1
|
Angelis N, Baulies A, Hubl F, Kucharska A, Kelly G, Llorian M, Boeing S, Li VSW. Loss of ARID3A perturbs intestinal epithelial proliferation-differentiation ratio and regeneration. J Exp Med 2024; 221:e20232279. [PMID: 39150450 DOI: 10.1084/jem.20232279] [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: 12/11/2023] [Revised: 06/08/2024] [Accepted: 07/19/2024] [Indexed: 08/17/2024] Open
Abstract
Intestinal stem cells at the crypt divide and give rise to progenitor cells that proliferate and differentiate into various mature cell types in the transit-amplifying (TA) zone. Here, we showed that the transcription factor ARID3A regulates intestinal epithelial cell proliferation and differentiation at the TA progenitors. ARID3A forms an expression gradient from the villus tip to the upper crypt mediated by TGF-β and WNT. Intestinal-specific deletion of Arid3a reduces crypt proliferation, predominantly in TA cells. Bulk and single-cell transcriptomic analysis shows increased enterocyte and reduced secretory differentiation in the Arid3a cKO intestine, accompanied by enriched upper-villus gene signatures of both cell lineages. We find that the enhanced epithelial differentiation in the Arid3a-deficient intestine is caused by increased binding and transcription of HNF1 and HNF4. Finally, we show that loss of Arid3a impairs irradiation-induced regeneration with sustained cell death and reprogramming. Our findings imply that Arid3a functions to fine-tune the proliferation-differentiation dynamics at the TA progenitors, which are essential for injury-induced regeneration.
Collapse
Affiliation(s)
- Nikolaos Angelis
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute , London, UK
| | - Anna Baulies
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute , London, UK
| | - Florian Hubl
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute , London, UK
| | - Anna Kucharska
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute , London, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute , London, UK
| | - Miriam Llorian
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute , London, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute , London, UK
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute , London, UK
| |
Collapse
|
2
|
Bildstein T, Charbit-Henrion F, Azabdaftari A, Cerf-Bensussan N, Uhlig HH. Cellular and molecular basis of proximal small intestine disorders. Nat Rev Gastroenterol Hepatol 2024:10.1038/s41575-024-00962-9. [PMID: 39117867 DOI: 10.1038/s41575-024-00962-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
The proximal part of the small intestine, including duodenum and jejunum, is not only dedicated to nutrient digestion and absorption but is also a highly regulated immune site exposed to environmental factors. Host-protective responses against pathogens and tolerance to food antigens are essential functions in the small intestine. The cellular ecology and molecular pathways to maintain those functions are complex. Maladaptation is highlighted by common immune-mediated diseases such as coeliac disease, environmental enteric dysfunction or duodenal Crohn's disease. An expanding spectrum of more than 100 rare monogenic disorders inform on causative molecular mechanisms of nutrient absorption, epithelial homeostasis and barrier function, as well as inflammatory immune responses and immune regulation. Here, after summarizing the architectural and cellular traits that underlie the functions of the proximal intestine, we discuss how the integration of tissue immunopathology and molecular mechanisms can contribute towards our understanding of disease and guide diagnosis. We propose an integrated mechanism-based taxonomy and discuss the latest experimental approaches to gain new mechanistic insight into these disorders with large disease burden worldwide as well as implications for therapeutic interventions.
Collapse
Affiliation(s)
- Tania Bildstein
- Great Ormond Street Hospital for Children, Department of Paediatric Gastroenterology, London, UK
| | - Fabienne Charbit-Henrion
- Department of Genomic Medicine for Rare Diseases, Necker-Enfants Malades Hospital, APHP, University of Paris-Cité, Paris, France
- INSERM UMR1163, Intestinal Immunity, Institut Imagine, Paris, France
| | - Aline Azabdaftari
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Oxford, UK
| | | | - Holm H Uhlig
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Oxford, UK.
- Department of Paediatrics, University of Oxford, Oxford, UK.
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK.
| |
Collapse
|
3
|
Mitrofanova O, Nikolaev M, Xu Q, Broguiere N, Cubela I, Camp JG, Bscheider M, Lutolf MP. Bioengineered human colon organoids with in vivo-like cellular complexity and function. Cell Stem Cell 2024; 31:1175-1186.e7. [PMID: 38876106 DOI: 10.1016/j.stem.2024.05.007] [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: 06/28/2023] [Revised: 03/19/2024] [Accepted: 05/20/2024] [Indexed: 06/16/2024]
Abstract
Organoids and organs-on-a-chip have emerged as powerful tools for modeling human gut physiology and disease in vitro. Although physiologically relevant, these systems often lack the environmental milieu, spatial organization, cell type diversity, and maturity necessary for mimicking human intestinal mucosa. To instead generate models closely resembling in vivo tissue, we herein integrated organoid and organ-on-a-chip technology to develop an advanced human organoid model, called "mini-colons." By employing an asymmetric stimulation with growth factors, we greatly enhanced tissue longevity and replicated in vivo-like diversity and patterning of proliferative and differentiated cell types. Mini-colons contain abundant mucus-producing goblet cells and, signifying mini-colon maturation, single-cell RNA sequencing reveals emerging mature and functional colonocytes. This methodology is expanded to generate microtissues from the small intestine and incorporate additional microenvironmental components. Finally, our bioengineered organoids provide a precise platform to systematically study human gut physiology and pathology, and a reliable preclinical model for drug safety assessment.
Collapse
Affiliation(s)
- Olga Mitrofanova
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel 4052, Switzerland
| | - Mikhail Nikolaev
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel 4052, Switzerland
| | - Quan Xu
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel 4052, Switzerland
| | - Nicolas Broguiere
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Irineja Cubela
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel 4052, Switzerland
| | - J Gray Camp
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel 4052, Switzerland
| | - Michael Bscheider
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel 4052, Switzerland
| | - Matthias P Lutolf
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel 4052, Switzerland; Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.
| |
Collapse
|
4
|
Harnik Y, Yakubovsky O, Hoefflin R, Novoselsky R, Bahar Halpern K, Barkai T, Korem Kohanim Y, Egozi A, Golani O, Addadi Y, Kedmi M, Keidar Haran T, Levin Y, Savidor A, Keren-Shaul H, Mayer C, Pencovich N, Pery R, Shouval DS, Tirosh I, Nachmany I, Itzkovitz S. A spatial expression atlas of the adult human proximal small intestine. Nature 2024; 632:1101-1109. [PMID: 39112711 DOI: 10.1038/s41586-024-07793-3] [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: 10/11/2023] [Accepted: 07/05/2024] [Indexed: 08/17/2024]
Abstract
The mouse small intestine shows profound variability in gene expression along the crypt-villus axis1,2. Whether similar spatial heterogeneity exists in the adult human gut remains unclear. Here we use spatial transcriptomics, spatial proteomics and single-molecule fluorescence in situ hybridization to reconstruct a comprehensive spatial expression atlas of the adult human proximal small intestine. We describe zonated expression and cell type representation for epithelial, mesenchymal and immune cell types. We find that migrating enterocytes switch from lipid droplet assembly and iron uptake at the villus bottom to chylomicron biosynthesis and iron release at the tip. Villus tip cells are pro-immunogenic, recruiting γδ T cells and macrophages to the tip, in contrast to their immunosuppressive roles in mouse. We also show that the human small intestine contains abundant serrated and branched villi that are enriched at the tops of circular folds. Our study presents a detailed resource for understanding the biology of the adult human small intestine.
Collapse
Affiliation(s)
- Yotam Harnik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Oran Yakubovsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rouven Hoefflin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Roy Novoselsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Barkai
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Sheba Medical Center, Ramat Gan, Israel
| | - Yael Korem Kohanim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yoseph Addadi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Kedmi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Keidar Haran
- Department of Pathology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Yishai Levin
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Mayer
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Niv Pencovich
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ron Pery
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dror S Shouval
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Nachmany
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
5
|
Wu Z, Xiao C, Wang J, Zhou M, You F, Li X. 17β-estradiol in colorectal cancer: friend or foe? Cell Commun Signal 2024; 22:367. [PMID: 39030619 PMCID: PMC11264751 DOI: 10.1186/s12964-024-01745-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/10/2024] [Indexed: 07/21/2024] Open
Abstract
Colorectal cancer (CRC) is a common gastrointestinal malignancy with higher incidence and mortality rates in men compared to women, potentially due to the effects of estrogen signaling. There is substantial evidence supporting the significant role of 17β-Estradiol (E2) in reducing CRC risk in females, although this perspective remains debated. E2 has been demonstrated to inhibit CRC cell proliferation and migration at the cellular level by enhancing DNA mismatch repair, modulating key gene expression, triggering cell cycle arrest, and reducing activity of migration factors. Furthermore, E2 contributes to promote a tumor microenvironment unfavorable for CRC growth by stimulating ERβ expression, reducing inflammatory responses, reversing immunosuppression, and altering the gut microbiome composition. Conversely, under conditions of high oxidative stress, hypoxia, and nutritional deficiencies, E2 may facilitate CRC development through GPER-mediated non-genomic signaling. E2's influence on CRC involves the genomic and non-genomic signals mediated by ERβ and GPER, respectively, leading to its dual roles in anticancer activity and carcinogenesis. This review aims to summarize the potential mechanisms by which E2 directly or indirectly impacts CRC development, providing insights into the phenomenon of sexual dimorphism in CRC and suggesting potential strategies for prevention and treatment.
Collapse
Affiliation(s)
- Zihong Wu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Chong Xiao
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Jiamei Wang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Min Zhou
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University (Chongqing Health Center for Women and Children), Chongqing, 401147, China
| | - Fengming You
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China.
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China.
- Oncology Teaching and Research Department of Chengdu, University of Traditional Chinese Medicine, Chengdu, 610072, China.
| | - Xueke Li
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China.
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Díez-Sánchez A, Lindholm HT, Vornewald PM, Ostrop J, Yao R, Single AB, Marstad A, Parmar N, Shaw TN, Martín-Alonso M, Oudhoff MJ. LSD1 drives intestinal epithelial maturation and controls small intestinal immune cell composition independent of microbiota in a murine model. Nat Commun 2024; 15:3412. [PMID: 38649356 PMCID: PMC11035651 DOI: 10.1038/s41467-024-47815-2] [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: 09/10/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
Postnatal development of the gastrointestinal tract involves the establishment of the commensal microbiota, the acquisition of immune tolerance via a balanced immune cell composition, and maturation of the intestinal epithelium. While studies have uncovered an interplay between the first two, less is known about the role of the maturing epithelium. Here we show that intestinal-epithelial intrinsic expression of lysine-specific demethylase 1A (LSD1) is necessary for the postnatal maturation of intestinal epithelium and maintenance of this developed state during adulthood. Using microbiota-depleted mice, we find plasma cells, innate lymphoid cells (ILCs), and a specific myeloid population to depend on LSD1-controlled epithelial maturation. We propose that LSD1 controls the expression of epithelial-derived chemokines, such as Cxcl16, and that this is a mode of action for this epithelial-immune cell interplay in local ILC2s but not ILC3s. Together, our findings suggest that the maturing epithelium plays a dominant role in regulating the local immune cell composition, thereby contributing to gut homeostasis.
Collapse
Affiliation(s)
- Alberto Díez-Sánchez
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Håvard T Lindholm
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Pia M Vornewald
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jenny Ostrop
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rouan Yao
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Andrew B Single
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anne Marstad
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Naveen Parmar
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tovah N Shaw
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mara Martín-Alonso
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Menno J Oudhoff
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
- Department of Health Sciences, Carleton University, Ottawa, Ontario, ON, Canada.
| |
Collapse
|
8
|
Shirai K, Qiu S, Minowa H, Hashita T, Iwao T, Matsunaga T. Air-liquid interface culture and modified culture medium promote the differentiation of human induced pluripotent stem cells into intestinal epithelial cells. Drug Metab Pharmacokinet 2024; 55:100994. [PMID: 38452616 DOI: 10.1016/j.dmpk.2023.100994] [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: 08/21/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 03/09/2024]
Abstract
An in vitro system that evaluates pharmacokinetics in the small intestine is crucial for the development of oral drugs. We produced human induced pluripotent stem cell-derived small intestinal epithelial cells (hiSIECs) with high drug metabolizing enzyme and drug transporter activities. However, the gene expression of our hiSIECs partially differed from that of the human small intestine, with low drug metabolizing enzyme activities. Therefore, we used air-liquid interface (ALI) culture and 5-aza-2'-deoxycytidine (5AZA)-free medium to generate hiSIECs (novel hiSIECs). Novel hiSIECs showed enhanced gene expression of drug metabolizing enzymes, such as cytochrome P450 (CYP)3A4, CYP2C9, CYP2C19, and carboxylesterase 2 that are highly expressed in the small intestine. In addition, the expression of genes involved in nutrient absorption-one of the major functions of the small intestine-also increased. The novel hiSIECs expressed ZO-1 and E-cadherin. Moreover, the novel hiSIECs exhibited a barrier function that allowed low lucifer yellow permeation. The novel hiSIECs showed high activities of CYP3A4, CYP2C9, and CYP2C19, which are abundantly expressed in the small intestine. In conclusion, the novel hiSIECs have great potential as an in vitro system to evaluate pharmacokinetics in the small intestine.
Collapse
Affiliation(s)
- Kotaro Shirai
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
| | - Shimeng Qiu
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
| | - Hanako Minowa
- Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
| | - Tadahiro Hashita
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan; Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
| | - Takahiro Iwao
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan; Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
| | - Tamihide Matsunaga
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan; Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
| |
Collapse
|
9
|
Boretto M, Geurts MH, Gandhi S, Ma Z, Staliarova N, Celotti M, Lim S, He GW, Millen R, Driehuis E, Begthel H, Smabers L, Roodhart J, van Es J, Wu W, Clevers H. Epidermal growth factor receptor (EGFR) is a target of the tumor-suppressor E3 ligase FBXW7. Proc Natl Acad Sci U S A 2024; 121:e2309902121. [PMID: 38483988 PMCID: PMC10962967 DOI: 10.1073/pnas.2309902121] [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: 06/12/2023] [Accepted: 01/08/2024] [Indexed: 03/19/2024] Open
Abstract
FBXW7 is an E3 ubiquitin ligase that targets proteins for proteasome-mediated degradation and is mutated in various cancer types. Here, we use CRISPR base editors to introduce different FBXW7 hotspot mutations in human colon organoids. Functionally, FBXW7 mutation reduces EGF dependency of organoid growth by ~10,000-fold. Combined transcriptomic and proteomic analyses revealed increased EGFR protein stability in FBXW7 mutants. Two distinct phosphodegron motifs reside in the cytoplasmic tail of EGFR. Mutations in these phosphodegron motifs occur in human cancer. CRISPR-mediated disruption of the phosphodegron motif at T693 reduced EGFR degradation and EGF growth factor dependency. FBXW7 mutant organoids showed reduced sensitivity to EGFR-MAPK inhibitors. These observations were further strengthened in CRC-derived organoid lines and validated in a cohort of patients treated with panitumumab. Our data imply that FBXW7 mutations reduce EGF dependency by disabling EGFR turnover.
Collapse
Affiliation(s)
- Matteo Boretto
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Maarten H. Geurts
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Shashank Gandhi
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
- Department of Molecular and Cellular Biology, Miller Institute for Basic Research in Science, University of California, Berkeley, CA94720
| | - Ziliang Ma
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore138648, Singapore
- Department of Pharmacy, National University of Singapore, Singapore117543, Singapore
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Nadzeya Staliarova
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Martina Celotti
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Sangho Lim
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Gui-Wei He
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Rosemary Millen
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Else Driehuis
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Harry Begthel
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Lidwien Smabers
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CXUtrecht, the Netherlands
| | - Jeanine Roodhart
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CXUtrecht, the Netherlands
| | - Johan van Es
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Wei Wu
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore138648, Singapore
- Department of Pharmacy, National University of Singapore, Singapore117543, Singapore
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Hans Clevers
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| |
Collapse
|
10
|
Xu X, Foley E. Vibrio cholerae arrests intestinal epithelial proliferation through T6SS-dependent activation of the bone morphogenetic protein pathway. Cell Rep 2024; 43:113750. [PMID: 38340318 DOI: 10.1016/j.celrep.2024.113750] [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: 07/05/2023] [Revised: 12/19/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
To maintain an effective barrier, intestinal progenitor cells must divide at a rate that matches the loss of dead and dying cells. Otherwise, epithelial breaches expose the host to systemic infection by gut-resident microbes. Unlike most pathogens, Vibrio cholerae blocks tissue repair by arresting progenitor proliferation in the Drosophila model. At present, we do not understand how V. cholerae circumvents such a critical antibacterial defense. We find that V. cholerae blocks epithelial repair by activating the growth inhibitor bone morphogenetic protein (BMP) pathway in progenitors. Specifically, we show that interactions between V. cholerae and gut commensals initiate BMP signaling via host innate immune defenses. Notably, we find that V. cholerae also activates BMP and arrests proliferation in zebrafish intestines, indicating an evolutionarily conserved link between infection and failure in tissue repair. Our study highlights how enteric pathogens engage host immune and growth regulatory pathways to disrupt intestinal epithelial repair.
Collapse
Affiliation(s)
- Xinyue Xu
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Edan Foley
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2E1, Canada; Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| |
Collapse
|
11
|
I Kutyavin V, Korn LL, Medzhitov R. Nutrient-derived signals regulate eosinophil adaptation to the small intestine. Proc Natl Acad Sci U S A 2024; 121:e2316446121. [PMID: 38271336 PMCID: PMC10835075 DOI: 10.1073/pnas.2316446121] [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: 09/21/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024] Open
Abstract
Eosinophils are well recognized as effector cells of type 2 immunity, yet they also accumulate in many tissues under homeostatic conditions. However, the processes that govern homeostatic eosinophil accumulation and tissue-specific adaptation, and their functional significance, remain poorly defined. Here, we investigated how eosinophils adapt to the small intestine (SI) microenvironment and the local signals that regulate this process. We observed that eosinophils gradually migrate along the crypt-villus axis, giving rise to a villus-resident subpopulation with a distinct transcriptional signature. Retinoic acid signaling was specifically required for maintenance of this subpopulation, while IL-5 was largely dispensable outside of its canonical role in eosinophil production. Surprisingly, we found that a high-protein diet suppressed the accumulation of villus-resident eosinophils. Purified amino acids were sufficient for this effect, which was a consequence of accelerated eosinophil turnover within the tissue microenvironment and was not due to altered development in the bone marrow. Our study provides insight into the process of eosinophil adaptation to the SI, highlighting its reliance on nutrient-derived signals.
Collapse
Affiliation(s)
- Vassily I Kutyavin
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510
| | - Lisa L Korn
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510
- Department of Medicine (Rheumatology), Yale University School of Medicine, New Haven, CT 06510
| | - Ruslan Medzhitov
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510
- HHMI, Yale University School of Medicine, New Haven, CT 06510
| |
Collapse
|
12
|
Yousef Yengej FA, Pou Casellas C, Ammerlaan CME, Olde Hanhof CJA, Dilmen E, Beumer J, Begthel H, Meeder EMG, Hoenderop JG, Rookmaaker MB, Verhaar MC, Clevers H. Tubuloid differentiation to model the human distal nephron and collecting duct in health and disease. Cell Rep 2024; 43:113614. [PMID: 38159278 DOI: 10.1016/j.celrep.2023.113614] [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: 08/14/2023] [Revised: 11/09/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024] Open
Abstract
Organoid technology is rapidly gaining ground for studies on organ (patho)physiology. Tubuloids are long-term expanding organoids grown from adult kidney tissue or urine. The progenitor state of expanding tubuloids comes at the expense of differentiation. Here, we differentiate tubuloids to model the distal nephron and collecting ducts, essential functional parts of the kidney. Differentiation suppresses progenitor traits and upregulates genes required for function. A single-cell atlas reveals that differentiation predominantly generates thick ascending limb and principal cells. Differentiated human tubuloids express luminal NKCC2 and ENaC capable of diuretic-inhibitable electrolyte uptake and enable disease modeling as demonstrated by a lithium-induced tubulopathy model. Lithium causes hallmark AQP2 loss, induces proliferation, and upregulates inflammatory mediators, as seen in vivo. Lithium also suppresses electrolyte transport in multiple segments. In conclusion, this tubuloid model enables modeling of the human distal nephron and collecting duct in health and disease and provides opportunities to develop improved therapies.
Collapse
Affiliation(s)
- Fjodor A Yousef Yengej
- Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Department of Nephrology and Hypertension, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Carla Pou Casellas
- Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Department of Nephrology and Hypertension, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Carola M E Ammerlaan
- Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Department of Nephrology and Hypertension, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Charlotte J A Olde Hanhof
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, 6525 GA Nijmegen, the Netherlands
| | - Emre Dilmen
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, 6525 GA Nijmegen, the Netherlands
| | - Joep Beumer
- Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, 3584 CT Utrecht, the Netherlands; Institute of Human Biology, Roche Pharma Research and Early Development, 4058 Basel, Switzerland
| | - Harry Begthel
- Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, 3584 CT Utrecht, the Netherlands
| | - Elise M G Meeder
- Department of Psychiatry, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Joost G Hoenderop
- Department of Medical BioSciences, Radboud Institute for Medical Innovation, 6525 GA Nijmegen, the Netherlands
| | - Maarten B Rookmaaker
- Department of Nephrology and Hypertension, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Marianne C Verhaar
- Department of Nephrology and Hypertension, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands.
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute-KNAW, 3584 CT Utrecht, the Netherlands.
| |
Collapse
|
13
|
Wu H, Mu C, Xu L, Yu K, Shen L, Zhu W. Host-microbiota interaction in intestinal stem cell homeostasis. Gut Microbes 2024; 16:2353399. [PMID: 38757687 PMCID: PMC11110705 DOI: 10.1080/19490976.2024.2353399] [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: 02/02/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024] Open
Abstract
Intestinal stem cells (ISCs) play a pivotal role in gut physiology by governing intestinal epithelium renewal through the precise regulation of proliferation and differentiation. The gut microbiota interacts closely with the epithelium through myriad of actions, including immune and metabolic interactions, which translate into tight connections between microbial activity and ISC function. Given the diverse functions of the gut microbiota in affecting the metabolism of macronutrients and micronutrients, dietary nutrients exert pronounced effects on host-microbiota interactions and, consequently, the ISC fate. Therefore, understanding the intricate host-microbiota interaction in regulating ISC homeostasis is imperative for improving gut health. Here, we review recent advances in understanding host-microbiota immune and metabolic interactions that shape ISC function, such as the role of pattern-recognition receptors and microbial metabolites, including lactate and indole metabolites. Additionally, the diverse regulatory effects of the microbiota on dietary nutrients, including proteins, carbohydrates, vitamins, and minerals (e.g. iron and zinc), are thoroughly explored in relation to their impact on ISCs. Thus, we highlight the multifaceted mechanisms governing host-microbiota interactions in ISC homeostasis. Insights gained from this review provide strategies for the development of dietary or microbiota-based interventions to foster gut health.
Collapse
Affiliation(s)
- Haiqin Wu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Chunlong Mu
- Food Informatics, AgResearch, Te Ohu Rangahau Kai, Palmerston North, New Zealand
| | - Laipeng Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Kaifan Yu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Le Shen
- Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
14
|
Bernier-Latmani J, González-Loyola A, Petrova TV. Mechanisms and functions of intestinal vascular specialization. J Exp Med 2024; 221:e20222008. [PMID: 38051275 PMCID: PMC10697212 DOI: 10.1084/jem.20222008] [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: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
The intestinal vasculature has been studied for the last 100 years, and its essential role in absorbing and distributing ingested nutrients is well known. Recently, fascinating new insights into the organization, molecular mechanisms, and functions of intestinal vessels have emerged. These include maintenance of intestinal epithelial cell function, coping with microbiota-induced inflammatory pressure, recruiting gut-specific immune cells, and crosstalk with other organs. Intestinal function is also regulated at the systemic and cellular levels, such that the postprandial hyperemic response can direct up to 30% of systemic blood to gut vessels, while micron-sized endothelial cell fenestrations are necessary for nutrient uptake. In this review, we will highlight past discoveries made about intestinal vasculature in the context of new findings of molecular mechanisms underpinning gut function. Such comprehensive understanding of the system will pave the way to breakthroughs in nutrient uptake optimization, drug delivery efficiency, and treatment of human diseases.
Collapse
Affiliation(s)
- Jeremiah Bernier-Latmani
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Lausanne, Switzerland
| | | | - Tatiana V. Petrova
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Lausanne, Switzerland
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| |
Collapse
|
15
|
Li G, Gao M, Zhang S, Dai T, Wang F, Geng J, Rao J, Qin X, Qian J, Zuo L, Zhou M, Liu L, Zhou H. Sleep Deprivation Impairs Intestinal Mucosal Barrier by Activating Endoplasmic Reticulum Stress in Goblet Cells. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:85-100. [PMID: 37918798 DOI: 10.1016/j.ajpath.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023]
Abstract
Sleep deficiency is associated with intestinal inflammatory conditions and is increasingly recognized as a public health concern worldwide. However, the effects of sleep deficiency on intestinal goblet cells (GCs), which play a major role in intestinal barrier formation, remain elusive. Herein, the effects of sleep deprivation on intestinal GCs were determined using a sleep-deprivation mouse model. Sleep deprivation impaired the intestinal mucosal barrier and decreased the expression of tight junction proteins. According to single-cell RNA sequencing and histologic assessments, sleep deprivation significantly reduced GC numbers and mucin protein levels in intestinal tissues. Furthermore, sleep deprivation initiated endoplasmic reticulum stress by activating transcription factor 6 and binding Ig protein. Treatment with melatonin, an endoplasmic reticulum stress regulator, significantly alleviated endoplasmic reticulum stress responses in intestinal GCs. In addition, melatonin increased the villus length, reduced the crypt depth, and restored intestinal barrier function in mice with sleep deprivation. Overall, the findings revealed that sleep deprivation could impair intestinal mucosal barrier integrity and GC function. Targeting endoplasmic reticulum stress could represent an ideal strategy for treating sleep deficiency-induced gastrointestinal disorders.
Collapse
Affiliation(s)
- Gaoxiang Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China; School of Life Sciences, Anhui Medical University, Hefei, China
| | - Mengru Gao
- Clinical Pathology Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Clinical Pathology Center, Anhui Public Health Clinical Center, Hefei, China
| | - Shuangshuang Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Tianliang Dai
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Fei Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Jinke Geng
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Jia Rao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Xuejia Qin
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Jizhao Qian
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Li Zuo
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Meng Zhou
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Lixin Liu
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Hong Zhou
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China; School of Life Sciences, Anhui Medical University, Hefei, China.
| |
Collapse
|
16
|
Gall L, Duckworth C, Jardi F, Lammens L, Parker A, Bianco A, Kimko H, Pritchard DM, Pin C. Homeostasis, injury, and recovery dynamics at multiple scales in a self-organizing mouse intestinal crypt. eLife 2023; 12:e85478. [PMID: 38063302 PMCID: PMC10789491 DOI: 10.7554/elife.85478] [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: 12/09/2022] [Accepted: 12/07/2023] [Indexed: 01/16/2024] Open
Abstract
The maintenance of the functional integrity of the intestinal epithelium requires a tight coordination between cell production, migration, and shedding along the crypt-villus axis. Dysregulation of these processes may result in loss of the intestinal barrier and disease. With the aim of generating a more complete and integrated understanding of how the epithelium maintains homeostasis and recovers after injury, we have built a multi-scale agent-based model (ABM) of the mouse intestinal epithelium. We demonstrate that stable, self-organizing behaviour in the crypt emerges from the dynamic interaction of multiple signalling pathways, such as Wnt, Notch, BMP, ZNRF3/RNF43, and YAP-Hippo pathways, which regulate proliferation and differentiation, respond to environmental mechanical cues, form feedback mechanisms, and modulate the dynamics of the cell cycle protein network. The model recapitulates the crypt phenotype reported after persistent stem cell ablation and after the inhibition of the CDK1 cycle protein. Moreover, we simulated 5-fluorouracil (5-FU)-induced toxicity at multiple scales starting from DNA and RNA damage, which disrupts the cell cycle, cell signalling, proliferation, differentiation, and migration and leads to loss of barrier integrity. During recovery, our in silico crypt regenerates its structure in a self-organizing, dynamic fashion driven by dedifferentiation and enhanced by negative feedback loops. Thus, the model enables the simulation of xenobiotic-, in particular chemotherapy-, induced mechanisms of intestinal toxicity and epithelial recovery. Overall, we present a systems model able to simulate the disruption of molecular events and its impact across multiple levels of epithelial organization and demonstrate its application to epithelial research and drug development.
Collapse
Affiliation(s)
- Louis Gall
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZenecaCambridgeUnited Kingdom
| | - Carrie Duckworth
- Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Ferran Jardi
- Preclinical Sciences and Translational Safety, JanssenBeerseBelgium
| | - Lieve Lammens
- Preclinical Sciences and Translational Safety, JanssenBeerseBelgium
| | - Aimee Parker
- Gut Microbes and Health Programme, Quadram InstituteNorwichUnited Kingdom
| | - Ambra Bianco
- Clinical Pharmacology and Safety Sciences, AstraZenecaCambridgeUnited Kingdom
| | - Holly Kimko
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZenecaCambridgeUnited Kingdom
| | - David Mark Pritchard
- Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Carmen Pin
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZenecaCambridgeUnited Kingdom
| |
Collapse
|
17
|
Zhou W, Yan K, Xi Q. BMP signaling in cancer stemness and differentiation. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:37. [PMID: 38049682 PMCID: PMC10695912 DOI: 10.1186/s13619-023-00181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023]
Abstract
The BMP (Bone morphogenetic protein) signaling pathway plays a central role in metazoan biology, intricately shaping embryonic development, maintaining tissue homeostasis, and influencing disease progression. In the context of cancer, BMP signaling exhibits context-dependent dynamics, spanning from tumor suppression to promotion. Cancer stem cells (CSCs), a modest subset of neoplastic cells with stem-like attributes, exert substantial influence by steering tumor growth, orchestrating therapy resistance, and contributing to relapse. A comprehensive grasp of the intricate interplay between CSCs and their microenvironment is pivotal for effective therapeutic strategies. Among the web of signaling pathways orchestrating cellular dynamics within CSCs, BMP signaling emerges as a vital conductor, overseeing CSC self-renewal, differentiation dynamics, and the intricate symphony within the tumor microenvironment. Moreover, BMP signaling's influence in cancer extends beyond CSCs, intricately regulating cellular migration, invasion, and metastasis. This multifaceted role underscores the imperative of comprehending BMP signaling's contributions to cancer, serving as the foundation for crafting precise therapies to navigate multifaceted challenges posed not only by CSCs but also by various dimensions of cancer progression. This article succinctly encapsulates the diverse roles of the BMP signaling pathway across different cancers, spanning glioblastoma multiforme (GBM), diffuse intrinsic pontine glioma (DIPG), colorectal cancer, acute myeloid leukemia (AML), lung cancer, prostate cancer, and osteosarcoma. It underscores the necessity of unraveling underlying mechanisms and molecular interactions. By delving into the intricate tapestry of BMP signaling's engagement in cancers, researchers pave the way for meticulously tailored therapies, adroitly leveraging its dualistic aspects-whether as a suppressor or promoter-to effectively counter the relentless march of tumor progression.
Collapse
Affiliation(s)
- Wei Zhou
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Kun Yan
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiaoran Xi
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Joint Graduate Program of Peking-Tsinghua-NIBS, Tsinghua University, Beijing, China.
| |
Collapse
|
18
|
Matsuoka Y, Tsujimoto Y. Housing conditions affect enterocyte death mode and turnover rate in mouse small intestine. Sci Rep 2023; 13:20423. [PMID: 37993588 PMCID: PMC10665386 DOI: 10.1038/s41598-023-47660-1] [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: 03/24/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023] Open
Abstract
Small intestinal enterocytes are continuously renewed. Shedding/death of enterocytes involves receptor-interacting protein kinase 1 (RIPK1)-dependent (but RIPK3-independent) necrotic death, but the regulatory mechanism of the processes is not fully understood. Here, we show that mouse housing conditions, such as the type of bedding material and the presence or absence of a Shepherd Shack, affect enterocyte turnover rate and determine whether enterocyte shedding/death is RIPK1-independent or -dependent. Mice housed with ALPHA-dri (αDri, hard paper chip) bedding material without a Shepherd Shack had a higher, largely RIPK1-dependent enterocyte turnover rate and higher blood corticosterone levels, suggesting the involvement of minor stress, whereas mice housed with αDri plus a Shepherd Shack or with Soft Chip had a lower, RIPK1-independent turnover rate and lower blood corticosterone levels. Corticosterone administration to a small intestine culture derived from mice housed with αDri plus a Shepherd Shack or with Soft Chip increased enterocyte shedding/death and turnover. By using kinase inhibitors and knockout mice, we showed that the switch from RIPK1-independent to RIPK1-dependent enterocyte shedding/death and turnover involves suppression of TANK-binding kinase 1. Our results demonstrate that housing conditions may cause minor stress, which alters the mode of enterocyte shedding/death and enterocyte turnover rate in mice.
Collapse
Affiliation(s)
- Yosuke Matsuoka
- Department of Oncogenesis and Growth Regulation, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka, 541-8567, Japan.
- Department of Molecular and Cellular Biology, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka, 541-8567, Japan.
| | - Yoshihide Tsujimoto
- Department of Molecular and Cellular Biology, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka, 541-8567, Japan.
| |
Collapse
|
19
|
Dinarello A, May M, Amo-Aparicio J, Azam T, Gaballa JM, Marchetti C, Tesoriere A, Ghirardo R, Redzic JS, Webber WS, Atif SM, Li S, Eisenmesser EZ, de Graaf DM, Dinarello CA. IL-38 regulates intestinal stem cell homeostasis by inducing WNT signaling and beneficial IL-1β secretion. Proc Natl Acad Sci U S A 2023; 120:e2306476120. [PMID: 37906644 PMCID: PMC10636342 DOI: 10.1073/pnas.2306476120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/13/2023] [Indexed: 11/02/2023] Open
Abstract
The IL-1 Family member IL-38 has been characterized primarily as an antiinflammatory cytokine in human and mouse models of systemic diseases. Here, we examined the role of IL-38 in the murine small intestine (SI). Immunostaining of SI revealed that IL-38 expression partially confines to intestinal stem cells. Cultures of intestinal organoids reveal IL-38 functions as a growth factor by increasing organoid size via inducing WNT3a. In contrast, organoids from IL-38-deficient mice develop more slowly. This reduction in size is likely due to the downregulation of intestinal stemness markers (i.e., Fzd5, Ephb2, and Olfm4) expression compared with wild-type organoids. The IL-38 binding to IL-1R6 and IL-1R9 is still a matter of debate. Therefore, to analyze the molecular mechanisms of IL-38 signaling, we also examined organoids from IL-1R9-deficient mice. Unexpectedly, these organoids, although significantly smaller than wild type, respond to IL-38, suggesting that IL-1R9 is not involved in IL-38 signaling in the stem cell crypt. Nevertheless, silencing of IL-1R6 disabled the organoid response to the growth property of IL-38, thus suggesting IL-1R6 as the main receptor used by IL-38 in the crypt compartment. In organoids from wild-type mice, IL-38 stimulation induced low concentrations of IL-1β which contribute to organoid growth. However, high concentrations of IL-1β have detrimental effects on the cultures that were prevented by treatment with recombinant IL-38. Overall, our data demonstrate an important regulatory function of IL-38 as a growth factor, and as an antiinflammatory molecule in the SI, maintaining homeostasis.
Collapse
Affiliation(s)
- Alberto Dinarello
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Makenna May
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Jesus Amo-Aparicio
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Tania Azam
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Joseph M. Gaballa
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Carlo Marchetti
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | | | | | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO80045
| | - William S. Webber
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Shaikh M. Atif
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Suzhao Li
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Elan Z. Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO80045
| | - Dennis M. de Graaf
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Charles A. Dinarello
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| |
Collapse
|
20
|
Doke M, Álvarez-Cubela S, Klein D, Altilio I, Schulz J, Mateus Gonçalves L, Almaça J, Fraker CA, Pugliese A, Ricordi C, Qadir MMF, Pastori RL, Domínguez-Bendala J. Dynamic scRNA-seq of live human pancreatic slices reveals functional endocrine cell neogenesis through an intermediate ducto-acinar stage. Cell Metab 2023; 35:1944-1960.e7. [PMID: 37898119 DOI: 10.1016/j.cmet.2023.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/23/2023] [Accepted: 10/03/2023] [Indexed: 10/30/2023]
Abstract
Human pancreatic plasticity is implied from multiple single-cell RNA sequencing (scRNA-seq) studies. However, these have been invariably based on static datasets from which fate trajectories can only be inferred using pseudotemporal estimations. Furthermore, the analysis of isolated islets has resulted in a drastic underrepresentation of other cell types, hindering our ability to interrogate exocrine-endocrine interactions. The long-term culture of human pancreatic slices (HPSs) has presented the field with an opportunity to dynamically track tissue plasticity at the single-cell level. Combining datasets from same-donor HPSs at different time points, with or without a known regenerative stimulus (BMP signaling), led to integrated single-cell datasets storing true temporal or treatment-dependent information. This integration revealed population shifts consistent with ductal progenitor activation, blurring of ductal/acinar boundaries, formation of ducto-acinar-endocrine differentiation axes, and detection of transitional insulin-producing cells. This study provides the first longitudinal scRNA-seq analysis of whole human pancreatic tissue, confirming its plasticity in a dynamic fashion.
Collapse
Affiliation(s)
- Mayur Doke
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Silvia Álvarez-Cubela
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Dagmar Klein
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Isabella Altilio
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Joseph Schulz
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Luciana Mateus Gonçalves
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Joana Almaça
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Christopher A Fraker
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Alberto Pugliese
- Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Camillo Ricordi
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mirza M F Qadir
- Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Ricardo L Pastori
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Juan Domínguez-Bendala
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| |
Collapse
|
21
|
Wang Y, Lou R, Zhang Z, Xiao C, Yu S, Wei S, Liu Y, Fu W, Li B, Chen YG. Stromal BMP signaling regulates mucin production in the large intestine via interleukin-1/17. SCIENCE ADVANCES 2023; 9:eadi1827. [PMID: 37889976 PMCID: PMC10610902 DOI: 10.1126/sciadv.adi1827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023]
Abstract
Bone morphogenic protein (BMP) signaling is critical for intestinal development, homeostasis, and function performance. Although the function of BMP signaling in the intestinal epithelium is well appreciated, the direct effect of BMP on intestinal stromal cells is poorly understood. Here, we show that disruption of BMP signaling by genetic ablation of Alk3 or Smad4 expands the stromal cell pool, the mucosa tumefaction, and colonic polyposis in the large intestine. Interleukin (IL) secretion by stromal cells is notably increased, including IL-1, IL-11, and IL-17. Specifically, IL-1 and IL-17a hyperactivate the mucin production by goblet cells through nuclear factor κB signaling, and abnormal mucin accumulation results in the morphological changes, epithelial barrier destruction, and polyposis development. Together, our results provide an insight into the role of BMP signaling in intestinal stromal cells to regulate epithelium function. This study further highlights the role of mucin-producing goblet cells in intestinal homeostasis and colitis development.
Collapse
Affiliation(s)
- Yalong Wang
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou National Laboratory, Guangzhou 510005, China
| | - Ruoyu Lou
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhe Zhang
- Guangzhou National Laboratory, Guangzhou 510005, China
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Chuyu Xiao
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shicheng Yu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou National Laboratory, Guangzhou 510005, China
| | - Siting Wei
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuan Liu
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Fu
- Department of General Surgery, Peking University Third Hospital, Beijing 100191, China
| | - Baojie Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ye-Guang Chen
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Guangzhou National Laboratory, Guangzhou 510005, China
- School of Basic Medicine, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| |
Collapse
|
22
|
Vornewald PM, Forman R, Yao R, Parmar N, Lindholm HT, Lee LSK, Martín-Alonso M, Else KJ, Oudhoff MJ. Mmp17-deficient mice exhibit heightened goblet cell effector expression in the colon and increased resistance to chronic Trichuris muris infection. Front Immunol 2023; 14:1243528. [PMID: 37869014 PMCID: PMC10587605 DOI: 10.3389/fimmu.2023.1243528] [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: 06/20/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Intestinal epithelial homeostasis is maintained by intrinsic and extrinsic signals. The extrinsic signals include those provided by mesenchymal cell populations that surround intestinal crypts and is further facilitated by the extracellular matrix (ECM), which is modulated by proteases such as matrix metalloproteinases (MMPs). Extrinsic signals ensure an appropriate balance between intestinal epithelial proliferation and differentiation. This study explores the role of MMP17, which is preferentially expressed by smooth muscle cells in the intestine, in intestinal homeostasis and during immunity to infection. Mice lacking MMP17 expressed high levels of goblet-cell associated genes and proteins, such as CLCA1 and RELM-β, which are normally associated with immune responses to infection. Nevertheless, Mmp17 KO mice did not have altered resistance during a bacterial Citrobacter rodentium infection. However, when challenged with a low dose of the helminth Trichuris muris, Mmp17 KO mice had increased resistance, without a clear role for an altered immune response during infection. Mechanistically, we did not find changes in traditional modulators of goblet cell effectors such as the NOTCH pathway or specific cytokines. We found MMP17 expression in smooth muscle cells as well as lamina propria cells such as macrophages. Together, our data suggest that MMP17 extrinsically alters goblet cell maturation which is sufficient to alter clearance in a helminth infection model.
Collapse
Affiliation(s)
- Pia M. Vornewald
- CEMIR – Center of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU – Norwegian University of Science and Technology, Trondheim, Norway
| | - Ruth Forman
- Lydia Becker Institute of Immunology & Inflammation, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
| | - Rouan Yao
- CEMIR – Center of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU – Norwegian University of Science and Technology, Trondheim, Norway
| | - Naveen Parmar
- CEMIR – Center of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU – Norwegian University of Science and Technology, Trondheim, Norway
| | - Håvard T. Lindholm
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lilith S. K. Lee
- CEMIR – Center of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU – Norwegian University of Science and Technology, Trondheim, Norway
| | - Mara Martín-Alonso
- CEMIR – Center of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU – Norwegian University of Science and Technology, Trondheim, Norway
| | - Kathryn J. Else
- Lydia Becker Institute of Immunology & Inflammation, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
| | - Menno J. Oudhoff
- CEMIR – Center of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU – Norwegian University of Science and Technology, Trondheim, Norway
- Department of Health Sciences, Carleton University, Ottawa, ON, Canada
| |
Collapse
|
23
|
Brügger MD, Basler K. The diverse nature of intestinal fibroblasts in development, homeostasis, and disease. Trends Cell Biol 2023; 33:834-849. [PMID: 37080817 DOI: 10.1016/j.tcb.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 04/22/2023]
Abstract
Only in recent years have we begun to appreciate the involvement of fibroblasts in intestinal development, tissue homeostasis, and disease. These insights followed the advent of single-cell transcriptomics that allowed researchers to explore the heterogeneity of intestinal fibroblasts in unprecedented detail. Since researchers often defined cell types and their associated function based on the biological process they studied, there are a plethora of partially overlapping markers for different intestinal fibroblast populations. This ambiguity complicates putting different research findings into context. Here, we provide a census on the function and identity of intestinal fibroblasts in mouse and human. We propose a simplified framework consisting of three colonic and four small intestinal fibroblast populations to aid navigating the diversity of intestinal fibroblasts.
Collapse
Affiliation(s)
- Michael David Brügger
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Konrad Basler
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| |
Collapse
|
24
|
Berková L, Fazilaty H, Yang Q, Kubovčiak J, Stastna M, Hrckulak D, Vojtechova M, Dalessi T, Brügger MD, Hausmann G, Liberali P, Korinek V, Basler K, Valenta T. Terminal differentiation of villus tip enterocytes is governed by distinct Tgfβ superfamily members. EMBO Rep 2023; 24:e56454. [PMID: 37493498 PMCID: PMC10481656 DOI: 10.15252/embr.202256454] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/27/2023] Open
Abstract
The protective and absorptive functions of the intestinal epithelium rely on differentiated enterocytes in the villi. The differentiation of enterocytes is orchestrated by sub-epithelial mesenchymal cells producing distinct ligands along the villus axis, in particular Bmps and Tgfβ. Here, we show that individual Bmp ligands and Tgfβ drive distinct enterocytic programs specific to villus zonation. Bmp4 is expressed from the centre to the upper part of the villus and activates preferentially genes connected to lipid uptake and metabolism. In contrast, Bmp2 is produced by villus tip mesenchymal cells and it influences the adhesive properties of villus tip epithelial cells and the expression of immunomodulators. Additionally, Tgfβ induces epithelial gene expression programs similar to those triggered by Bmp2. Bmp2-driven villus tip program is activated by a canonical Bmp receptor type I/Smad-dependent mechanism. Finally, we establish an organoid cultivation system that enriches villus tip enterocytes and thereby better mimics the cellular composition of the intestinal epithelium. Our data suggest that not only a Bmp gradient but also the activity of individual Bmp drives specific enterocytic programs.
Collapse
Affiliation(s)
- Linda Berková
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Hassan Fazilaty
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Qiutan Yang
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and Regeneration, Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jan Kubovčiak
- Laboratory of Genomics and BioinformaticsInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Monika Stastna
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Dusan Hrckulak
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Martina Vojtechova
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Tosca Dalessi
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | | | - George Hausmann
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
| | - Vladimir Korinek
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Konrad Basler
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Tomas Valenta
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| |
Collapse
|
25
|
Aita R, Chen L, Verzi M. Evaluating Performance of IsoformSwitchAnalyzeR and mRNA Isoform Switching in Small Intestine Epithelial Differentiation. GASTRO HEP ADVANCES 2023; 2:1077-1081. [PMID: 38094226 PMCID: PMC10718563 DOI: 10.1016/j.gastha.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/04/2023] [Indexed: 12/17/2023]
Affiliation(s)
- R. Aita
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Division of Environmental & Population Health Biosciences, EOHSI, New Brunswick, New Jersey
| | - L. Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Division of Environmental & Population Health Biosciences, EOHSI, New Brunswick, New Jersey
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China
| | - M.P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Division of Environmental & Population Health Biosciences, EOHSI, New Brunswick, New Jersey
| |
Collapse
|
26
|
Leo S, Kato Y, Wu Y, Yokota M, Koike M, Yui S, Tsuchiya K, Shiraki N, Kume S. The Effect of Vitamin D3 and Valproic Acid on the Maturation of Human-Induced Pluripotent Stem Cell-Derived Enterocyte-Like Cells. Stem Cells 2023; 41:775-791. [PMID: 37228023 DOI: 10.1093/stmcls/sxad042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/17/2023] [Indexed: 05/27/2023]
Abstract
Cytochrome P450 3A4 (CYP3A4) is involved in first-pass metabolism in the small intestine and is heavily implicated in oral drug bioavailability and pharmacokinetics. We previously reported that vitamin D3 (VD3), a known CYP enzyme inducer, induces functional maturation of iPSC-derived enterocyte-like cells (iPSC-ent). Here, we identified a Notch activator and CYP modulator valproic acid (VPA), as a promotor for the maturation of iPSC-ent. We performed bulk RNA sequencing to investigate the changes in gene expression during the differentiation and maturation periods of these cells. VPA potentiated gene expression of key enterocyte markers ALPI, FABP2, and transporters such as SULT1B1. RNA-sequencing analysis further elucidated several function-related pathways involved in fatty acid metabolism, significantly upregulated by VPA when combined with VD3. Particularly, VPA treatment in tandem with VD3 significantly upregulated key regulators of enterohepatic circulation, such as FGF19, apical bile acid transporter SLCO1A2 and basolateral bile acid transporters SLC51A and SLC51B. To sum up, we could ascertain the genetic profile of our iPSC-ent cells to be specialized toward fatty acid absorption and metabolism instead of transporting other nutrients, such as amino acids, with the addition of VD3 and VPA in tandem. Together, these results suggest the possible application of VPA-treated iPSC-ent for modelling enterohepatic circulation.
Collapse
Affiliation(s)
- Sylvia Leo
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Yusuke Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Yumeng Wu
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Mutsumi Yokota
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Masato Koike
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shiro Yui
- Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kiichiro Tsuchiya
- Department of Gastroenterology, Institute of Medicine, University of Tsukuba, Tennoudai, Tsukuba, Ibaraki, Japan
| | - Nobuaki Shiraki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Shoen Kume
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| |
Collapse
|
27
|
Wei S, Li M, Song W, Liu J, Yu S, Wang Y, Zhang M, Du H, Liu Y, Liu H, Fu W, Li B, Chen YG. The cyclooxygenase-expressing mesenchyme resists intestinal epithelial injury by paracrine signaling. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:30. [PMID: 37574502 PMCID: PMC10423710 DOI: 10.1186/s13619-023-00174-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Abstract
Paracrine signals play pivotal roles in organ homeostasis. Mesenchymal stromal cells (MSCs) play a key role in regulating epithelium homeostasis in the intestine while their paracrine effects are poorly characterized. Here, we identified prostaglandin E2 (PGE2) secreted by cyclooxygenase (COX)-expressing MSCs as a vital factor to maintain the intestinal mucosal barrier. We found that MSCs-induced organoid swelling through paracrine effect in vitro, a process due to enhanced water adsorption and is mediated by the COX-PGE2-EP4 axis. To further explore the regulatory effect of this axis on the intestinal epithelial barrier in vivo, we established the conditional knockout mouse model to specifically delete COX in MSCs and found that PGE2 reduction downregulated the gene Muc2 and induced a gastric metaplasia-like phenotype. Moreover, PGE2 defects increased the susceptibility of intestinal epithelium to colitis. Our study uncovers the paracrine signaling of COX-expressing MSCs in intestinal mucosal barrier maintenance, providing a basis for understanding the role of mesenchymal cells in the pathophysiological function of the intestine.
Collapse
Affiliation(s)
- Siting Wei
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meng Li
- Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Wanlu Song
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jiaye Liu
- Department of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shicheng Yu
- Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Yalong Wang
- Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Mengxian Zhang
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huijun Du
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuan Liu
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huidong Liu
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wei Fu
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Baojie Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuro- Psychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ye-Guang Chen
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Guangzhou National Laboratory, Guangzhou, 510005, China.
- School of Basic Medicine, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
| |
Collapse
|
28
|
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.
Collapse
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.
| |
Collapse
|
29
|
Zhang W, Jiang A, Yu H, Dong B. Comparative Transcriptomic Analysis Reveals the Functionally Segmented Intestine in Tunicate Ascidian. Int J Mol Sci 2023; 24:6270. [PMID: 37047242 PMCID: PMC10094616 DOI: 10.3390/ijms24076270] [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: 03/03/2023] [Revised: 03/16/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023] Open
Abstract
The vertebrate intestinal system consists of separate segments that remarkably differ in morphology and function. However, the origin of intestinal segmentation remains unclear. In this study, we investigated the segmentation of the intestine in a tunicate ascidian species, Ciona savignyi, by performing RNA sequencing. The gene expression profiles showed that the whole intestine was separated into three segments. Digestion, ion transport and signal transduction, and immune-related pathway genes were enriched in the proximal, middle, and distal parts of the intestine, respectively, implying that digestion, absorption, and immune function appear to be regional specializations in the ascidian intestine. We further performed a multi-species comparison analysis and found that the Ciona intestine showed a similar gene expression pattern to vertebrates, indicating tunicates and vertebrates might share the conserved intestinal functions. Intriguingly, vertebrate pancreatic homologous genes were expressed in the digestive segment of the Ciona intestine, suggesting that the proximal intestine might play the part of pancreatic functions in C. savignyi. Our results demonstrate that the tunicate intestine can be functionally separated into three distinct segments, which are comparable to the corresponding regions of the vertebrate intestinal system, offering insights into the functional evolution of the digestive system in chordates.
Collapse
Affiliation(s)
- Wei Zhang
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - An Jiang
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Haiyan Yu
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Bo Dong
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laoshan Laboratory for Marine Science and Technology, Qingdao 266237, China
- MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| |
Collapse
|
30
|
Smirnov A, Melino G, Candi E. Gene expression in organoids: an expanding horizon. Biol Direct 2023; 18:11. [PMID: 36964575 PMCID: PMC10038780 DOI: 10.1186/s13062-023-00360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/20/2023] [Indexed: 03/26/2023] Open
Abstract
Recent development of human three-dimensional organoid cultures has opened new doors and opportunities ranging from modelling human development in vitro to personalised cancer therapies. These new in vitro systems are opening new horizons to the classic understanding of human development and disease. However, the complexity and heterogeneity of these models requires cutting-edge techniques to capture and trace global changes in gene expression to enable identification of key players and uncover the underlying molecular mechanisms. Rapid development of sequencing approaches made possible global transcriptome analyses and epigenetic profiling. Despite challenges in organoid culture and handling, these techniques are now being adapted to embrace organoids derived from a wide range of human tissues. Here, we review current state-of-the-art multi-omics technologies, such as single-cell transcriptomics and chromatin accessibility assays, employed to study organoids as a model for development and a platform for precision medicine.
Collapse
Affiliation(s)
- Artem Smirnov
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00166, Rome, Italy.
| |
Collapse
|
31
|
Zheng D, Mohapatra G, Kern L, He Y, Shmueli MD, Valdés-Mas R, Kolodziejczyk AA, Próchnicki T, Vasconcelos MB, Schorr L, Hertel F, Lee YS, Rufino MC, Ceddaha E, Shimshy S, Hodgetts RJ, Dori-Bachash M, Kleimeyer C, Goldenberg K, Heinemann M, Stettner N, Harmelin A, Shapiro H, Puschhof J, Chen M, Flavell RA, Latz E, Merbl Y, Abdeen SK, Elinav E. Epithelial Nlrp10 inflammasome mediates protection against intestinal autoinflammation. Nat Immunol 2023; 24:585-594. [PMID: 36941399 DOI: 10.1038/s41590-023-01450-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/06/2023] [Indexed: 03/23/2023]
Abstract
Unlike other nucleotide oligomerization domain-like receptors, Nlrp10 lacks a canonical leucine-rich repeat domain, suggesting that it is incapable of signal sensing and inflammasome formation. Here we show that mouse Nlrp10 is expressed in distal colonic intestinal epithelial cells (IECs) and modulated by the intestinal microbiome. In vitro, Nlrp10 forms an Apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC)-dependent, m-3M3FBS-activated, polyinosinic:polycytidylic acid-modulated inflammasome driving interleukin-1β and interleukin-18 secretion. In vivo, Nlrp10 signaling is dispensable during steady state but becomes functional during autoinflammation in antagonizing mucosal damage. Importantly, whole-body or conditional IEC Nlrp10 depletion leads to reduced IEC caspase-1 activation, coupled with enhanced susceptibility to dextran sodium sulfate-induced colitis, mediated by altered inflammatory and healing programs. Collectively, understanding Nlrp10 inflammasome-dependent and independent activity, regulation and possible human relevance might facilitate the development of new innate immune anti-inflammatory interventions.
Collapse
Affiliation(s)
- Danping Zheng
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Gayatree Mohapatra
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Lara Kern
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Yiming He
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Merav D Shmueli
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Rafael Valdés-Mas
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | | | - Tomasz Próchnicki
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | | | - Lena Schorr
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Franziska Hertel
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
| | - Ye Seul Lee
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
| | | | - Emmanuelle Ceddaha
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Sandy Shimshy
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Ryan James Hodgetts
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Mally Dori-Bachash
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Christian Kleimeyer
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Kim Goldenberg
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Melina Heinemann
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Stettner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Hagit Shapiro
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Jens Puschhof
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Eicke Latz
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Yifat Merbl
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Suhaib K Abdeen
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
- Division of Cancer-Microbiome Research, German Cancer Research Center, Heidelberg, Germany.
| |
Collapse
|
32
|
González-Loyola A, Bernier-Latmani J, Roci I, Wyss T, Langer J, Durot S, Munoz O, Prat-Luri B, Delorenzi M, Lutolf MP, Zamboni N, Verdeil G, Petrova TV. c-MAF coordinates enterocyte zonation and nutrient uptake transcriptional programs. J Exp Med 2022; 219:213478. [PMID: 36121415 PMCID: PMC9486085 DOI: 10.1084/jem.20212418] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/15/2022] [Accepted: 08/24/2022] [Indexed: 12/13/2022] Open
Abstract
Small intestinal villi are structural and functional units present in higher vertebrates and uniquely adapted to nutrient absorption. Villus enterocytes are organized in transcriptional "zones" dedicated to specialized tasks such as absorption of specific nutrients. We report that the transcription factor c-MAF is expressed in differentiated lower and mid-villus enterocytes and is a target of BMP signaling. Maf inactivation perturbed the villus zonation program by increasing carbohydrate-related transcripts while suppressing transcripts linked to amino-acid and lipid absorption. The formation of cytoplasmic lipid droplets, shuttling dietary fat to chylomicrons, was impaired upon Maf loss indicating its role in dietary lipid handling. Maf inactivation under homeostatic conditions expanded tuft cells and led to compensatory gut lengthening, preventing weight loss. However, delayed Maf-/- enterocyte maturation impaired weight recovery after acute intestinal injury, resulting in reduced survival. Our results identify c-MAF as a regulator of the intestinal villus zonation program, while highlighting the importance of coordination between stem/progenitor and differentiation programs for intestinal regeneration.
Collapse
Affiliation(s)
- Alejandra González-Loyola
- Department of Oncology, University of Lausanne, and Ludwig Institute for Cancer Research, Lausanne, Epalinges, Switzerland
| | - Jeremiah Bernier-Latmani
- Department of Oncology, University of Lausanne, and Ludwig Institute for Cancer Research, Lausanne, Epalinges, Switzerland
| | - Irena Roci
- Department of Oncology, University of Lausanne, and Ludwig Institute for Cancer Research, Lausanne, Epalinges, Switzerland
| | - Tania Wyss
- Department of Oncology, University of Lausanne, and Ludwig Institute for Cancer Research, Lausanne, Epalinges, Switzerland.,Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jakob Langer
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stephan Durot
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Olivia Munoz
- Department of Oncology, University of Lausanne, and Ludwig Institute for Cancer Research, Lausanne, Epalinges, Switzerland
| | - Borja Prat-Luri
- Department of Oncology, University of Lausanne, and Ludwig Institute for Cancer Research, Lausanne, Epalinges, Switzerland
| | - Mauro Delorenzi
- Department of Oncology, University of Lausanne, and Ludwig Institute for Cancer Research, Lausanne, Epalinges, Switzerland.,Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Grégory Verdeil
- Department of Oncology, University of Lausanne, and Ludwig Institute for Cancer Research, Lausanne, Epalinges, Switzerland
| | - Tatiana V Petrova
- Department of Oncology, University of Lausanne, and Ludwig Institute for Cancer Research, Lausanne, Epalinges, Switzerland
| |
Collapse
|
33
|
Corominas-Murtra B, Hannezo E. Modelling the dynamics of mammalian gut homeostasis. Semin Cell Dev Biol 2022:S1084-9521(22)00317-2. [DOI: 10.1016/j.semcdb.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/26/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
|
34
|
An analysis of intestinal morphology and incretin-producing cells using tissue optical clearing and 3-D imaging. Sci Rep 2022; 12:17530. [PMID: 36266531 PMCID: PMC9584944 DOI: 10.1038/s41598-022-22511-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 10/17/2022] [Indexed: 01/13/2023] Open
Abstract
Tissue optical clearing permits detailed evaluation of organ three-dimensional (3-D) structure as well as that of individual cells by tissue staining and autofluorescence. In this study, we evaluated intestinal morphology, intestinal epithelial cells (IECs), and enteroendocrine cells, such as incretin-producing cells, in reporter mice by intestinal 3-D imaging. 3-D intestinal imaging of reporter mice using optical tissue clearing enabled us to evaluate both detailed intestinal morphologies and cell numbers, villus length and crypt depth in the same samples. In disease mouse model of lipopolysaccharide (LPS)-injected mice, the results of 3-D imaging using tissue optical clearing in this study was consistent with those of 2-D imaging in previous reports and could added the new data of intestinal morphology. In analysis of incretin-producing cells of reporter mice, we could elucidate the number, the percentage, and the localization of incretin-producing cells in intestine and the difference of those between L cells and K cells. Thus, we established a novel method of intestinal analysis using tissue optical clearing and 3-D imaging. 3-D evaluation of intestine enabled us to clarify not only detailed intestinal morphology but also the precise number and localization of IECs and incretin-producing cells in the same samples.
Collapse
|
35
|
Oda M, Hatano Y, Sato T. Intestinal epithelial organoids: regeneration and maintenance of the intestinal epithelium. Curr Opin Genet Dev 2022; 76:101977. [PMID: 36058061 DOI: 10.1016/j.gde.2022.101977] [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: 05/30/2022] [Revised: 07/24/2022] [Accepted: 07/26/2022] [Indexed: 11/18/2022]
Abstract
Vital functions of the intestines: digestion, absorption, and surface barrier are performed by the intestinal epithelium, which consists of various differentiated cells and intestinal stem cells. Recent technological advances in sequencing technology, including single-cell transcriptomics and epigenetic analysis, have facilitated the genetic characterization of diverse intestinal epithelial cell types and surrounding mesenchymal niche environments. Organoids have allowed biological analysis of the human intestinal epithelium in coordination with genome engineering, genetic lineage tracing, and transplantation into orthotopic tissue. Together, these technologies have prompted the development of organoid-based regenerative therapies for intestinal diseases, including short-bowel syndrome. This article provides an overview of the current understanding of intestinal epithelial self-renewal during homeostasis and regeneration and provides a perspective for future organoid medicine.
Collapse
Affiliation(s)
- Mayumi Oda
- Department of Organoid Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Yoshiko Hatano
- Department of Organoid Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| |
Collapse
|
36
|
Applications of human organoids in the personalized treatment for digestive diseases. Signal Transduct Target Ther 2022; 7:336. [PMID: 36167824 PMCID: PMC9513303 DOI: 10.1038/s41392-022-01194-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/09/2022] [Accepted: 09/13/2022] [Indexed: 11/15/2022] Open
Abstract
Digestive system diseases arise primarily through the interplay of genetic and environmental influences; there is an urgent need in elucidating the pathogenic mechanisms of these diseases and deploy personalized treatments. Traditional and long-established model systems rarely reproduce either tissue complexity or human physiology faithfully; these shortcomings underscore the need for better models. Organoids represent a promising research model, helping us gain a more profound understanding of the digestive organs; this model can also be used to provide patients with precise and individualized treatment and to build rapid in vitro test models for drug screening or gene/cell therapy, linking basic research with clinical treatment. Over the past few decades, the use of organoids has led to an advanced understanding of the composition of each digestive organ and has facilitated disease modeling, chemotherapy dose prediction, CRISPR-Cas9 genetic intervention, high-throughput drug screening, and identification of SARS-CoV-2 targets, pathogenic infection. However, the existing organoids of the digestive system mainly include the epithelial system. In order to reveal the pathogenic mechanism of digestive diseases, it is necessary to establish a completer and more physiological organoid model. Combining organoids and advanced techniques to test individualized treatments of different formulations is a promising approach that requires further exploration. This review highlights the advancements in the field of organoid technology from the perspectives of disease modeling and personalized therapy.
Collapse
|
37
|
Wang Y, Song W, Yu S, Liu Y, Chen YG. Intestinal cellular heterogeneity and disease development revealed by single-cell technology. CELL REGENERATION 2022; 11:26. [PMID: 36045190 PMCID: PMC9433512 DOI: 10.1186/s13619-022-00127-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 07/15/2022] [Indexed: 11/10/2022]
Abstract
The intestinal epithelium is responsible for food digestion and nutrient absorption and plays a critical role in hormone secretion, microorganism defense, and immune response. These functions depend on the integral single-layered intestinal epithelium, which shows diversified cell constitution and rapid self-renewal and presents powerful regeneration plasticity after injury. Derailment of homeostasis of the intestine epithelium leads to the development of diseases, most commonly including enteritis and colorectal cancer. Therefore, it is important to understand the cellular characterization of the intestinal epithelium at the molecular level and the mechanisms underlying its homeostatic maintenance. Single-cell technologies allow us to gain molecular insights at the single-cell level. In this review, we summarize the single-cell RNA sequencing applications to understand intestinal cell characteristics, spatiotemporal evolution, and intestinal disease development.
Collapse
|
38
|
|
39
|
Chalkidi N, Paraskeva C, Koliaraki V. Fibroblasts in intestinal homeostasis, damage, and repair. Front Immunol 2022; 13:924866. [PMID: 36032088 PMCID: PMC9399414 DOI: 10.3389/fimmu.2022.924866] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/20/2022] [Indexed: 12/02/2022] Open
Abstract
The mammalian intestine is a self-renewing tissue that ensures nutrient absorption while acting as a barrier against environmental insults. This is achieved by mature intestinal epithelial cells, the renewing capacity of intestinal stem cells at the base of the crypts, the development of immune tolerance, and the regulatory functions of stromal cells. Upon intestinal injury or inflammation, this tightly regulated mucosal homeostasis is disrupted and is followed by a series of events that lead to tissue repair and the restoration of organ function. It is now well established that fibroblasts play significant roles both in the maintenance of epithelial and immune homeostasis in the intestine and the response to tissue damage mainly through the secretion of a variety of soluble mediators and ligands and the remodeling of the extracellular matrix. In addition, recent advances in single-cell transcriptomics have revealed an unexpected heterogeneity of fibroblasts that comprise distinct cell subsets in normal and inflammatory conditions, indicative of diverse functions. However, there is still little consensus on the number, terminology, and functional properties of these subsets. Moreover, it is still unclear how individual fibroblast subsets can regulate intestinal repair processes and what is their impact on the pathogenesis of inflammatory bowel disease. In this mini-review, we aim to provide a concise overview of recent advances in the field, that we believe will help clarify current concepts on fibroblast heterogeneity and functions and advance our understanding of the contribution of fibroblasts in intestinal damage and repair.
Collapse
|
40
|
Wu CWK, Reid M, Leedham S, Lui RN. The emerging era of personalized medicine in advanced colorectal cancer. J Gastroenterol Hepatol 2022; 37:1411-1425. [PMID: 35815339 DOI: 10.1111/jgh.15937] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 12/09/2022]
Abstract
Colorectal cancer (CRC) is a genetically heterogeneous disease with its pathogenesis often driven by varying genetic or epigenetic alterations. This has led to a substantial number of patients developing chemoresistance and treatment failure, resulting in a high mortality rate for advanced disease. Deep molecular analysis has allowed for the discovery of key intestinal signaling pathways which impacts colonic epithelial cell fate, and the integral role of the tumor microenvironment on cancer growth and dissemination. Through transitioning pre-clinical knowledge in research into clinical practice, many potential druggable targets within these pathways have been discovered in the hopes of overcoming the roadblocks encountered by conventional therapies. A personalized approach tailoring treatment according to the histopathological and molecular features of individual tumors can hopefully translate to better patient outcomes, and reduce the rate of recurrence in patients with advanced CRC. Herein, the latest understanding on the molecular science behind CRC tumorigenesis, and the potential treatment targets currently at the forefront of research are summarized.
Collapse
Affiliation(s)
- Claudia W K Wu
- Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong, China.,Division of Gastroenterology and Hepatology, Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China
| | - Madeleine Reid
- Translational Gastroenterology Unit, John Radcliffe hospital, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simon Leedham
- Translational Gastroenterology Unit, John Radcliffe hospital, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rashid N Lui
- Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong, China.,Division of Gastroenterology and Hepatology, Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China.,Department of Clinical Oncology, Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|