1
|
Lei J, Fu J, Wang T, Guo Y, Gong M, Xia T, Shang S, Xu Y, Cheng L, Lin B. Molecular subtype identification and prognosis stratification by a immunogenic cell death-related gene expression signature in colorectal cancer. Expert Rev Anticancer Ther 2024; 24:635-647. [PMID: 38407877 DOI: 10.1080/14737140.2024.2320187] [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: 08/31/2023] [Accepted: 12/28/2023] [Indexed: 02/27/2024]
Abstract
OBJECTIVES This study intended to develop a new immunogenic cell death (ICD)-related prognostic signature for colorectal cancer (CRC) patients. RESEARCH DESIGN AND METHODS The Non-Negative Matrix Factorization (NMF) algorithm was adopted to cluster tumor samples based on ICD gene expression to obtain ICD-related subtypes. Survival analysis and immune microenvironment analysis were conducted among different subtypes. Regression analysis was used to construct the model. Based on riskscore median, cancer patients were classified into high and low risk groups, and independent prognostic ability of the model was analyzed. The CIBERSORT algorithm was adopted to determine the immune infiltration level of both groups. RESULTS We analyzed the differential genes between cluster 4 and cluster 1-3 and obtained 12 genes with the best prognostic features finally (NLGN1, SLC30A3, C3orf20, ADAD2, ATOH1, ATP6V1B1, KCNQ2, MUCL3, RGCC, CLEC17A, COL6A5, and INSL4). In addition, patients with lower risk had higher levels of infiltration of most immune cells, lower Tumor Immune Dysfunction and Exclusion (TIDE) level and higher immunophenscore (IPS) level than those with higher risk. CONCLUSIONS This study constructed and validated the ICD feature signature predicting CRC prognosis and provide a reference criteria for guiding the prognosis and immunotherapy of CRC cancer patients.
Collapse
Affiliation(s)
- Junping Lei
- Department of Colorectal and Anal Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, P.R, China
| | - Jia Fu
- Department of Pulmonary and Critical Care Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, P.R, China
| | - Tianyang Wang
- Department of Colorectal and Anal Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, P.R, China
| | - Yu Guo
- Department of Colorectal and Anal Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, P.R, China
| | - Mingmin Gong
- Department of Colorectal and Anal Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, P.R, China
| | - Tian Xia
- Department of Colorectal and Anal Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, P.R, China
| | - Song Shang
- Department of Colorectal and Anal Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, P.R, China
| | - Yan Xu
- Department of Colorectal and Anal Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, P.R, China
| | - Ling Cheng
- Zhejiang Luoxi Medical Technology Co. Ltd, Hangzhou, P.R, China
| | - Binghu Lin
- Department of Colorectal and Anal Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, P.R, China
| |
Collapse
|
2
|
Liu Y, Wang D, Luan Y, Tao B, Li Q, Feng Q, Zhou H, Mu J, Yu J. The application of organoids in colorectal diseases. Front Pharmacol 2024; 15:1412489. [PMID: 38983913 PMCID: PMC11231380 DOI: 10.3389/fphar.2024.1412489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/07/2024] [Indexed: 07/11/2024] Open
Abstract
Intestinal organoids are a three-dimensional cell culture model derived from colon or pluripotent stem cells. Intestinal organoids constructed in vitro strongly mimic the colon epithelium in cell composition, tissue architecture, and specific functions, replicating the colon epithelium in an in vitro culture environment. As an emerging biomedical technology, organoid technology has unique advantages over traditional two-dimensional culture in preserving parental gene expression and mutation, cell function, and biological characteristics. It has shown great potential in the research and treatment of colorectal diseases. Organoid technology has been widely applied in research on colorectal topics, including intestinal tumors, inflammatory bowel disease, infectious diarrhea, and intestinal injury regeneration. This review focuses on the application of organoid technology in colorectal diseases, including the basic principles and preparation methods of organoids, and explores the pathogenesis of and personalized treatment plans for various colorectal diseases to provide a valuable reference for organoid technology development and application.
Collapse
Affiliation(s)
- Yanxin Liu
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Dongxu Wang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Yanhong Luan
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Boqiang Tao
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
| | - Qirong Li
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Qiang Feng
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Hengzong Zhou
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Jianfeng Mu
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Jinhai Yu
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| |
Collapse
|
3
|
Singh A, Beaupre M, Villegas-Novoa C, Shiomitsu K, Gaudino SJ, Tawch S, Damle R, Kempen C, Choudhury B, McAleer JP, Sheridan BS, Denoya P, Blumberg RS, Hearing P, Allbritton NL, Kumar P. IL-22 promotes mucin-type O-glycosylation and MATH1 + cell-mediated amelioration of intestinal inflammation. Cell Rep 2024; 43:114206. [PMID: 38733584 PMCID: PMC11328608 DOI: 10.1016/j.celrep.2024.114206] [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: 08/30/2023] [Revised: 03/26/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
The interleukin (IL)-22 cytokine can be protective or inflammatory in the intestine. It is unclear if IL-22 receptor (IL-22Ra1)-mediated protection involves a specific type of intestinal epithelial cell (IEC). By using a range of IEC type-specific Il22Ra1 conditional knockout mice and a dextran sulfate sodium (DSS) colitis model, we demonstrate that IL-22Ra1 signaling in MATH1+ cells (goblet and progenitor cells) is essential for maintaining the mucosal barrier and intestinal tissue regeneration. The IL-22Ra1 signaling in IECs promotes mucin core-2 O-glycan extension and induces beta-1,3-galactosyltransferase 5 (B3GALT5) expression in the colon. Adenovirus-mediated expression of B3galt5 is sufficient to rescue Il22Ra1IEC mice from DSS colitis. Additionally, we observe a reduction in the expression of B3GALT5 and the Tn antigen, which indicates defective mucin O-glycan, in the colon tissue of patients with ulcerative colitis. Lastly, IL-22Ra1 signaling in MATH1+ progenitor cells promotes organoid regeneration after DSS injury. Our findings suggest that IL-22-dependent protective responses involve O-glycan modification, proliferation, and differentiation in MATH1+ progenitor cells.
Collapse
Affiliation(s)
- Ankita Singh
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael Beaupre
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Kiyoshi Shiomitsu
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Stephen J Gaudino
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Suzanne Tawch
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ruhee Damle
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Cody Kempen
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Biswa Choudhury
- GlycoAnalytics Core, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeremy P McAleer
- Department of Pharmaceutical Sciences, Marshall University School of Pharmacy, Huntington, WV 25701, USA
| | - Brian S Sheridan
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Paula Denoya
- Division of Colon and Rectal Surgery, Department of Surgery, Stony Brook University Hospital, Stony Brook, NY 11794, USA
| | - Richard S Blumberg
- Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick Hearing
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Pawan Kumar
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
| |
Collapse
|
4
|
Bao L, Fu L, Su Y, Chen Z, Peng Z, Sun L, Gonzalez FJ, Wu C, Zhang H, Shi B, Shi YB. Amino acid transporter SLC7A5 regulates cell proliferation and secretary cell differentiation and distribution in the mouse intestine. Int J Biol Sci 2024; 20:2187-2201. [PMID: 38617535 PMCID: PMC11008275 DOI: 10.7150/ijbs.94297] [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: 01/15/2024] [Accepted: 02/16/2024] [Indexed: 04/16/2024] Open
Abstract
The intestine is critical for not only processing nutrients but also protecting the organism from the environment. These functions are mainly carried out by the epithelium, which is constantly being self-renewed. Many genes and pathways can influence intestinal epithelial cell proliferation. Among them is mTORC1, whose activation increases cell proliferation. Here, we report the first intestinal epithelial cell (IEC)-specific knockout (ΔIEC) of an amino acid transporter capable of activating mTORC1. We show that the transporter, SLC7A5, is highly expressed in mouse intestinal crypt and Slc7a5ΔIEC reduces mTORC1 signaling. Surprisingly, adult Slc7a5ΔIEC intestinal crypts have increased cell proliferation but reduced mature Paneth cells. Goblet cells, the other major secretory cell type in the small intestine, are increased in the crypts but reduced in the villi. Analyses with scRNA-seq and electron microscopy have revealed dedifferentiation of Paneth cells in Slc7a5ΔIEC mice, leading to markedly reduced secretory granules with little effect on Paneth cell number. Thus, SLC7A5 likely regulates secretory cell differentiation to affect stem cell niche and indirectly regulate cell proliferation.
Collapse
Affiliation(s)
- Lingyu Bao
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, MD, USA
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine. No.277, Yanta West Road, Xi'an, Shaanxi, 710061, P.R. China
| | - Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, MD, USA
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging and Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Zuojia Chen
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhaoyi Peng
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, MD, USA
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine. No.277, Yanta West Road, Xi'an, Shaanxi, 710061, P.R. China
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J. Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hongen Zhang
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Bingyin Shi
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine. No.277, Yanta West Road, Xi'an, Shaanxi, 710061, P.R. China
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, MD, USA
| |
Collapse
|
5
|
Beumer J, Clevers H. Hallmarks of stemness in mammalian tissues. Cell Stem Cell 2024; 31:7-24. [PMID: 38181752 PMCID: PMC10769195 DOI: 10.1016/j.stem.2023.12.006] [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: 11/06/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
All adult tissues experience wear and tear. Most tissues can compensate for cell loss through the activity of resident stem cells. Although the cellular maintenance strategies vary greatly between different adult (read: postnatal) tissues, the function of stem cells is best defined by their capacity to replace lost tissue through division. We discuss a set of six complementary hallmarks that are key enabling features of this basic function. These include longevity and self-renewal, multipotency, transplantability, plasticity, dependence on niche signals, and maintenance of genome integrity. We discuss these hallmarks in the context of some of the best-understood adult stem cell niches.
Collapse
Affiliation(s)
- Joep Beumer
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Basel, Switzerland.
| | - Hans Clevers
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Basel, Switzerland.
| |
Collapse
|
6
|
Boers R, Boers J, Tan B, van Leeuwen ME, Wassenaar E, Sanchez EG, Sleddens E, Tenhagen Y, Mulugeta E, Laven J, Creyghton M, Baarends W, van IJcken WFJ, Gribnau J. Retrospective analysis of enhancer activity and transcriptome history. Nat Biotechnol 2023; 41:1582-1592. [PMID: 36823354 PMCID: PMC10635829 DOI: 10.1038/s41587-023-01683-1] [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: 07/01/2021] [Accepted: 01/20/2023] [Indexed: 02/25/2023]
Abstract
Cell state changes in development and disease are controlled by gene regulatory networks, the dynamics of which are difficult to track in real time. In this study, we used an inducible DCM-RNA polymerase subunit b fusion protein which labels active genes and enhancers with a bacterial methylation mark that does not affect gene transcription and is propagated in S-phase. This DCM-RNA polymerase fusion protein enables transcribed genes and active enhancers to be tagged and then examined at later stages of development or differentiation. We apply this DCM-time machine (DCM-TM) technology to study intestinal homeostasis, revealing rapid and coordinated activation of enhancers and nearby genes during enterocyte differentiation. We provide new insights in absorptive-secretory lineage decision-making in intestinal stem cell (ISC) differentiation and show that ISCs retain a unique chromatin landscape required to maintain ISC identity and delineate future expression of differentiation-associated genes. DCM-TM has wide applicability in tracking cell states, providing new insights in the regulatory networks underlying cell state changes.
Collapse
Affiliation(s)
- Ruben Boers
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Joachim Boers
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Beatrice Tan
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marieke E van Leeuwen
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Erlantz Gonzalez Sanchez
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Esther Sleddens
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Yasha Tenhagen
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Joop Laven
- Department of Obstetrics and Gynaecology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Menno Creyghton
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Willy Baarends
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.
| |
Collapse
|
7
|
Campillo Poveda M, Britton C, Devaney E, McNeilly TN, Gerbe F, Jay P, Maizels RM. Tuft Cells: Detectors, Amplifiers, Effectors and Targets in Parasite Infection. Cells 2023; 12:2477. [PMID: 37887321 PMCID: PMC10605326 DOI: 10.3390/cells12202477] [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: 08/25/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Tuft cells have recently emerged as the focus of intense interest following the discovery of their chemosensory role in the intestinal tract, and their ability to activate Type 2 immune responses to helminth parasites. Moreover, they populate a wide range of mucosal tissues and are intimately connected to immune and neuronal cells, either directly or through the release of pharmacologically active mediators. They are now recognised to fulfil both homeostatic roles, in metabolism and tissue integrity, as well as acting as the first sensors of parasite infection, immunity to which is lost in their absence. In this review we focus primarily on the importance of tuft cells in the intestinal niche, but also link to their more generalised physiological role and discuss their potential as targets for the treatment of gastrointestinal disorders.
Collapse
Affiliation(s)
- Marta Campillo Poveda
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK;
| | - Collette Britton
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK; (C.B.); (E.D.)
| | - Eileen Devaney
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK; (C.B.); (E.D.)
| | - Tom N. McNeilly
- Disease Control Department, Moredun Research Institute, Penicuik EH26 0PZ, UK;
| | - François Gerbe
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, F-34094 Montpellier, France; (F.G.); (P.J.)
| | - Philippe Jay
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, F-34094 Montpellier, France; (F.G.); (P.J.)
| | - Rick M. Maizels
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK;
| |
Collapse
|
8
|
Orzechowska-Licari EJ, Bialkowska AB, Yang VW. Sonic Hedgehog and WNT Signaling Regulate a Positive Feedback Loop Between Intestinal Epithelial and Stromal Cells to Promote Epithelial Regeneration. Cell Mol Gastroenterol Hepatol 2023; 16:607-642. [PMID: 37481204 PMCID: PMC10470419 DOI: 10.1016/j.jcmgh.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/24/2023]
Abstract
BACKGROUND AND AIMS Active intestinal stem cells are prone to injury by ionizing radiation. We previously showed that upon radiation-induced injury, normally quiescent reserve intestinal stem cells (rISCs) (marked by BMI1) are activated by Musashi-1 (MSI1) and exit from the quiescent state to regenerate the intestinal epithelium. This study aims to further establish the mechanism that regulates activation of Bmi1-CreER;Rosa26eYFP (Bmi1-CreER) rISCs following γ radiation-induced injury. METHODS Bmi1-CreER mice were treated with tamoxifen to initiate lineage tracing of BMI1 (eYFP+) cells and exposed to 12 Gy of total body γ irradiation or sham. Intestinal tissues were collected and analyzed by immunofluorescence, Western blot, reverse-transcription quantitative polymerase chain reaction, enzyme-linked immunosorbent assay, and chromatin immunoprecipitation real-time polymerase chain reaction. RESULTS After irradiation, increased expression of Msi1 in eYFP+ cells was accompanied by increased expression of Axin2, a WNT marker. Promoter studies of the Msi1 gene indicated that Msi1 is a WNT target gene. Coculture of stromal cells isolated from irradiated mice stimulated Bmi1-CreER-derived organoid regeneration more effectively than those from sham mice. Expression of WNT ligands, including Wnt2b, Wnt4, Wnt5a, and Rspo3, was increased in irradiated stromal cells compared with sham-treated stromal cells. Moreover, expression of the Sonic hedgehog (SHH) effector Gli1 was increased in stromal cells from irradiated mice. This was correlated with an increased expression of SHH in epithelial cells postirradiation, indicating epithelial-stromal interaction. Finally, preinjury treatment with SHH inhibitor cyclopamine significantly reduced intestinal epithelial regeneration and Msi1 expression postirradiation. CONCLUSIONS Upon ionizing radiation-induced injury, intestinal epithelial cells increase SHH secretion, stimulating stromal cells to secrete WNT ligands. WNT activators induce Msi1 expression in the Bmi1-CreER cells. This stromal-epithelial interaction leads to Bmi1-CreER rISCs induction and epithelial regeneration.
Collapse
Affiliation(s)
| | - Agnieszka B Bialkowska
- Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York.
| | - Vincent W Yang
- Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York; Department of Physiology and Biophysics, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York.
| |
Collapse
|
9
|
Bao L, Fu L, Su Y, Chen Z, Peng Z, Sun L, Gonzalez FJ, Wu C, Zhang H, Shi B, Shi YB. Amino acid transporter SLC7A5 regulates Paneth cell function to affect the intestinal inflammatory response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.524966. [PMID: 36789439 PMCID: PMC9928054 DOI: 10.1101/2023.01.24.524966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The intestine is critical for not only processing and resorbing nutrients but also protecting the organism from the environment. These functions are mainly carried out by the epithelium, which is constantly being self-renewed. Many genes and pathways can influence intestinal epithelial cell proliferation. Among them is mTORC1, whose activation increases cell proliferation. Here, we report the first intestinal epithelial cell-specific knockout ( ΔIEC ) of an amino acid transporter capable of activating mTORC1. We show that the transporter, SLC7A5, is highly expressed in mouse intestinal crypt and Slc7a5 ΔIEC reduces mTORC1 signaling. Surprisingly, Slc7a5 ΔIEC mice have increased cell proliferation but reduced secretory cells, particularly mature Paneth cells. scRNA-seq and electron microscopic analyses revealed dedifferentiation of Paneth cells in Slc7a5 ΔIEC mice, leading to markedly reduced secretory granules with little effect on Paneth cell number. We further show that Slc7a5 ΔIEC mice are prone to experimental colitis. Thus, SLC7A5 regulates secretory cell differentiation to affect stem cell niche and/or inflammatory response to regulate cell proliferation.
Collapse
|
10
|
Du Y, Gao H, He C, Xin S, Wang B, Zhang S, Gong F, Yu X, Pan L, Sun F, Wang W, Xu J. An update on the biological characteristics and functions of tuft cells in the gut. Front Cell Dev Biol 2023; 10:1102978. [PMID: 36704202 PMCID: PMC9872863 DOI: 10.3389/fcell.2022.1102978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
The intestine is a powerful digestive system and one of the most sophisticated immunological organs. Evidence shows that tuft cells (TCs), a kind of epithelial cell with distinct morphological characteristics, play a significant role in various physiological processes. TCs can be broadly categorized into different subtypes depending on different molecular criteria. In this review, we discuss its biological properties and role in maintaining homeostasis in the gastrointestinal tract. We also emphasize its relevance to the immune system and highlight its powerful influence on intestinal diseases, including inflammations and tumors. In addition, we provide fresh insights into future clinical diagnostic and therapeutic strategies related to TCs.
Collapse
Affiliation(s)
- Yixuan Du
- Department of Oral Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Han Gao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Chengwei He
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Shuzi Xin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Boya Wang
- Undergraduate Student of 2018 Eight Program of Clinical Medicine, Peking University People’s Hospital, Beijing, China
| | - Sitian Zhang
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Fengrong Gong
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xinyi Yu
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Luming Pan
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Fanglin Sun
- Department of Laboratory Animal Research, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Wen Wang
- Department of Laboratory Animal Research, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Jingdong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China,*Correspondence: Jingdong Xu,
| |
Collapse
|
11
|
Che J, Yu S. Ecological niches for colorectal cancer stem cell survival and thrival. Front Oncol 2023; 13:1135364. [PMID: 37124519 PMCID: PMC10134776 DOI: 10.3389/fonc.2023.1135364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/17/2023] [Indexed: 05/02/2023] Open
Abstract
To date, colorectal cancer is still ranking top three cancer types severely threatening lives. According to cancer stem cell hypothesis, malignant colorectal lumps are cultivated by a set of abnormal epithelial cells with stem cell-like characteristics. These vicious stem cells are derived from intestinal epithelial stem cells or transformed by terminally differentiated epithelial cells when they accumulate an array of transforming genomic alterations. Colorectal cancer stem cells, whatever cell-of-origin, give rise to all morphologically and functionally heterogenous tumor daughter cells, conferring them with overwhelming resilience to intrinsic and extrinsic stresses. On the other hand, colorectal cancer stem cells and their daughter cells continuously participate in constructing ecological niches for their survival and thrival by communicating with adjacent stromal cells and circulating immune guardians. In this review, we first provide an overview of the normal cell-of-origin populations contributing to colorectal cancer stem cell reservoirs and the niche architecture which cancer stem cells depend on at early stage. Then we survey recent advances on how these aberrant niches are fostered by cancer stem cells and their neighbors. We also discuss recent research on how niche microenvironment affects colorectal cancer stem cell behaviors such as plasticity, metabolism, escape of immune surveillance as well as resistance to clinical therapies, therefore endowing them with competitive advantages compared to their normal partners. In the end, we explore therapeutic strategies available to target malignant stem cells.
Collapse
Affiliation(s)
- Jiayun Che
- Shanghai Institute of Precision Medicine, 9 Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiyan Yu
- Shanghai Institute of Precision Medicine, 9 Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Oncology, 9 Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Shiyan Yu,
| |
Collapse
|
12
|
Yagishita Y, Joshi T, Kensler TW, Wakabayashi N. Transcriptional Regulation of Math1 by Aryl Hydrocarbon Receptor: Effect on Math1 + Progenitor Cells in Mouse Small Intestine. Mol Cell Biol 2023; 43:43-63. [PMID: 36720468 PMCID: PMC9937019 DOI: 10.1080/10985549.2022.2160610] [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: 09/13/2022] [Accepted: 11/29/2022] [Indexed: 01/28/2023] Open
Abstract
The physiological roles of aryl hydrocarbon receptor (AhR) in the small intestine have been revealed as immunomodulatory and barrier functions. However, its contributions to cell fate regulation are incompletely understood. The Notch-activated signaling cascade is a central component of intestinal cell fate determinations. The lateral inhibitory mechanism governed by Notch directs cell fates toward distinct cell lineages (i.e., absorptive and secretory cell lineages) through its downstream effector, mouse atonal homolog 1 (MATH1). An investigation employing cell lines and intestinal crypt cells revealed that AhR regulates Math1 expression in a xenobiotic response element (XRE)-dependent manner. The AhR-Math1 axis was further addressed using intestinal organoids, where AhR-Math1 and HES1-Math1 axes appeared to coexist within the underlying Math1 transcriptional machinery. When the HES1-Math1 axis was pharmacologically suppressed, β-naphthoflavone-mediated AhR activation increased the number of goblet and Math1+ progenitor cells in the organoids. The same pharmacological dissection of the AhR-Math1 axis was applied in vivo, demonstrating an enhanced number of Math1+ progenitor cells in the small intestine following AhR activation. We report here that AhR-Math1 is a direct transcriptional axis with effects on Math1+ progenitor cells in the small intestine, highlighting a novel molecular basis for fine-tuning Notch-mediated cell fate regulation.
Collapse
Affiliation(s)
- Yoko Yagishita
- Translational Research Program, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Tanvi Joshi
- Translational Research Program, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Thomas W. Kensler
- Translational Research Program, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Nobunao Wakabayashi
- Translational Research Program, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| |
Collapse
|
13
|
Dou Y, Pizarro T, Zhou L. Organoids as a Model System for Studying Notch Signaling in Intestinal Epithelial Homeostasis and Intestinal Cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1347-1357. [PMID: 35752229 PMCID: PMC9552028 DOI: 10.1016/j.ajpath.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/16/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Organoid culture is an approach that allows three-dimensional growth for stem cells to self-organize and develop multicellular structures. Intestinal organoids have been widely used to study cellular or molecular processes in stem cell and cancer research. These cultures possess the ability to maintain cellular complexity as well as recapitulate many properties of the human intestinal epithelium, thereby providing an ideal in vitro model to investigate cellular and molecular signaling pathways. These include, but are not limited to, the mechanisms required for maintaining balanced populations of epithelial cells. Notch signaling is one of the major pathways of regulating stem cell functions in the gut, driving proliferation and controlling cell fate determination. Notch also plays an important role in regulating tumor progression and metastasis. Understanding how Notch pathway regulates epithelial regeneration and differentiation by using intestinal organoids is critical for studying both homeostasis and pathogenesis of intestinal stem cells that can lead to discoveries of new targets for drug development to treat intestinal diseases. In addition, use of patient-derived organoids can provide effective personalized medicine. This review summarizes the current literature regarding epithelial Notch pathways regulating intestinal homeostasis and regeneration, highlighting the use of organoid cultures and their potential therapeutic applications.
Collapse
Affiliation(s)
- Yingtong Dou
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Theresa Pizarro
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Lan Zhou
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio.
| |
Collapse
|
14
|
Wang J, Shang L, Zhang J, Yu Z, Huang J, Jin J, Lv C. Nfatc1 + colonic stem cells contribute to regeneration upon colitis. J Gastroenterol Hepatol 2022; 37:734-740. [PMID: 35102609 DOI: 10.1111/jgh.15790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/14/2021] [Accepted: 01/03/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND AND AIM Colonic stem cells play important roles in both normal epithelial turnover and injury repair. Lgr5+ colonic stem cells are highly susceptible to DSS-induced damage. However, it is still unclear how colonic stem cells regenerate injured epithelium during colitis. Here, we explored the functions of a new population of NFATc1+ colonic stem cells in experimental colitis. METHODS Nfatc1+ colonic stem cells were labeled using Nfatc1CreERT2 ;R26mTmG reporter mice. Immunostaining assays were used to detect Goblet cells, enteroendocrine cells, and intestinal stem/progenitor cells. We performed lineage tracing assay to investigate whether Nfatc1+ cells are real colonic stem cells using Nfatc1CreERT2 ;R26mTmG mice. The contribution of Nfatc1+ stem cells on epithelial regeneration was detected in experimental colitis induced by DSS. RESULTS Nfatc1-reporter marked cells are enriched for +3 to +5 position in colonic crypts, and they are overlapped with Sox9+ cells and Hopx+ cells that have been identified as stem cells in small intestine. However, Nfatc1-reporter marked cells are not overlapped with Lgr5+ colonic stem cells, as well as differentiated goblet cells and enteroendocrine cells. Furthermore, Nfatc1-reporter marked cells are able to give rise to all lineages of the colonic epithelium, and they preferentially contribute to the regeneration of colonic epithelium in DSS-induced experimental colitis. CONCLUSION Nfatc1+ cells were identified as a novel population of colonic stem cells that are primarily located at +3 to +5 position and contribute to epithelial regeneration during colitis.
Collapse
Affiliation(s)
- Jianyang Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Linkuo Shang
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Jiahui Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Zhengquan Yu
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiaqiang Huang
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Jing Jin
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Cong Lv
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, Department of Nutrition and Health, China Agricultural University, Beijing, China
| |
Collapse
|
15
|
Medina A, Bellec K, Polcowñuk S, Cordero JB. Investigating local and systemic intestinal signalling in health and disease with Drosophila. Dis Model Mech 2022; 15:274860. [PMID: 35344037 PMCID: PMC8990086 DOI: 10.1242/dmm.049332] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Whole-body health relies on complex inter-organ signalling networks that enable organisms to adapt to environmental perturbations and to changes in tissue homeostasis. The intestine plays a major role as a signalling centre by producing local and systemic signals that are relayed to the body and that maintain intestinal and organismal homeostasis. Consequently, disruption of intestinal homeostasis and signalling are associated with systemic diseases and multi-organ dysfunction. In recent years, the fruit fly Drosophila melanogaster has emerged as a prime model organism to study tissue-intrinsic and systemic signalling networks of the adult intestine due to its genetic tractability and functional conservation with mammals. In this Review, we highlight Drosophila research that has contributed to our understanding of how the adult intestine interacts with its microenvironment and with distant organs. We discuss the implications of these findings for understanding intestinal and whole-body pathophysiology, and how future Drosophila studies might advance our knowledge of the complex interplay between the intestine and the rest of the body in health and disease. Summary: We outline work in the fruit fly Drosophila melanogaster that has contributed knowledge on local and whole-body signalling coordinated by the adult intestine, and discuss its implications in intestinal pathophysiology and associated systemic dysfunction.
Collapse
Affiliation(s)
- Andre Medina
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK.,CRUK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Karen Bellec
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Sofia Polcowñuk
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Julia B Cordero
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK.,CRUK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| |
Collapse
|
16
|
Abstract
Complex multicellular organisms have evolved specific mechanisms to replenish cells in homeostasis and during repair. Here, we discuss how emerging technologies (e.g., single-cell RNA sequencing) challenge the concept that tissue renewal is fueled by unidirectional differentiation from a resident stem cell. We now understand that cell plasticity, i.e., cells adaptively changing differentiation state or identity, is a central tissue renewal mechanism. For example, mature cells can access an evolutionarily conserved program (paligenosis) to reenter the cell cycle and regenerate damaged tissue. Most tissues lack dedicated stem cells and rely on plasticity to regenerate lost cells. Plasticity benefits multicellular organisms, yet it also carries risks. For one, when long-lived cells undergo paligenotic, cyclical proliferation and redif-ferentiation, they can accumulate and propagate acquired mutations that activate oncogenes and increase the potential for developing cancer. Lastly, we propose a new framework for classifying patterns of cell proliferation in homeostasis and regeneration, with stem cells representing just one of the diverse methods that adult tissues employ.
Collapse
Affiliation(s)
- Jeffrey W. Brown
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Charles J. Cho
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA,Current affiliation: Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Jason C. Mills
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA,Current affiliation: Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA,Departments of Pathology and Immunology and Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA,Current affiliation: Departments of Medicine, Pathology and Immunology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
17
|
Lin X, Gaudino SJ, Jang KK, Bahadur T, Singh A, Banerjee A, Beaupre M, Chu T, Wong HT, Kim CK, Kempen C, Axelrad J, Huang H, Khalid S, Shah V, Eskiocak O, Parks OB, Berisha A, McAleer JP, Good M, Hoshino M, Blumberg R, Bialkowska AB, Gaffen SL, Kolls JK, Yang VW, Beyaz S, Cadwell K, Kumar P. IL-17RA-signaling in Lgr5 + intestinal stem cells induces expression of transcription factor ATOH1 to promote secretory cell lineage commitment. Immunity 2022; 55:237-253.e8. [PMID: 35081371 PMCID: PMC8895883 DOI: 10.1016/j.immuni.2021.12.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/06/2021] [Accepted: 12/20/2021] [Indexed: 12/14/2022]
Abstract
The Th17 cell-lineage-defining cytokine IL-17A contributes to host defense and inflammatory disease by coordinating multicellular immune responses. The IL-17 receptor (IL-17RA) is expressed by diverse intestinal cell types, and therapies targeting IL-17A induce adverse intestinal events, suggesting additional tissue-specific functions. Here, we used multiple conditional deletion models to identify a role for IL-17A in secretory epithelial cell differentiation in the gut. Paneth, tuft, goblet, and enteroendocrine cell numbers were dependent on IL-17A-mediated induction of the transcription factor ATOH1 in Lgr5+ intestinal epithelial stem cells. Although dispensable at steady state, IL-17RA signaling in ATOH1+ cells was required to regenerate secretory cells following injury. Finally, IL-17A stimulation of human-derived intestinal organoids that were locked into a cystic immature state induced ATOH1 expression and rescued secretory cell differentiation. Our data suggest that the cross talk between immune cells and stem cells regulates secretory cell lineage commitment and the integrity of the mucosa.
Collapse
Affiliation(s)
- Xun Lin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Stephen J Gaudino
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Kyung Ku Jang
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Tej Bahadur
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Ankita Singh
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Anirban Banerjee
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Michael Beaupre
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Timothy Chu
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Hoi Tong Wong
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Chang-Kyung Kim
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Cody Kempen
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Jordan Axelrad
- Division of Gastroenterology and Hepatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Huakang Huang
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Saba Khalid
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Vyom Shah
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Onur Eskiocak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Olivia B Parks
- University of Pittsburgh School of Medicine, Medical Scientist Training Program, Pittsburgh, PA 15213, USA
| | - Artan Berisha
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Jeremy P McAleer
- Department of Pharmaceutical Science, Marshall University School of Pharmacy, Huntington, WV 25701, USA
| | - Misty Good
- Washington University School of Medicine, Department of Pediatrics, Division of Newborn Medicine, St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - Miko Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Richard Blumberg
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Agnieszka B Bialkowska
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sarah L Gaffen
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jay K Kolls
- Center for Translational Research in Infection and Inflammation, Tulane School of Medicine, New Orleans, LA 70112, USA
| | - Vincent W Yang
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - Pawan Kumar
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA.
| |
Collapse
|
18
|
Ramadan R, van Driel MS, Vermeulen L, van Neerven SM. Intestinal stem cell dynamics in homeostasis and cancer. Trends Cancer 2022; 8:416-425. [DOI: 10.1016/j.trecan.2022.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 12/31/2022]
|
19
|
Meyer AR, Brown ME, McGrath PS, Dempsey PJ. Injury-Induced Cellular Plasticity Drives Intestinal Regeneration. Cell Mol Gastroenterol Hepatol 2021; 13:843-856. [PMID: 34915204 PMCID: PMC8803615 DOI: 10.1016/j.jcmgh.2021.12.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022]
Abstract
The epithelial lining of the intestine, particularly the stem cell compartment, is affected by harsh conditions in the luminal environment and also is susceptible to genotoxic agents such as radiation and chemotherapy. Therefore, the ability for intestinal epithelial cells to revert to a stem cell state is an important physiological damage response to regenerate the intestinal epithelium at sites of mucosal injury. Many signaling networks involved in maintaining the stem cell niche are activated as part of the damage response to promote cellular plasticity and regeneration. The relative contribution of each cell type and signaling pathway is a critical area of ongoing research, likely dependent on the nature of injury as well as the regional specification within the intestine. Here, we review the current understanding of the multicellular cooperation to restore the intestinal epithelium after damage.
Collapse
Affiliation(s)
| | | | | | - Peter J. Dempsey
- Correspondence Address correspondence to: Peter J. Dempsey, PhD, Section of Developmental Biology, Department of Pediatrics, University of Colorado School of Medicine, 1775 Aurora Court, Barbara Davis Center, M20–3306, Aurora, Colorado 80045. fax: (303) 724-6538.
| |
Collapse
|
20
|
Hayakawa Y, Nakagawa H, Rustgi AK, Que J, Wang TC. Stem cells and origins of cancer in the upper gastrointestinal tract. Cell Stem Cell 2021; 28:1343-1361. [PMID: 34129814 DOI: 10.1016/j.stem.2021.05.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The esophagus and stomach, joined by a unique transitional zone, contain actively dividing epithelial stem cells required for organ homeostasis. Upon prolonged inflammation, epithelial cells in both organs can undergo a cell fate switch leading to intestinal metaplasia, predisposing to malignancy. Here we discuss the biology of gastroesophageal stem cells and their role as cells of origin in cancer. We summarize the interactions between the stromal niche and gastroesophageal stem cells in metaplasia and early expansion of mutated stem-cell-derived clones during carcinogenesis. Finally, we review new approaches under development to better study gastroesophageal stem cells and advance the field.
Collapse
Affiliation(s)
- Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyoku, Tokyo 113-8655, Japan
| | - Hiroshi Nakagawa
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Anil K Rustgi
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Jianwen Que
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Columbia Center for Human Development, Department of Medicine, Columbia University, College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA.
| | - Timothy C Wang
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, 1130 St. Nicholas Avenue, New York, NY 10032, USA.
| |
Collapse
|
21
|
Mitoyan L, Chevrier V, Hernandez-Vargas H, Ollivier A, Homayed Z, Pannequin J, Poizat F, De Biasi-Cador C, Charafe-Jauffret E, Ginestier C, Guasch G. A stem cell population at the anorectal junction maintains homeostasis and participates in tissue regeneration. Nat Commun 2021; 12:2761. [PMID: 33980830 PMCID: PMC8115161 DOI: 10.1038/s41467-021-23034-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/11/2021] [Indexed: 11/09/2022] Open
Abstract
At numerous locations of the body, transition zones are localized at the crossroad between two types of epithelium and are frequently associated with neoplasia involving both type of tissues. These transition zones contain cells expressing markers of adult stem cells that can be the target of early transformation. The mere fact that transition zone cells can merge different architecture with separate functions implies for a unique plasticity that these cells must display in steady state. However, their roles during tissue regeneration in normal and injured state remain unknown. Here, by using in vivo lineage tracing, single-cell transcriptomics, computational modeling and a three-dimensional organoid culture system of transition zone cells, we identify a population of Krt17+ basal cells with multipotent properties at the squamo-columnar anorectal junction that maintain a squamous epithelium during normal homeostasis and can participate in the repair of a glandular epithelium following tissue injury.
Collapse
Affiliation(s)
- Louciné Mitoyan
- Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Véronique Chevrier
- Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Hector Hernandez-Vargas
- Department of Immunity, Virus and Inflammation, Cancer Research Center of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, Lyon Cedex 08, France.,Department of Translational Research and Innovation, Centre Léon Bérard, Lyon Cedex 08, France
| | - Alexane Ollivier
- Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Zeinab Homayed
- CNRS, UMR5203, Inserm U661, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Julie Pannequin
- CNRS, UMR5203, Inserm U661, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Flora Poizat
- Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | | | - Emmanuelle Charafe-Jauffret
- Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France.,Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | - Christophe Ginestier
- Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Géraldine Guasch
- Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France.
| |
Collapse
|
22
|
Sphyris N, Hodder MC, Sansom OJ. Subversion of Niche-Signalling Pathways in Colorectal Cancer: What Makes and Breaks the Intestinal Stem Cell. Cancers (Basel) 2021; 13:1000. [PMID: 33673710 PMCID: PMC7957493 DOI: 10.3390/cancers13051000] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
The intestinal epithelium fulfils pleiotropic functions in nutrient uptake, waste elimination, and immune surveillance while also forming a barrier against luminal toxins and gut-resident microbiota. Incessantly barraged by extraneous stresses, the intestine must continuously replenish its epithelial lining and regenerate the full gamut of specialized cell types that underpin its functions. Homeostatic remodelling is orchestrated by the intestinal stem cell (ISC) niche: a convergence of epithelial- and stromal-derived cues, which maintains ISCs in a multipotent state. Following demise of homeostatic ISCs post injury, plasticity is pervasive among multiple populations of reserve stem-like cells, lineage-committed progenitors, and/or fully differentiated cell types, all of which can contribute to regeneration and repair. Failure to restore the epithelial barrier risks seepage of toxic luminal contents, resulting in inflammation and likely predisposing to tumour formation. Here, we explore how homeostatic niche-signalling pathways are subverted in tumorigenesis, enabling ISCs to gain autonomy from niche restraints ("ISC emancipation") and transform into cancer stem cells capable of driving tumour initiation, progression, and therapy resistance. We further consider the implications of the pervasive plasticity of the intestinal epithelium for the trajectory of colorectal cancer, the emergence of distinct molecular subtypes, the propensity to metastasize, and the development of effective therapeutic strategies.
Collapse
Affiliation(s)
- Nathalie Sphyris
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; (N.S.); (M.C.H.)
| | - Michael C. Hodder
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; (N.S.); (M.C.H.)
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; (N.S.); (M.C.H.)
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| |
Collapse
|
23
|
Iwaya M, Ota H, Nakajima T, Uehara T, Riddell R, Conner J. Most colitis associated carcinomas lack expression of LGR5: a preliminary study with implications for unique pathways of carcinogenesis compared to sporadic colorectal carcinoma. BMC Cancer 2021; 21:119. [PMID: 33541282 PMCID: PMC7863293 DOI: 10.1186/s12885-021-07835-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
Background Leucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5), a component of the Wnt receptor complex, is thought to lineage label gastric and intestinal stem cells. LGR5 expression is increased in colorectal carcinoma (CRC) compared to normal tissue. Colitis associated colorectal adenocarcinoma (CAC) often shows distinct morphologic and molecular phenotypes compared to sporadic cases. However, the expression profile of LGR5, and by extension the potential role of an intestinal stem cell phenotype, has not been well described in a series of human CAC. Method RNA in situ hybridization (ISH) for LGR5 expression on 30 CACs (12 cases with conventional morphology and 18 cases with non-conventional type morphology) from 29 inflammatory bowel disease (IBD) patients was performed and compared the expression profile to a control group of 10 sporadic CRCs. Immunohistochemistry for beta-catenin and SATB2 was performed on the 30 CACs. Result LGR5 was positive in 30% (9/30) of CAC cases and 90% (9/10) of sporadic CRCs (p = 0.002). A large majority (89%) of LGR5 positive CACs were of the conventional histologic type, and conventional type CAC showed a significantly higher LGR5 score (median 3.0; interquartile range 1.75–3.25) than non-conventional type CAC (median 1.5; interquartile range 1.00–2.00) (p = 0.034). CAC with conventional morphology did have a lower level of LGR5 expression than sporadic CRC. Sporadic CRCs showed a significantly higher LGR5 level score than non-conventional type CACs (p < 0.001). Nuclear translocation of beta-catenin was strongly associated with LGR5 expression (p = 0.003), however no significant association was identified between SATB2 expression and LGR5 expression status in CACs. Conclusion These findings suggest that the wider spectrum of tumor morphology in CAC may be associated with absence of a LGR5-expressing intestinal stem cell phenotype.
Collapse
Affiliation(s)
- Mai Iwaya
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada. .,Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano, Japan.
| | - Hiroyoshi Ota
- Department of Clinical Laboratory Sciences, School of Health Sciences, Shinshu University, Matsumoto, Japan
| | - Tomoyuki Nakajima
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano, Japan
| | - Takeshi Uehara
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano, Japan
| | - Robert Riddell
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - James Conner
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| |
Collapse
|
24
|
Hageman JH, Heinz MC, Kretzschmar K, van der Vaart J, Clevers H, Snippert HJG. Intestinal Regeneration: Regulation by the Microenvironment. Dev Cell 2021; 54:435-446. [PMID: 32841594 DOI: 10.1016/j.devcel.2020.07.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Accepted: 07/13/2020] [Indexed: 01/05/2023]
Abstract
Damage to the intestinal stem cell niche can result from mechanical stress, infections, chronic inflammation or cytotoxic therapies. Progenitor cells can compensate for insults to the stem cell population through dedifferentiation. The microenvironment modulates this regenerative response by influencing the activity of signaling pathways, including Wnt, Notch, and YAP/TAZ. For instance, mesenchymal cells and immune cells become more abundant after damage and secrete signaling molecules that promote the regenerative process. Furthermore, regeneration is influenced by the nutritional state, microbiome, and extracellular matrix. Here, we review how all these components cooperate to restore epithelial homeostasis in the intestine after injury.
Collapse
Affiliation(s)
- Joris H Hageman
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Maria C Heinz
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Kai Kretzschmar
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Mildred-Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Jelte van der Vaart
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands.
| |
Collapse
|
25
|
Rees WD, Tandun R, Yau E, Zachos NC, Steiner TS. Regenerative Intestinal Stem Cells Induced by Acute and Chronic Injury: The Saving Grace of the Epithelium? Front Cell Dev Biol 2020; 8:583919. [PMID: 33282867 PMCID: PMC7688923 DOI: 10.3389/fcell.2020.583919] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
The intestinal epithelium is replenished every 3-4 days through an orderly process that maintains important secretory and absorptive functions while preserving a continuous mucosal barrier. Intestinal epithelial cells (IECs) derive from a stable population of intestinal stem cells (ISCs) that reside in the basal crypts. When intestinal injury reaches the crypts and damages IECs, a mechanism to replace them is needed. Recent research has highlighted the existence of distinct populations of acute and chronic damage-associated ISCs and their roles in maintaining homeostasis in several intestinal perturbation models. What remains unknown is how the damage-associated regenerative ISC population functions in the setting of chronic inflammation, as opposed to acute injury. What long-term consequences result from persistent inflammation and other cellular insults to the ISC niche? What particular "regenerative" cell types provide the most efficacious restorative properties? Which differentiated IECs maintain the ability to de-differentiate and restore the ISC niche? This review will cover the latest research on damage-associated regenerative ISCs and epigenetic factors that determine ISC fate, as well as provide opinions on future studies that need to be undertaken to understand the repercussions of the emergence of these cells, their contribution to relapses in inflammatory bowel disease, and their potential use in therapeutics for chronic intestinal diseases.
Collapse
Affiliation(s)
- William D Rees
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Rene Tandun
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Enoch Yau
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Nicholas C Zachos
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Theodore S Steiner
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| |
Collapse
|
26
|
Improved detection of tumor suppressor events in single-cell RNA-Seq data. NPJ Genom Med 2020; 5:43. [PMID: 33083012 PMCID: PMC7541488 DOI: 10.1038/s41525-020-00151-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/21/2020] [Indexed: 12/17/2022] Open
Abstract
Tissue-specific transcription factors are frequently inactivated in cancer. To fully dissect the heterogeneity of such tumor suppressor events requires single-cell resolution, yet this is challenging because of the high dropout rate. Here we propose a simple yet effective computational strategy called SCIRA to infer regulatory activity of tissue-specific transcription factors at single-cell resolution and use this tool to identify tumor suppressor events in single-cell RNA-Seq cancer studies. We demonstrate that tissue-specific transcription factors are preferentially inactivated in the corresponding cancer cells, suggesting that these are driver events. For many known or suspected tumor suppressors, SCIRA predicts inactivation in single cancer cells where differential expression does not, indicating that SCIRA improves the sensitivity to detect changes in regulatory activity. We identify NKX2-1 and TBX4 inactivation as early tumor suppressor events in normal non-ciliated lung epithelial cells from smokers. In summary, SCIRA can help chart the heterogeneity of tumor suppressor events at single-cell resolution.
Collapse
|
27
|
Sei Y, Feng J, Zhao X, Wank SA. Role of an active reserve stem cell subset of enteroendocrine cells in intestinal stem cell dynamics and the genesis of small intestinal neuroendocrine tumors. Am J Physiol Gastrointest Liver Physiol 2020; 319:G494-G501. [PMID: 32845170 PMCID: PMC7654644 DOI: 10.1152/ajpgi.00278.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Small intestinal neuroendocrine tumors (SI-NET) are serotonin-secreting well-differentiated neuroendocrine tumors of putative enterochromaffin (EC) cell origin. Recent studies recognize a subset of EC cells that is label-retaining at the +4 position in the crypt and functions as a reserve intestinal stem cell. Importantly, this +4 reserve EC cell subset not only contributes to regeneration of the intestinal epithelium during injury and inflammation but also to basal crypt homeostasis at a constant rate. The latter function suggests that the +4 EC cell subset serves as an active reserve stem cell via a constant rate of dedifferentiation. Characterization of early tumor formation of SI-NET, observed as crypt-based EC cell clusters in many cases of familial SI-NETs, suggests that the +4 active reserve EC cell subset is the cell of origin. This newly discovered active reserve stem cell property of EC cells can account for unique biological mechanisms and processes associated with the genesis and development of SI-NETs. The recognition of this property of the +4 active reserve EC cell subset may provide novel opportunities to explore NETs in the gastrointestinal tract and other organs.
Collapse
Affiliation(s)
- Yoshitatsu Sei
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jianying Feng
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Xilin Zhao
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Stephen A. Wank
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
28
|
Liu Y, Chen YG. Intestinal epithelial plasticity and regeneration via cell dedifferentiation. CELL REGENERATION 2020; 9:14. [PMID: 32869114 PMCID: PMC7459029 DOI: 10.1186/s13619-020-00053-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/01/2020] [Indexed: 12/21/2022]
Abstract
The intestinal epithelium possesses a great capacity of self-renewal under normal homeostatic conditions and of regeneration upon damages. The renewal and regenerative processes are driven by intestinal stem cells (ISCs), which reside at the base of crypts and are marked by Lgr5. As Lgr5+ ISCs undergo fast cycling and are vulnerable to damages, there must be other types of cells that can replenish the lost Lgr5+ ISCs and then regenerate the damage epithelium. In addition to Lgr5+ ISCs, quiescent ISCs at the + 4 position in the crypt have been proposed to convert to Lgr5+ ISCs during regeneration. However, this “reserve stem cell” model still remains controversial. Different from the traditional view of a hierarchical organization of the intestinal epithelium, recent works support the dynamic “dedifferentiation” model, in which various cell types within the epithelium can de-differentiate to revert to the stem cell state and then regenerate the epithelium upon tissue injury. Here, we provide an overview of the cell identity and features of two distinct models and discuss the possible mechanisms underlying the intestinal epithelial plasticity.
Collapse
Affiliation(s)
- Yuan Liu
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, 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.
| |
Collapse
|
29
|
Li Q, Dai W, Liu J, Sang Q, Li YX, Li YY. Gene dysregulation analysis builds a mechanistic signature for prognosis and therapeutic benefit in colorectal cancer. J Mol Cell Biol 2020; 12:881-893. [PMID: 32717065 PMCID: PMC7883816 DOI: 10.1093/jmcb/mjaa041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/21/2020] [Accepted: 07/01/2020] [Indexed: 12/09/2022] Open
Abstract
The implementation of cancer precision medicine requires biomarkers or signatures for predicting prognosis and therapeutic benefits. Most of current efforts in this field are paying much more attention to predictive accuracy than to molecular mechanistic interpretability. Mechanism-driven strategy has recently emerged, aiming to build signatures with both predictive power and explanatory power. Driven by this strategy, we developed a robust gene dysregulation analysis framework with machine learning algorithms, which is capable of exploring gene dysregulations underlying carcinogenesis from high-dimensional data with cooperativity and synergy between regulators and several other transcriptional regulation rules taken into consideration. We then applied the framework to a colorectal cancer (CRC) cohort from The Cancer Genome Atlas. The identified CRC-related dysregulations significantly covered known carcinogenic processes and exhibited good prognostic effect. By choosing dysregulations with greedy strategy, we built a four-dysregulation (4-DysReg) signature, which has the capability of predicting prognosis and adjuvant chemotherapy benefit. 4-DysReg has the potential to explain carcinogenesis in terms of dysfunctional transcriptional regulation. These results demonstrate that our gene dysregulation analysis framework could be used to develop predictive signature with mechanistic interpretability for cancer precision medicine, and furthermore, elucidate the mechanisms of carcinogenesis.
Collapse
Affiliation(s)
- Quanxue Li
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.,Shanghai Center for Bioinformation Technology, Shanghai 201203, China
| | - Wentao Dai
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China.,Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Engineering Research Center of Pharmaceutical Translation and Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Jixiang Liu
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China.,Shanghai Engineering Research Center of Pharmaceutical Translation and Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Qingqing Sang
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yi-Xue Li
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.,Shanghai Center for Bioinformation Technology, Shanghai 201203, China.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Engineering Research Center of Pharmaceutical Translation and Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China.,Shanghai Engineering Research Center of Pharmaceutical Translation and Shanghai Industrial Technology Institute, Shanghai 201203, China
| |
Collapse
|
30
|
Characterization of radioresistant epithelial stem cell heterogeneity in the damaged mouse intestine. Sci Rep 2020; 10:8308. [PMID: 32444673 PMCID: PMC7244543 DOI: 10.1038/s41598-020-64987-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/24/2020] [Indexed: 12/15/2022] Open
Abstract
The small intestine has a robust regenerative capacity, and various cell types serve as "cells-of-origin" in the epithelial regeneration process after injury. However, how much each population contributes to regeneration remains unclear. Using lineage tracing, we found that Lgr5-expressing cell derivatives contained radioresistant intestinal stem cells (ISCs) crucial for epithelial regeneration in the damaged intestine after irradiation. Single-cell qRT-PCR analysis showed that surviving Lgr5-expressing cell derivatives in the damaged intestine are remarkably heterogeneous, and that the expression levels of a YAP-target gene Sca1 were inversely correlated with their "stemness", suggesting that the YAP/Wnt signal balance in surviving crypt epithelial cells determines the cellular contribution to epithelial regeneration. Single-cell RNA sequencing of Sca1-Lgr5-derivatives revealed that expression of a tetraspanin family member CD81 correlated well with the expression of ISC- and proliferation-related genes. Consistent with these findings, organoid-forming ability was confined to the CD81hiSca1- fraction within the damaged crypt epithelial cells. Characterization of radioresistant epithelial stem cell heterogeneity in the damaged intestine may contribute to therapeutic strategies for gastrointestinal diseases.
Collapse
|
31
|
Karmakar S, Deng L, He XC, Li L. Intestinal epithelial regeneration: active versus reserve stem cells and plasticity mechanisms. Am J Physiol Gastrointest Liver Physiol 2020; 318:G796-G802. [PMID: 32003604 PMCID: PMC7191462 DOI: 10.1152/ajpgi.00126.2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The gastrointestinal system is arguably one of the most complicated developmental systems in a multicellular organism, as it carries out at least four major functions: digestion of food, absorption of nutrients, excretion of hormones, and defense against pathogens. Anatomically, the fetal gut has a tubular structure with an outer layer of smooth muscle derived from lateral splanchnic mesoderm and an inner lining of epithelium derived from the definitive endoderm. During morphogenesis of the gut tube, the definitive endoderm transforms into a primitive gut tube with a foregut, midgut, and hindgut. During the course of further development, the midgut gives rise to the small and proximal large intestine and the hindgut gives rise to the distal large intestine and rectum. The small intestine is subdivided into three parts: duodenum, jejunum, and ileum, whereas the large intestine is subdivided into the cecum, colon, and rectum.
Collapse
Affiliation(s)
- Soham Karmakar
- 1Stowers Institute for Medical Research, Kansas City, Missouri
| | - Lu Deng
- 1Stowers Institute for Medical Research, Kansas City, Missouri
| | - Xi C. He
- 1Stowers Institute for Medical Research, Kansas City, Missouri
| | - Linheng Li
- 1Stowers Institute for Medical Research, Kansas City, Missouri,2University of Kansas Medical Center, Kansas City, Kansas
| |
Collapse
|
32
|
Gao Y, Yan Y, Tripathi S, Pentinmikko N, Amaral A, Päivinen P, Domènech-Moreno E, Andersson S, Wong IPL, Clevers H, Katajisto P, Mäkelä TP. LKB1 Represses ATOH1 via PDK4 and Energy Metabolism and Regulates Intestinal Stem Cell Fate. Gastroenterology 2020; 158:1389-1401.e10. [PMID: 31930988 DOI: 10.1053/j.gastro.2019.12.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 12/02/2019] [Accepted: 12/30/2019] [Indexed: 01/16/2023]
Abstract
BACKGROUND & AIMS In addition to the Notch and Wnt signaling pathways, energy metabolism also regulates intestinal stem cell (ISC) function. Tumor suppressor and kinase STK11 (also called LKB1) regulates stem cells and cell metabolism. We investigated whether loss of LKB1 alters ISC homeostasis in mice. METHODS We deleted LKB1 from ISCs in mice using Lgr5-regulated CRE-ERT2 (Lkb1Lgr5-KO mice) and the traced lineages by using a CRE-dependent TdTomato reporter. Intestinal tissues were collected and analyzed by immunohistochemical and immunofluorescence analyses. We purified ISCs and intestinal progenitors using flow cytometry and performed RNA-sequencing analysis. We measured organoid-forming capacity and ISC percentages using intestinal tissues from Lkb1Lgr5-KO mice. We analyzed human Ls174t cells with knockdown of LKB1 or other proteins by immunoblotting, real-time quantitative polymerase chain reaction, and the Seahorse live-cell metabolic assay. RESULTS Some intestinal crypts from Lkb1Lgr5-KO mice lost ISCs compared with crypts from control mice. However, most crypts from Lkb1Lgr5-KO mice contained functional ISCs that expressed increased levels of Atoh1 messenger RNA (mRNA), acquired a gene expression signature associated with secretory cells, and generated more cells in the secretory lineage compared with control mice. Knockdown of LKB1 in Ls174t cells induced expression of Atoh1 mRNA and a phenotype of increased mucin production; knockdown of ATOH1 prevented induction of this phenotype. The increased expression of Atoh1 mRNA after LKB1 loss from ISCs or Ls174t cells did not involve Notch or Wnt signaling. Knockdown of pyruvate dehydrogenase kinase 4 (PDK4) or inhibition with dichloroacetate reduced the up-regulation of Atoh1 mRNA after LKB1 knockdown in Ls174t cells. Cells with LKB1 knockdown had a reduced rate of oxygen consumption, which was partially restored by PDK4 inhibition with dichloroacetate. ISCs with knockout of LKB1 increased the expression of PDK4 and had an altered metabolic profile. CONCLUSIONS LKB1 represses transcription of ATOH1, via PDK4, in ISCs, restricting their differentiation into secretory lineages. These findings provide a connection between metabolism and the fate determination of ISCs.
Collapse
Affiliation(s)
- Yajing Gao
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Finland; HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Yan Yan
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Finland; HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Finland.
| | - Sushil Tripathi
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Finland; HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Nalle Pentinmikko
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Finland; HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
| | - Ana Amaral
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Pekka Päivinen
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Finland; HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Eva Domènech-Moreno
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Finland; HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Simon Andersson
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Finland; HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
| | - Iris P L Wong
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Finland
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and Cancer Genomics Netherlands, University Medical Center Utrecht and Princess Máxima Centre, Utrecht, The Netherlands
| | - Pekka Katajisto
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Finland; HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Tomi P Mäkelä
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Finland; HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Finland.
| |
Collapse
|
33
|
Murata K, Jadhav U, Madha S, van Es J, Dean J, Cavazza A, Wucherpfennig K, Michor F, Clevers H, Shivdasani RA. Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells. Cell Stem Cell 2020; 26:377-390.e6. [PMID: 32084390 DOI: 10.1016/j.stem.2019.12.011] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/07/2019] [Accepted: 12/23/2019] [Indexed: 12/28/2022]
Abstract
Ablation of LGR5+ intestinal stem cells (ISCs) is associated with rapid restoration of the ISC compartment. Different intestinal crypt populations dedifferentiate to provide new ISCs, but the transcriptional and signaling trajectories that guide this process are unclear, and a large body of work suggests that quiescent "reserve" ISCs contribute to regeneration. By timing the interval between LGR5+ lineage tracing and lethal injury, we show that ISC regeneration is explained nearly completely by dedifferentiation, with contributions from absorptive and secretory progenitors. The ISC-restricted transcription factor ASCL2 confers measurable competitive advantage to resting ISCs and is essential to restore the ISC compartment. Regenerating cells re-express Ascl2 days before Lgr5, and single-cell RNA sequencing (scRNA-seq) analyses reveal transcriptional paths underlying dedifferentiation. ASCL2 target genes include the interleukin-11 (IL-11) receptor Il11ra1, and recombinant IL-11 enhances crypt cell regenerative potential. These findings reveal cell dedifferentiation as the principal means for ISC restoration and highlight an ASCL2-regulated signal that enables this adaptive response.
Collapse
Affiliation(s)
- Kazutaka Murata
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Unmesh Jadhav
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Shariq Madha
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Johan van Es
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC) Utrecht, 3584 CT Utrecht, the Netherlands
| | - Justin Dean
- Department of Cancer Data Sciences, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alessia Cavazza
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Kai Wucherpfennig
- Department of Cancer Immunology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Franziska Michor
- Department of Cancer Data Sciences, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC) Utrecht, 3584 CT Utrecht, the Netherlands
| | - Ramesh A Shivdasani
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| |
Collapse
|
34
|
Pereira B, Amaral AL, Dias A, Mendes N, Muncan V, Silva AR, Thibert C, Radu AG, David L, Máximo V, van den Brink GR, Billaud M, Almeida R. MEX3A regulates Lgr5 + stem cell maintenance in the developing intestinal epithelium. EMBO Rep 2020; 21:e48938. [PMID: 32052574 PMCID: PMC7132344 DOI: 10.15252/embr.201948938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
Intestinal stem cells (ISCs) fuel the lifelong self‐renewal of the intestinal tract and are paramount for epithelial repair. In this context, the Wnt pathway component LGR5 is the most consensual ISC marker to date. Still, the effort to better understand ISC identity and regulation remains a challenge. We have generated a Mex3a knockout mouse model and show that this RNA‐binding protein is crucial for the maintenance of the Lgr5+ISC pool, as its absence disrupts epithelial turnover during postnatal development and stereotypical organoid maturation ex vivo. Transcriptomic profiling of intestinal crypts reveals that Mex3a deletion induces the peroxisome proliferator‐activated receptor (PPAR) pathway, along with a decrease in Wnt signalling and loss of the Lgr5+ stem cell signature. Furthermore, we identify PPARγ activity as a molecular intermediate of MEX3A‐mediated regulation. We also show that high PPARγ signalling impairs Lgr5+ISC function, thus uncovering a new layer of post‐transcriptional regulation that critically contributes to intestinal homeostasis.
Collapse
Affiliation(s)
- Bruno Pereira
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Ana L Amaral
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Alexandre Dias
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Nuno Mendes
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Vanesa Muncan
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Tytgat Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Ana R Silva
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Chantal Thibert
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Anca G Radu
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Leonor David
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,FMUP-Faculty of Medicine, University of Porto, Porto, Portugal
| | - Valdemar Máximo
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,FMUP-Faculty of Medicine, University of Porto, Porto, Portugal
| | - Gijs R van den Brink
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Tytgat Institute, University of Amsterdam, Amsterdam, The Netherlands.,Medicines Research Center, GSK, Stevenage, UK
| | - Marc Billaud
- Clinical and Experimental Model of Lymphomagenesis, INSERM U1052, CNRS UMR5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Raquel Almeida
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,FMUP-Faculty of Medicine, University of Porto, Porto, Portugal.,Biology Department, Faculty of Sciences, University of Porto, Porto, Portugal
| |
Collapse
|
35
|
Wang Y, Chiang IL, Ohara TE, Fujii S, Cheng J, Muegge BD, Ver Heul A, Han ND, Lu Q, Xiong S, Chen F, Lai CW, Janova H, Wu R, Whitehurst CE, VanDussen KL, Liu TC, Gordon JI, Sibley LD, Stappenbeck TS. Long-Term Culture Captures Injury-Repair Cycles of Colonic Stem Cells. Cell 2019; 179:1144-1159.e15. [PMID: 31708126 PMCID: PMC6904908 DOI: 10.1016/j.cell.2019.10.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/15/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023]
Abstract
The colonic epithelium can undergo multiple rounds of damage and repair, often in response to excessive inflammation. The responsive stem cell that mediates this process is unclear, in part because of a lack of in vitro models that recapitulate key epithelial changes that occur in vivo during damage and repair. Here, we identify a Hopx+ colitis-associated regenerative stem cell (CARSC) population that functionally contributes to mucosal repair in mouse models of colitis. Hopx+ CARSCs, enriched for fetal-like markers, transiently arose from hypertrophic crypts known to facilitate regeneration. Importantly, we established a long-term, self-organizing two-dimensional (2D) epithelial monolayer system to model the regenerative properties and responses of Hopx+ CARSCs. This system can reenact the "homeostasis-injury-regeneration" cycles of epithelial alterations that occur in vivo. Using this system, we found that hypoxia and endoplasmic reticulum stress, insults commonly present in inflammatory bowel diseases, mediated the cyclic switch of cellular status in this process.
Collapse
Affiliation(s)
- Yi Wang
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - I-Ling Chiang
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Takahiro E Ohara
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Satoru Fujii
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jiye Cheng
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Brian D Muegge
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Aaron Ver Heul
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Nathan D Han
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Qiuhe Lu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Feidi Chen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chin-Wen Lai
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Hana Janova
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Renee Wu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Charles E Whitehurst
- Boehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Disease Research, Ridgefield, CT 06877, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| |
Collapse
|
36
|
Li S, Peppelenbosch MP, Smits R. Bacterial biofilms as a potential contributor to mucinous colorectal cancer formation. Biochim Biophys Acta Rev Cancer 2019; 1872:74-79. [DOI: 10.1016/j.bbcan.2019.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023]
|
37
|
Shimizu H, Suzuki K, Watanabe M, Okamoto R. Stem cell-based therapy for inflammatory bowel disease. Intest Res 2019; 17:311-316. [PMID: 31352774 PMCID: PMC6667367 DOI: 10.5217/ir.2019.00043] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/11/2019] [Indexed: 12/19/2022] Open
Abstract
Inflammatory bowel disease (IBD) is an idiopathic, multi-etiological disease characterized by inflammation and mucosal destruction of the gastrointestinal tract. Despite the remarkable advance in immunomodulating therapies, there still remains a certain population of patients who are refractory to conventional as well as biologic therapies and fail to achieve mucosal healing. To improve the prognosis of those patients, at least 2 types of stem cells have been tested for their potential therapeutic use. Transplantation of hematopoietic stem cells or mesenchymal stem cells have been tested in several clinical studies, but their beneficial effect still remains controversial. In this review, we would like to overview the recent clinical challenges of stem cell-based therapies in IBD and also introduce our new therapeutic plan of intestinal stem cell transplantation for IBD, based on our ex vivo intestinal organoid culture technique.
Collapse
Affiliation(s)
- Hiromichi Shimizu
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Endoscopy, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kohei Suzuki
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Endoscopy, Tokyo Medical and Dental University, Tokyo, Japan
| | - Mamoru Watanabe
- Institute of Advanced Study, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryuichi Okamoto
- Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
38
|
Buczacki S. Fate plasticity in the intestine: The devil is in the detail. World J Gastroenterol 2019; 25:3116-3122. [PMID: 31333305 PMCID: PMC6626720 DOI: 10.3748/wjg.v25.i25.3116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/14/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023] Open
Abstract
The intestinal epithelium possesses a remarkable ability for both proliferation and regeneration. The last two decades have generated major advances in our understanding of the stem cell populations responsible for its maintenance during homeostasis and more recently the events that occur during injury induced regeneration. These fundamental discoveries have capitalised on the use of transgenic mouse models and in vivo lineage tracing to make their conclusions. It is evident that maintenance is driven by rapidly proliferating crypt base stem cells, but complexities associated with the technicality of mouse modelling have led to several overlapping populations being held responsible for the same behaviour. Similarly, it has been shown that essentially any population in the intestinal crypt can revert to a stem cell state given the correct stimulus during epithelial regeneration. Whilst these observations are profound it is uncertain how relevant they are to human intestinal homeostasis and pathology. Here, these recent studies are presented, in context with technical considerations of the models used, to argue that their conclusions may indeed not be applicable in understanding "homeostatic regeneration" and experimental suggestions presented for validating their results in human tissue.
Collapse
Affiliation(s)
- Simon Buczacki
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Addenbrooke’s Biomedical Campus, Cambridge CB2 0AF, United Kingdom
| |
Collapse
|
39
|
Hirata A, Hatano Y, Niwa M, Hara A, Tomita H. Heterogeneity in Colorectal Cancer Stem Cells. Cancer Prev Res (Phila) 2019; 12:413-420. [DOI: 10.1158/1940-6207.capr-18-0482] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/07/2019] [Accepted: 05/14/2019] [Indexed: 11/16/2022]
|
40
|
Abstract
Intestinal homeostasis and regeneration are driven by intestinal stem cells (ISCs) lying in the crypt. In addition to the actively cycling ISCs that maintain daily homeostasis, accumulating evidence supports the existence of other pools of stem/progenitor cells with the capacity to repair damaged tissue and facilitate rapid restoration of intestinal integrity after injuries. Appropriate control of ISCs and other populations of intestinal epithelial cells with stem cell activity is essential for intestinal homeostasis and regeneration while their deregulation is implicated in colorectal tumorigenesis. In this review, we will summarize the recent findings about ISC identity and cellular plasticity in intestine, discuss regulatory mechanisms that control ISCs for intestinal homeostasis and regeneration, and put a particular emphasis on extrinsic niche-derived signaling and intrinsic epigenetic regulation. Moreover, we highlight several fundamental questions about the precise mechanisms conferring robust capacity for intestine to maintain physiological homeostasis and repair injuries.
Collapse
Affiliation(s)
- Deqing Hu
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics; Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Heping, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Heping, Tianjin, China
| | - Han Yan
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics; Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Heping, Tianjin, China
| | - Xi C He
- Stowers Institute for Medical Research, Kansas City, USA
| | - Linheng Li
- Stowers Institute for Medical Research, Kansas City, USA.,Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, China
| |
Collapse
|
41
|
Castillo-Azofeifa D, Fazio EN, Nattiv R, Good HJ, Wald T, Pest MA, de Sauvage FJ, Klein OD, Asfaha S. Atoh1 + secretory progenitors possess renewal capacity independent of Lgr5 + cells during colonic regeneration. EMBO J 2019; 38:embj.201899984. [PMID: 30635334 DOI: 10.15252/embj.201899984] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022] Open
Abstract
During homeostasis, the colonic epithelium is replenished every 3-5 days by rapidly cycling Lgr5 + stem cells. However, various insults can lead to depletion of Lgr5 + stem cells, and colonic epithelium can be regenerated from Lgr5-negative cells. While studies in the small intestine have addressed the lineage identity of the Lgr5-negative regenerative cell population, in the colon this question has remained unanswered. Here, we set out to identify which cell(s) contribute to colonic regeneration by performing genetic fate-mapping studies of progenitor populations in mice. First, using keratin-19 (Krt19) to mark a heterogeneous population of cells, we found that Lgr5-negative cells can regenerate colonic crypts and give rise to Lgr5 + stem cells. Notch1 + absorptive progenitor cells did not contribute to epithelial repair after injury, whereas Atoh1 + secretory progenitors did contribute to this process. Additionally, while colonic Atoh1 + cells contributed minimally to other lineages during homeostasis, they displayed plasticity and contributed to epithelial repair during injury, independent of Lgr5 + cells. Our findings suggest that promotion of secretory progenitor plasticity could enable gut healing in colitis.
Collapse
Affiliation(s)
- David Castillo-Azofeifa
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Elena N Fazio
- Department of Medicine, University of Western Ontario, London, ON, Canada
| | - Roy Nattiv
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Hayley J Good
- Department of Medicine, University of Western Ontario, London, ON, Canada
| | - Tomas Wald
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Michael A Pest
- Department of Physiology & Pharmacology, University of Western Ontario, London, ON, Canada
| | | | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA .,Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Samuel Asfaha
- Department of Medicine, University of Western Ontario, London, ON, Canada
| |
Collapse
|
42
|
Tomic G, Morrissey E, Kozar S, Ben-Moshe S, Hoyle A, Azzarelli R, Kemp R, Chilamakuri CSR, Itzkovitz S, Philpott A, Winton DJ. Phospho-regulation of ATOH1 Is Required for Plasticity of Secretory Progenitors and Tissue Regeneration. Cell Stem Cell 2018; 23:436-443.e7. [PMID: 30100168 PMCID: PMC6138952 DOI: 10.1016/j.stem.2018.07.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/25/2018] [Accepted: 07/06/2018] [Indexed: 01/07/2023]
Abstract
The intestinal epithelium is largely maintained by self-renewing stem cells but with apparently committed progenitors also contributing, particularly following tissue damage. However, the mechanism of, and requirement for, progenitor plasticity in mediating pathological response remain unknown. Here we show that phosphorylation of the transcription factor Atoh1 is required for both the contribution of secretory progenitors to the stem cell pool and for a robust regenerative response. As confirmed by lineage tracing, Atoh1+ cells (Atoh1(WT)CreERT2 mice) give rise to multilineage intestinal clones both in the steady state and after tissue damage. In a phosphomutant Atoh1(9S/T-A)CreERT2 line, preventing phosphorylation of ATOH1 protein acts to promote secretory differentiation and inhibit the contribution of progenitors to self-renewal. Following chemical colitis, Atoh1+ cells of Atoh1(9S/T-A)CreERT2 mice have reduced clonogenicity that affects overall regeneration. Progenitor plasticity maintains robust self-renewal in the intestinal epithelium, and the balance between stem and progenitor fate is directly coordinated by ATOH1 multisite phosphorylation.
Collapse
Affiliation(s)
- Goran Tomic
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Edward Morrissey
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sarah Kozar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Shani Ben-Moshe
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alice Hoyle
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Roberta Azzarelli
- Department of Oncology, Hutchison/Medical Research Council (MRC) Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Richard Kemp
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Philpott
- Department of Oncology, Hutchison/Medical Research Council (MRC) Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK.
| | - Douglas J Winton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
| |
Collapse
|
43
|
Weichselbaum L, Klein OD. The intestinal epithelial response to damage. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1205-1211. [PMID: 30194677 DOI: 10.1007/s11427-018-9331-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/01/2018] [Indexed: 12/27/2022]
Abstract
The constant renewal of the intestinal epithelium is fueled by intestinal stem cells (ISCs) lying at the base of crypts, and these ISCs continuously give rise to transit-amplifying progenitor cells during homeostasis. Upon injury and loss of ISCs, the epithelium has the ability to regenerate by the dedifferentiation of progenitor cells that then regain stemness and repopulate the pool of ISCs. Epithelial cells receive cues from immune cells, mesenchymal cells and the microbiome to maintain homeostasis. This review focuses on the response of the epithelium to damage and the interplay between the different intestinal compartments.
Collapse
Affiliation(s)
- Laura Weichselbaum
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, 94143, USA.,Institute for Medical Immunology, Université Libre de Bruxelles, Gosselies, 6041, Belgium.,Laboratory of Experimental Gastroenterology, Université libre de Bruxelles, Brussels, 1070, Belgium
| | - Ophir D Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, CA, 94143, USA. .,Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA.
| |
Collapse
|
44
|
Suzuki K, Murano T, Shimizu H, Ito G, Nakata T, Fujii S, Ishibashi F, Kawamoto A, Anzai S, Kuno R, Kuwabara K, Takahashi J, Hama M, Nagata S, Hiraguri Y, Takenaka K, Yui S, Tsuchiya K, Nakamura T, Ohtsuka K, Watanabe M, Okamoto R. Single cell analysis of Crohn's disease patient-derived small intestinal organoids reveals disease activity-dependent modification of stem cell properties. J Gastroenterol 2018; 53:1035-1047. [PMID: 29374777 PMCID: PMC6132922 DOI: 10.1007/s00535-018-1437-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 01/21/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND Intestinal stem cells (ISCs) play indispensable roles in the maintenance of homeostasis, and also in the regeneration of the damaged intestinal epithelia. However, whether the inflammatory environment of Crohn's disease (CD) affects properties of resident small intestinal stem cells remain uncertain. METHODS CD patient-derived small intestinal organoids were established from enteroscopic biopsy specimens taken from active lesions (aCD-SIO), or from mucosa under remission (rCD-SIO). Expression of ISC-marker genes in those organoids was examined by immunohistochemistry, and also by microfluid-based single-cell multiplex gene expression analysis. The ISC-specific function of organoid cells was evaluated using a single-cell organoid reformation assay. RESULTS ISC-marker genes, OLFM4 and SLC12A2, were expressed by an increased number of small intestinal epithelial cells in the active lesion of CD. aCD-SIOs, rCD-SIOs or those of non-IBD controls (NI-SIOs) were successfully established from 9 patients. Immunohistochemistry showed a comparable level of OLFM4 and SLC12A2 expression in all organoids. Single-cell gene expression data of 12 ISC-markers were acquired from a total of 1215 cells. t-distributed stochastic neighbor embedding analysis identified clusters of candidate ISCs, and also revealed a distinct expression pattern of SMOC2 and LGR5 in ISC-cluster classified cells derived from aCD-SIOs. Single-cell organoid reformation assays showed significantly higher reformation efficiency by the cells of the aCD-SIOs compared with that of cells from NI-SIOs. CONCLUSIONS aCD-SIOs harbor ISCs with modified marker expression profiles, and also with high organoid reformation ability. Results suggest modification of small intestinal stem cell properties by unidentified factors in the inflammatory environment of CD.
Collapse
Affiliation(s)
- Kohei Suzuki
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Tatsuro Murano
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Hiromichi Shimizu
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Go Ito
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Toru Nakata
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Satoru Fujii
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Fumiaki Ishibashi
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Ami Kawamoto
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Sho Anzai
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Reiko Kuno
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Konomi Kuwabara
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Junichi Takahashi
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Minami Hama
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Sayaka Nagata
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Yui Hiraguri
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Kento Takenaka
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Shiro Yui
- Center for Stem Cell and Regenerative Medicine, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Kiichiro Tsuchiya
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Tetsuya Nakamura
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
- Department of Advanced Therapeutics in GI Diseases, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Kazuo Ohtsuka
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Mamoru Watanabe
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Ryuichi Okamoto
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan.
- Center for Stem Cell and Regenerative Medicine, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| |
Collapse
|