 04/13/2024]
Abstract
Intestinal epithelial cell (IEC) responses to interferon (IFN) favor antiviral defense with minimal cytotoxicity, but IEC-specific factors that regulate these responses remain poorly understood. Interferon regulatory factors (IRFs) are a family of nine related transcription factors, and IRF6 is preferentially expressed by epithelial cells, but its roles in IEC immunity are unknown. In this study, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) screens found that Irf6 deficiency enhanced IFN-stimulated antiviral responses in transformed mouse IECs but not macrophages. Furthermore, knockout (KO) of Irf6 in IEC organoids resulted in profound changes to homeostasis and immunity gene expression. Irf6 KO organoids grew more slowly, and single-cell ribonucleic acid sequencing indicated reduced expression of genes in epithelial differentiation and immunity pathways. IFN-stimulated gene expression was also significantly different in Irf6 KO organoids, with increased expression of stress and apoptosis-associated genes. Functionally, the transcriptional changes in Irf6 KO organoids were associated with increased cytotoxicity upon IFN treatment or inflammasome activation. These data indicate a previously unappreciated role for IRF6 in IEC biology, including regulation of epithelial development and moderation of innate immune responses to minimize cytotoxicity and maintain barrier function.
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Affiliation(s)
- Austin P Wright
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Sydney Harris
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Shelby Madden
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Bryan Ramirez Reyes
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Ethan Mulamula
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Alexis Gibson
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - David A Constant
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Timothy J Nice
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA.
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2
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LaBella KA, Reyes EA, Vermeulen L. Oscillation steers differentiation. Cell Stem Cell 2024; 31:943-945. [PMID: 38971144 DOI: 10.1016/j.stem.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/08/2024]
Abstract
The differentiation trajectories defining enteroendocrine (EE) cell heterogeneity remain obscure. In this issue of Cell Stem Cell, Singh et al.1 map the differentiation landscape of EE cells, identifying early oscillating cell progenitor states, which play a critical role in generating terminal EE cell diversity.
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Affiliation(s)
- Kyle A LaBella
- Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Efren A Reyes
- Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Louis Vermeulen
- Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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3
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Bustamante-Madrid P, Barbáchano A, Albandea-Rodríguez D, Rodríguez-Cobos J, Rodríguez-Salas N, Prieto I, Burgos A, Martínez de Villarreal J, Real FX, González-Sancho JM, Larriba MJ, Lafarga M, Muñoz A, Fernández-Barral A. Vitamin D opposes multilineage cell differentiation induced by Notch inhibition and BMP4 pathway activation in human colon organoids. Cell Death Dis 2024; 15:301. [PMID: 38684650 PMCID: PMC11058856 DOI: 10.1038/s41419-024-06680-z] [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: 12/11/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Understanding the mechanisms involved in colonic epithelial differentiation is key to unraveling the alterations causing inflammatory conditions and cancer. Organoid cultures provide an unique tool to address these questions but studies are scarce. We report a differentiation system toward enterocytes and goblet cells, the two major colonic epithelial cell lineages, using colon organoids generated from healthy tissue of colorectal cancer patients. Culture of these organoids in medium lacking stemness agents resulted in a modest ultrastructural differentiation phenotype with low-level expression of enterocyte (KLF4, KRT20, CA1, FABP2) and goblet cell (TFF2, TFF3, AGR2) lineage markers. BMP pathway activation through depletion of Noggin and addition of BMP4 resulted in enterocyte-biased differentiation. Contrarily, blockade of the Notch pathway using the γ-secretase inhibitor dibenzazepine (DBZ) favored goblet cell differentiation. Combination treatment with BMP4 and DBZ caused a balanced strong induction of both lineages. In contrast, colon tumor organoids responded poorly to BMP4 showing only weak signals of cell differentiation, and were unresponsive to DBZ. We also investigated the effects of 1α,25-dihydroxyvitamin D3 (calcitriol) on differentiation. Calcitriol attenuated the effects of BMP4 and DBZ on colon normal organoids, with reduced expression of differentiation genes and phenotype. Consistently, in normal organoids, calcitriol inhibited early signaling by BMP4 as assessed by reduction of the level of phospho-SMAD1/5/8. Our results show that BMP and Notch signaling play key roles in human colon stem cell differentiation to the enterocytic and goblet cell lineages and that calcitriol modulates these processes favoring stemness features.
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Affiliation(s)
- Pilar Bustamante-Madrid
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - Antonio Barbáchano
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - David Albandea-Rodríguez
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - Javier Rodríguez-Cobos
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - Nuria Rodríguez-Salas
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
- Servicio de Oncología Médica, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Isabel Prieto
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
- Servicio de Cirugía General, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Aurora Burgos
- Servicio de Digestivo, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Jaime Martínez de Villarreal
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - Francisco X Real
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - José Manuel González-Sancho
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - María Jesús Larriba
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain
| | - Miguel Lafarga
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria-IDIVAL, 39008, Santander, Spain
| | - Alberto Muñoz
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain.
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain.
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain.
| | - Asunción Fernández-Barral
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC-UAM, 28029, Madrid, Spain.
- Centro de Investigación Biomédica en Red-Cáncer (CIBERONC), 28029, Madrid, Spain.
- Instituto de Investigación Sanitaria Hospital Universitario La Paz (IdiPAZ), 28046, Madrid, Spain.
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Jiang KL, Jia YB, Liu XJ, Jia QL, Guo LK, Wang XX, Yang KM, Wu CH, Liang BB, Ling JH. Bibliometrics analysis based on the Web of Science: Current trends and perspective of gastric organoid during 2010-2023. World J Gastroenterol 2024; 30:969-983. [PMID: 38516239 PMCID: PMC10950634 DOI: 10.3748/wjg.v30.i8.969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/02/2024] [Accepted: 02/01/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND Three-dimensional organoid culture systems have been established as a robust tool for elucidating mechanisms and performing drug efficacy testing. The use of gastric organoid models holds significant promise for advancing personalized medicine research. However, a comprehensive bibliometric review of this bur-geoning field has not yet been published. AIM To analyze and understand the development, impact, and direction of gastric organoid research using bibliometric methods using data from the Web of Science Core Collection (WoSCC) database. METHODS This analysis encompassed literature pertaining to gastric organoids published between 2010 and 2023, as indexed in the WoSCC. CiteSpace and VOSviewer were used to depict network maps illustrating collaborations among authors, institutions and keywords related to gastric organoid. Citation, co-citation, and burst analysis methodologies were applied to assess the impact and progress of research. RESULTS A total of 656 relevant studies were evaluated. The majority of research was published in gastroenterology-focused journals. Globally, Yana Zavros, Hans Clevers, James M Wells, Sina Bartfeld, and Chen Zheng were the 5 most productive authors, while Hans Clevers, Huch Meritxell, Johan H van Es, Marc Van de Wetering, and Sato Toshiro were the foremost influential scientists in this area. Institutions from the University Medical Center Utrecht, Netherlands Institute for Developmental Biology (Utrecht), and University of Cincinnati (Cincinnati, OH, United States) made the most significant contributions. Currently, gastric organoids are used mainly in studies investigating gastric cancer (GC), Helicobacter pylori-infective gastritis, with a focus on the mechanisms of GC, and drug screening tests. CONCLUSION Key focus areas of research using gastric organoids include unraveling disease mechanisms and enhancing drug screening techniques. Major contributions from renowned academic institutions highlight this field's dynamic growth.
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Affiliation(s)
- Kai-Lin Jiang
- Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200021, China
- Laboratory of Cancer Biology, University of Oxford, Oxford OX37DQ, United Kingdom
| | - Yue-Bo Jia
- Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200021, China
| | - Xue-Jiao Liu
- Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200021, China
| | - Qing-Ling Jia
- Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200021, China
| | - Li-Kun Guo
- Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200021, China
| | - Xiang-Xiang Wang
- School of Traditional Chinese Medicine, Shanghai University of Chinese Medicine, Shanghai 200021, China
| | - Ke-Ming Yang
- Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200021, China
| | - Chen-Heng Wu
- Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200021, China
| | - Bei-Bei Liang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Jiang-Hong Ling
- Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200021, China
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Ladaika CA, Ghobashi AH, Boulton WC, Miller SA, O'Hagan HM. Single-cell multi-omics reveals insights into differentiation of rare cell types in mucinous colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578409. [PMID: 38370733 PMCID: PMC10871185 DOI: 10.1101/2024.02.01.578409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Neuroendocrine cells have been implicated in therapeutic resistance and worse overall survival in many cancer types. Mucinous colorectal cancer (mCRC) is uniquely enriched for enteroendocrine cells (EECs), the neuroendocrine cell of the normal colon epithelium, as compared to non-mucinous CRC. Therefore, targeting EEC differentiation may have clinical value in mCRC. Here, single cell multi-omics was used to uncover epigenetic alterations that accompany EEC differentiation, identify STAT3 as a novel regulator of EEC specification, and discover a rare cancer-specific cell type with enteric neuron-like characteristics. Further experiments demonstrated that lysine-specific demethylase 1 (LSD1) and CoREST2 mediate STAT3 demethylation and regulate STAT3 chromatin binding. Knockdown of CoREST2 in an orthotopic xenograft mouse model resulted in decreased primary tumor growth and lung metastases. In culmination, these results provide rationale for new LSD1 inhibitors that target the interaction between LSD1 with STAT3 or CoREST2, which may improve clinical outcomes for patients with mCRC.
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6
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Lin L, Clevers H. Decoding endocrine cell differentiation: insights from high-throughput CRISPR screening in human gut organoids. Clin Transl Med 2024; 14:e1526. [PMID: 38279896 PMCID: PMC10819080 DOI: 10.1002/ctm2.1526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/29/2024] Open
Affiliation(s)
- Lin Lin
- Hubrecht InstituteRoyal Netherlands Academy of Arts and Sciences (KNAW) and UMC UtrechtUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
- Princess Maxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Hans Clevers
- Hubrecht InstituteRoyal Netherlands Academy of Arts and Sciences (KNAW) and UMC UtrechtUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
- Princess Maxima Center for Pediatric OncologyUtrechtThe Netherlands
- Present address:
Pharma, Research and Early Development (pRED) of F. Hoffmann‐La Roche LtdBaselSwitzerland
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7
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Zhao D, Tang H. Staying stably cool in the sunlight. Science 2023; 382:644-645. [PMID: 37943902 DOI: 10.1126/science.adk9614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Microporous ceramics passively cool buildings and reduce the need for air conditioners.
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Affiliation(s)
- Dongliang Zhao
- School of Energy and Environment, Engineering Research Center of Building Equipment, Energy, and Environment, Southeast University, Nanjing 210096, China
- Institute of Science and Technology for Carbon Neutrality, Southeast University, Nanjing 210096, China
| | - Huajie Tang
- School of Energy and Environment, Engineering Research Center of Building Equipment, Energy, and Environment, Southeast University, Nanjing 210096, China
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