1
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Shaban HA, Friman ET, Deluz C, Tollenaere A, Katanayeva N, Suter DM. Individual transcription factors modulate both the micromovement of chromatin and its long-range structure. Proc Natl Acad Sci U S A 2024; 121:e2311374121. [PMID: 38648478 PMCID: PMC11067044 DOI: 10.1073/pnas.2311374121] [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: 07/05/2023] [Accepted: 03/13/2024] [Indexed: 04/25/2024] Open
Abstract
The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear how nucleus-wide chromatin organization responds dynamically to the activity of specific TFs. Here, we examined how two TFs with opposite effects on local chromatin accessibility modulate chromatin dynamics nucleus-wide. We combine high-resolution diffusion mapping and dense flow reconstruction and correlation in living cells to obtain an imaging-based, nanometer-scale analysis of local diffusion processes and long-range coordinated movements of both chromatin and TFs. We show that the expression of either an individual transcriptional activator (CDX2) or repressor (SIX6) with large numbers of binding sites increases chromatin mobility nucleus-wide, yet they induce opposite coherent chromatin motions at the micron scale. Hi-C analysis of higher-order chromatin structures shows that induction of the pioneer factor CDX2 leads both to changes in local chromatin interactions and the distribution of A and B compartments, thus relating the micromovement of chromatin with changes in compartmental structures. Given that inhibition of transcription initiation and elongation by RNA Pol II has a partial impact on the global chromatin dynamics induced by CDX2, we suggest that CDX2 overexpression alters chromatin structure dynamics both dependently and independently of transcription. Our biophysical analysis shows that sequence-specific TFs can influence chromatin structure on multiple architectural levels, arguing that local chromatin changes brought by TFs alter long-range chromatin mobility and its organization.
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Affiliation(s)
- Haitham A. Shaban
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
- Spectroscopy Department, Institute of Physics Research, National Research Centre, Cairo12622, Egypt
| | - Elias T. Friman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
| | - Cédric Deluz
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Armelle Tollenaere
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - David M. Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
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2
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Su Y, Yu Z, Yang Y, Wong KC, Li X. Distribution-Agnostic Deep Learning Enables Accurate Single-Cell Data Recovery and Transcriptional Regulation Interpretation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307280. [PMID: 38380499 DOI: 10.1002/advs.202307280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/16/2024] [Indexed: 02/22/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a robust method for studying gene expression at the single-cell level, but accurately quantifying genetic material is often hindered by limited mRNA capture, resulting in many missing expression values. Existing imputation methods rely on strict data assumptions, limiting their broader application, and lack reliable supervision, leading to biased signal recovery. To address these challenges, authors developed Bis, a distribution-agnostic deep learning model for accurately recovering missing sing-cell gene expression from multiple platforms. Bis is an optimal transport-based autoencoder model that can capture the intricate distribution of scRNA-seq data while addressing the characteristic sparsity by regularizing the cellular embedding space. Additionally, they propose a module using bulk RNA-seq data to guide reconstruction and ensure expression consistency. Experimental results show Bis outperforms other models across simulated and real datasets, showcasing superiority in various downstream analyses including batch effect removal, clustering, differential expression analysis, and trajectory inference. Moreover, Bis successfully restores gene expression levels in rare cell subsets in a tumor-matched peripheral blood dataset, revealing developmental characteristics of cytokine-induced natural killer cells within a head and neck squamous cell carcinoma microenvironment.
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Affiliation(s)
- Yanchi Su
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Zhuohan Yu
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Yuning Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
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3
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Mzoughi S, Schwarz M, Wang X, Demircioglu D, Ulukaya G, Mohammed K, Tullio FD, Company C, Dramaretska Y, Leushacke M, Giotti B, Lannagan T, Lozano-Ojalvo D, Hasson D, Tsankov AM, Sansom OJ, Marine JC, Barker N, Gargiulo G, Guccione E. A Mutation-driven oncofetal regression fuels phenotypic plasticity in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570854. [PMID: 38106050 PMCID: PMC10723414 DOI: 10.1101/2023.12.10.570854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Targeting cancer stem cells (CSCs) is crucial for effective cancer treatment 1 . However, the molecular mechanisms underlying resistance to LGR5 + CSCs depletion in colorectal cancer (CRC) 2,3 remain largely elusive. Here, we unveil the existence of a primitive cell state dubbed the oncofetal (OnF) state, which works in tandem with the LGR5 + stem cells (SCs) to fuel tumor evolution in CRC. OnF cells emerge early during intestinal tumorigenesis and exhibit features of lineage plasticity. Normally suppressed by the Retinoid X Receptor (RXR) in mature SCs, the OnF program is triggered by genetic deletion of the gatekeeper APC. We demonstrate that diminished RXR activity unlocks an epigenetic circuity governed by the cooperative action of YAP and AP1, leading to OnF reprogramming. This high-plasticity state is inherently resistant to conventional chemotherapies and its adoption by LGR5 + CSCs enables them to enter a drug-tolerant state. Furthermore, through phenotypic tracing and ablation experiments, we uncover a functional redundancy between the OnF and stem cell (SC) states and show that targeting both cellular states is essential for sustained tumor regression in vivo . Collectively, these findings establish a mechanistic foundation for developing effective combination therapies with enduring impact on CRC treatment.
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4
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Liu S, Xu H, Li Z. Linoleic acid derivatives target miR-361-3p/BTG2 to confer anticancer effects in acute myeloid leukemia. J Biochem Mol Toxicol 2023; 37:e23481. [PMID: 37497988 DOI: 10.1002/jbt.23481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/12/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023]
Abstract
Acute myeloid leukemia (AML) is a deadly hematologic malignancy. In this study, miR-361-3p and BTG2 gene expression in AML blood and healthy specimens were analyzed using quantitative real-time reverse transcription polymerase chain reaction. A significant negative correlation between miR-361-3p and BTG2 was observed. The cell viability and apoptosis were measured by CCK-8 assay, EdU incorporation assay and flow cytometry. A dual-luciferase reporter gene assay was performed to confirm the binding sequence between miR-361-3p and BTG2 messenger RNA 3'-untranslated region. 9s-Hydroxyoctadecadienoic acid (9s-HODE), a major active derivative of linoleic acid, reduced the viability and induced cell apoptosis of HL-60 cells. Furthermore, the miR-361-3p mimics and siBTG2 reversed the above effects of 9s-HODE. 9s-HODE exerted an anti-AML effect through, at least partly, regulating the miR-361-3p/BTG2 axis.
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Affiliation(s)
- Shili Liu
- Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
- Clinical Laboratory, Suizhou Central Hospital, Suizhou, Hubei Province, People's Republic of China
| | - Huijuan Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Zhen Li
- Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
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5
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Li J, Simmons AJ, Chiron S, Ramirez-Solano MA, Tasneem N, Kaur H, Xu Y, Revetta F, Vega PN, Bao S, Cui C, Tyree RN, Raber LW, Conner AN, Beaulieu DB, Dalal RL, Horst SN, Pabla BS, Huo Y, Landman BA, Roland JT, Scoville EA, Schwartz DA, Washington MK, Shyr Y, Wilson KT, Coburn LA, Lau KS, Liu Q. A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.560293. [PMID: 37873404 PMCID: PMC10592875 DOI: 10.1101/2023.09.30.560293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Crohn's disease (CD) is a complex chronic inflammatory disorder that may affect any part of gastrointestinal tract with extra-intestinal manifestations and associated immune dysregulation. To characterize heterogeneity in CD, we profiled single-cell transcriptomics of 170 samples from 65 CD patients and 18 non-inflammatory bowel disease (IBD) controls in both the terminal ileum (TI) and ascending colon (AC). Analysis of 202,359 cells identified a novel epithelial cell type in both TI and AC, featuring high expression of LCN2, NOS2, and DUOX2, and thus is named LND. LND cells, confirmed by high-resolution in-situ RNA imaging, were rarely found in non-IBD controls, but expanded significantly in active CD. Compared to other epithelial cells, genes defining LND cells were enriched in antimicrobial response and immunoregulation. Moreover, multiplexed protein imaging demonstrated that LND cell abundance was associated with immune infiltration. Cross-talk between LND and immune cells was explored by ligand-receptor interactions and further evidenced by their spatial colocalization. LND cells showed significant enrichment of expression specificity of IBD/CD susceptibility genes, revealing its role in immunopathogenesis of CD. Investigating lineage relationships of epithelial cells detected two LND cell subpopulations with different origins and developmental potential, early and late LND. The ratio of the late to early LND cells was related to anti-TNF response. These findings emphasize the pathogenic role of the specialized LND cell type in both Crohn's ileitis and Crohn's colitis and identify novel biomarkers associated with disease activity and treatment response.
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Affiliation(s)
- Jia Li
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Alan J. Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marisol A. Ramirez-Solano
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Naila Tasneem
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Harsimran Kaur
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yanwen Xu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paige N. Vega
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shunxing Bao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Can Cui
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Regina N. Tyree
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Larry W. Raber
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna N. Conner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dawn B. Beaulieu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robin L. Dalal
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara N. Horst
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Baldeep S. Pabla
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuankai Huo
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Bennett A. Landman
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Joseph T. Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville TN, USA
| | - Elizabeth A. Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - David A. Schwartz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Lori A. Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Ken S. Lau
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
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6
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Kim HM, Kang B, Park S, Park H, Kim C, Lee H, Yoo M, Kweon MN, Im SH, Kim T, Roh TY. Forkhead box protein D2 suppresses colorectal cancer by reprogramming enhancer interactions. Nucleic Acids Res 2023; 51:6143-6155. [PMID: 37158258 PMCID: PMC10325893 DOI: 10.1093/nar/gkad361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/10/2023] Open
Abstract
Somatic stem cells contribute to normal tissue homeostasis, and their epigenomic features play an important role in regulating tissue identities or developing disease states. Enhancers are one of the key players controlling chromatin context-specific gene expression in a spatial and temporal manner while maintaining tissue homeostasis, and their dysregulation leads to tumorigenesis. Here, epigenomic and transcriptomic analyses reveal that forkhead box protein D2 (FOXD2) is a hub for the gene regulatory network exclusive to large intestinal stem cells, and its overexpression plays a significant role in colon cancer regression. FOXD2 is positioned at the closed chromatin and facilitates mixed-lineage leukemia protein-4 (MLL4/KMT2D) binding to deposit H3K4 monomethylation. De novo FOXD2-mediated chromatin interactions rewire the regulation of p53-responsive genes and induction of apoptosis. Taken together, our findings illustrate the novel mechanistic details of FOXD2 in suppressing colorectal cancer growth and suggest its function as a chromatin-tuning factor and a potential therapeutic target for colorectal cancer.
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Affiliation(s)
- Hyo-Min Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Byunghee Kang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Sohyun Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Hyorim Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Chan Johng Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Hyeonji Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Mijoung Yoo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Mi-Na Kweon
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, Seoul 03722, Republic of Korea
- ImmunoBiome, Inc., Pohang 37666, Republic of Korea
| | - Tae Il Kim
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
- Sysgenlab Inc., Pohang 37673, Republic of Korea
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7
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Fritsche K, Boccellato F, Schlaermann P, Koeppel M, Denecke C, Link A, Malfertheiner P, Gut I, Meyer TF, Berger H. DNA methylation in human gastric epithelial cells defines regional identity without restricting lineage plasticity. Clin Epigenetics 2022; 14:193. [PMID: 36585699 PMCID: PMC9801550 DOI: 10.1186/s13148-022-01406-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Epigenetic modifications in mammalian DNA are commonly manifested by DNA methylation. In the stomach, altered DNA methylation patterns have been observed following chronic Helicobacter pylori infections and in gastric cancer. In the context of epigenetic regulation, the regional nature of the stomach has been rarely considered in detail. RESULTS Here, we establish gastric mucosa derived primary cell cultures as a reliable source of native human epithelium. We describe the DNA methylation landscape across the phenotypically different regions of the healthy human stomach, i.e., antrum, corpus, fundus together with the corresponding transcriptomes. We show that stable regional DNA methylation differences translate to a limited extent into regulation of the transcriptomic phenotype, indicating a largely permissive epigenetic regulation. We identify a small number of transcription factors with novel region-specific activity and likely epigenetic impact in the stomach, including GATA4, IRX5, IRX2, PDX1 and CDX2. Detailed analysis of the Wnt pathway reveals differential regulation along the craniocaudal axis, which involves non-canonical Wnt signaling in determining cell fate in the proximal stomach. By extending our analysis to pre-neoplastic lesions and gastric cancers, we conclude that epigenetic dysregulation characterizes intestinal metaplasia as a founding basis for functional changes in gastric cancer. We present insights into the dynamics of DNA methylation across anatomical regions of the healthy stomach and patterns of its change in disease. Finally, our study provides a well-defined resource of regional stomach transcription and epigenetics.
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Affiliation(s)
- Kristin Fritsche
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Francesco Boccellato
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Philipp Schlaermann
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Max Koeppel
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Christian Denecke
- Center for Bariatric and Metabolic Surgery, Center of Innovative Surgery (ZIC), Department of Surgery, Campus Virchow Klinikum and Campus Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University Hospital, Magdeburg, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University Hospital, Magdeburg, Germany
| | - Ivo Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Barcelona, Spain
| | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
- Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian Albrecht University of Kiel and University Hospital Schleswig-Holstein - Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany.
| | - Hilmar Berger
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
- Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian Albrecht University of Kiel and University Hospital Schleswig-Holstein - Campus Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany.
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8
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Giolito MV, La Rosa T, Farhat D, Bodoirat S, Guardia GDA, Domon‐Dell C, Galante PAF, Freund J, Plateroti M. Regulation of the THRA gene, encoding the thyroid hormone nuclear receptor TRα1, in intestinal lesions. Mol Oncol 2022; 16:3975-3993. [PMID: 36217307 PMCID: PMC9718118 DOI: 10.1002/1878-0261.13298] [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: 10/16/2021] [Revised: 07/05/2022] [Accepted: 07/29/2022] [Indexed: 12/24/2022] Open
Abstract
The THRA gene, encoding the thyroid hormone nuclear receptor TRα1, is expressed in an increasing gradient at the bottom of intestinal crypts, overlapping with high Wnt and Notch activities. Importantly, THRA is upregulated in colorectal cancers, particularly in the high-Wnt molecular subtype. The basis of this specific and/or altered expression pattern has remained unknown. To define the mechanisms controlling THRA transcription and TRα1 expression, we used multiple in vitro and ex vivo approaches. Promoter analysis demonstrated that transcription factors important for crypt homeostasis and altered in colorectal cancers, such as transcription factor 7-like 2 (TCF7L2; Wnt pathway), recombining binding protein suppressor of hairless (RBPJ; Notch pathway), and homeobox protein CDX2 (epithelial cell identity), modulate THRA activity. Specifically, although TCF7L2 and CDX2 stimulated THRA, RBPJ induced its repression. In-depth analysis of the Wnt-dependent increase showed direct regulation of the THRA promoter in cells and of TRα1 expression in murine enteroids. Given our previous results on the control of the Wnt pathway by TRα1, our new results unveil a complex regulatory loop and synergy between these endocrine and epithelial-cell-intrinsic signals. Our work describes, for the first time, the regulation of the THRA gene in specific cell and tumor contexts.
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Affiliation(s)
- Maria Virginia Giolito
- Inserm, IRFAC/UMR‐S1113, FMTS, Université de StrasbourgFrance,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de LyonFrance
| | - Théo La Rosa
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de LyonFrance,Present address:
Stem‐Cell and Brain Research Institute, U1208 INSERM, USC1361 INRABronFrance
| | - Diana Farhat
- Inserm, IRFAC/UMR‐S1113, FMTS, Université de StrasbourgFrance,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de LyonFrance
| | | | | | | | | | | | - Michelina Plateroti
- Inserm, IRFAC/UMR‐S1113, FMTS, Université de StrasbourgFrance,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de LyonFrance
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9
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Jin Q, Gao Y, Shuai S, Chen Y, Wang K, Chen J, Peng J, Gao C. Cdx1b protects intestinal cell fate by repressing signaling networks for liver specification. J Genet Genomics 2022; 49:1101-1113. [PMID: 36460297 DOI: 10.1016/j.jgg.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
Abstract
In mammals, the expression of the homeobox family member Cdx2/CDX2 is restricted within the intestine. Conditional ablation of the mouse Cdx2 in the endodermal cells causes a homeotic transformation of the intestine towards the esophagus or gastric fate. In this report, we show that null mutants of zebrafish cdx1b, encoding the counterpart of mammalian CDX2, could survive more than 10 days post fertilization, a stage when the zebrafish digestive system has been well developed. Through RNA sequencing (RNA-seq) and single-cell sequencing (scRNA-seq) of the dissected intestine from the mutant embryos, we demonstrate that the loss-of-function of the zebrafish cdx1b yields hepatocyte-like intestinal cells, a phenotype never observed in the mouse model. Further RNA-seq data analysis, and genetic double mutants and signaling inhibitor studies reveal that Cdx1b functions to guard the intestinal fate by repressing, directly or indirectly, a range of transcriptional factors and signaling pathways for liver specification. Finally, we demonstrate that heat shock-induced overexpression of cdx1b in a transgenic fish abolishes the liver formation. Therefore, we demonstrate that Cdx1b is a key repressor of hepatic fate during the intestine specification in zebrafish.
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Affiliation(s)
- Qingxia Jin
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuqi Gao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shimin Shuai
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yayue Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Kaiyuan Wang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Ce Gao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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10
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CDX2 expression in primary skin tumors-case series and review of the literature. Hum Pathol 2022; 129:1-10. [PMID: 35926811 DOI: 10.1016/j.humpath.2022.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 12/14/2022]
Abstract
CDX2 expression characterizes tumors of gastrointestinal origin, including those of intestinal-type differentiation. In dermatopathology, CDX2 expression is reported in 4 settings: cutaneous metastases from carcinomas of intestinal origin or differentiation, extramammary Paget's disease associated with an underlying colorectal or urothelial tumor, pilomatricomas and pilomatrical carcinomas, and rare primary cutaneous (adeno)squamous carcinomas with intestinal immunophenotype. Over 4 years (10/2017-10/2021), 252 dermatopathology cases with CDX2 immunostain were reviewed, revealing 46 cases with confirmed positive staining. Among them, 11 cases confirmed as primary nonintestinal type cutaneous carcinoma with definitively positive CDX2 nuclear staining were further studied. All cases demonstrated basaloid morphology with atypia, variable necrosis, and brisk mitotic activity. Cases 1-5 had heterogeneous features that cannot be further classified, including 2 cases with neuroendocrine or pseudoglandular/pseudopapillary features, and 1 case with human papillomavirus high-risk E6/E7 ISH positivity. In cases 6 through 11, the diagnosis of pilomatrical carcinoma was supported morphologically. This study substantiates the association of CDX2 with pilomatrical carcinoma. In addition, CDX2 positivity was observed in a subset of basaloid cutaneous carcinomas of ambiguous classification. However, this finding also raises a diagnostic pitfall in clinical diagnostic specificity of the CDX2 immunostain in skin cancers, which can be observed in rare while heterogeneous subsets of primary cutaneous carcinomas with primitive cytomorphology.
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11
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Swoboda J, Mittelsdorf P, Chen Y, Weiskirchen R, Stallhofer J, Schüle S, Gassler N. Intestinal Wnt in the transition from physiology to oncology. World J Clin Oncol 2022; 13:168-185. [PMID: 35433295 PMCID: PMC8966512 DOI: 10.5306/wjco.v13.i3.168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/07/2021] [Accepted: 02/20/2022] [Indexed: 02/06/2023] Open
Abstract
Adult stem cells are necessary for self-renewal tissues and regeneration after damage. Especially in the intestine, which self-renews every few days, they play a key role in tissue homeostasis. Therefore, complex regulatory mechanisms are needed to prevent hyperproliferation, which can lead in the worst case to carcinogenesis or under-activation of stem cells, which can result in dysfunctional epithelial. One main regulatory signaling pathway is the Wnt/β-catenin signaling pathway. It is a highly conserved pathway, with β-catenin, a transcription factor, as target protein. Translocation of β-catenin from cytoplasm to nucleus activates the transcription of numerous genes involved in regulating stem cell pluripo-tency, proliferation, cell differentiation and regulation of cell death. This review presents a brief overview of the Wnt/β-catenin signaling pathway, the regulatory mechanism of this pathway and its role in intestinal homeostasis. Additionally, this review highlights the molecular mechanisms and the histomorphological features of Wnt hyperactivation. Furthermore, the central role of the Wnt signaling pathway in intestinal carcinogenesis as well as its clinical relevance in colorectal carcinoma are discussed.
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Affiliation(s)
- Julia Swoboda
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
| | - Patrick Mittelsdorf
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
| | - Yuan Chen
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, RWTH University Hospital Aachen, Aachen 52074, Germany
| | - Johannes Stallhofer
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena 07747, Germany
| | - Silke Schüle
- Department of General, Visceral and Vascular Surgery, Jena University Hospital, Jena 07747, Germany
| | - Nikolaus Gassler
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
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12
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Cloft SE, Kinstler SR, Reno KE, Sellers HS, Franca M, Ecco R, Lee MD, Maurer JJ, Wong EA. Runting Stunting Syndrome in Broiler Chickens Is Associated with Altered Intestinal Stem Cell Morphology and Gene Expression. Avian Dis 2022; 66:85-94. [DOI: 10.1637/21-00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/20/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Sara E. Cloft
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Sydney R. Kinstler
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Kaitlyn E. Reno
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Holly S. Sellers
- Department of Population Health, Poultry Diagnostic Research Center, University of Georgia, Athens, GA 30601
| | - Monique Franca
- Department of Population Health, Poultry Diagnostic Research Center, University of Georgia, Athens, GA 30601
| | - Roselene Ecco
- Department of Clinic and Surgery, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte 30123-970, Brazil
| | - Margie D. Lee
- Department of Biomedical Science and Pathobiology, Virginia Tech, Blacksburg, VA 24061
| | - John J. Maurer
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Eric A. Wong
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061
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13
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Foley T, Lohnes D. Cdx regulates gene expression through PRC2-mediated epigenetic mechanisms. Dev Biol 2021; 483:22-33. [PMID: 34973175 DOI: 10.1016/j.ydbio.2021.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/03/2022]
Abstract
The extra-embryonic yolk sac contains adjacent layers of mesoderm and visceral endoderm. The mesodermal layer serves as the first site of embryonic hematopoiesis, while the visceral endoderm provides a means of exchanging nutrients and waste until the development of the chorioallantoic placenta. While defects in chorioallantoic fusion and yolk sac hematopoiesis have been described in Cdx mutant mouse models, little is known about the gene targets and molecular mechanisms through which Cdx members regulate these processes. To this end, we used RNA-seq to examine Cdx-dependent gene expression changes in the yolk sac. We find that loss of Cdx function impacts the expression of genes involved in yolk sac hematopoiesis, as previously described, as well as novel Cdx2 target genes. In addition, we observed Cdx-dependent changes in PRC2 subunit expression accompanied by altered H3K27me3 deposition at a subset of Cdx target genes as early as E7.5 in the embryo proper. This study identifies additional Cdx target genes and provides further evidence for Cdx-dependent epigenetic regulation of gene expression in the early embryo, and that this regulation is required to maintain gene expression programs in the extra-embryonic yolk sac at later developmental stages.
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Affiliation(s)
- Tanya Foley
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada, K1H 8M5.
| | - David Lohnes
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada, K1H 8M5.
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14
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Distinct properties of pure- and mixed-type high-grade fetal lung adenocarcinomas by genetic profiling and transcription factor expression. Virchows Arch 2021; 480:609-619. [PMID: 34846611 DOI: 10.1007/s00428-021-03247-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/10/2021] [Accepted: 11/24/2021] [Indexed: 10/19/2022]
Abstract
The clinicopathological differences among high-grade fetal lung adenocarcinomas completely comprising tumor cells that resemble fetal lung epithelium (pure type) and those with fetal lung-like components admixed with conventional adenocarcinoma cells (mixed type) remain undetermined. Here, we examined the clinicopathological, immunohistochemical, and molecular features of 11 lung adenocarcinomas with fetal lung-like morphology among 3895 consecutive cases of primary lung cancer based on the expression pattern of transcription factors. According to the current WHO classification, two cases (0.05%) were categorized as low-grade fetal adenocarcinoma, two cases (0.05%) were pure-type high-grade fetal adenocarcinoma, five cases (0.1%) were mixed-type high-grade fetal adenocarcinoma, and the remaining two cases (0.05%) were lung adenocarcinoma with high-grade fetal features (fetal lung-like morphology occupied less than 50%). CTNNB1 mutations were exclusively identified in low-grade fetal adenocarcinomas. In contrast, mixed-type high-grade fetal adenocarcinoma or lung adenocarcinoma with high-grade fetal features frequently harbored mitogenic drivers including EGFR mutations. Furthermore, almost all tumor cells expressed CDX2 and HNF4α in both cases of pure-type high-grade fetal lung adenocarcinoma, but lacked TTF-1 positivity. In contrast, TTF-1 was frequently expressed in mixed-type high-grade fetal lung adenocarcinoma and in lung adenocarcinoma with high-grade fetal features. Our data suggest similar prevalence of low-grade fetal lung adenocarcinoma and pure-type high-grade fetal lung adenocarcinoma, and indicate that pure- and mixed-type high-grade fetal lung adenocarcinomas are distinct, with the former akin to low-grade fetal adenocarcinoma with respect to purely embryonic morphology and absence of common lung adenocarcinoma mitogenic drivers, and the latter being genetically and transcriptionally related to conventional lung adenocarcinoma.
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15
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Gourain V, Duluc I, Domon-Dell C, Freund JN. A Core Response to the CDX2 Homeoprotein During Development and in Pathologies. Front Genet 2021; 12:744165. [PMID: 34759958 PMCID: PMC8573415 DOI: 10.3389/fgene.2021.744165] [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: 07/20/2021] [Accepted: 10/07/2021] [Indexed: 01/18/2023] Open
Abstract
Whether a gene involved in distinct tissue or cell functions exerts a core of common molecular activities is a relevant topic in evolutionary, developmental, and pathological perspectives. Here, we addressed this question by focusing on the transcription factor and regulator of chromatin accessibility encoded by the Cdx2 homeobox gene that plays important functions during embryonic development and in adult diseases. By integrating RNAseq data in mouse embryogenesis, we unveiled a core set of common genes whose expression is responsive to the CDX2 homeoprotein during trophectoderm formation, posterior body elongation and intestinal specification. ChIPseq data analysis also identified a set of common chromosomal regions targeted by CDX2 at these three developmental steps. The transcriptional core set of genes was then validated with transgenic mouse models of loss or gain of function of Cdx2. Finally, based on human cancer data, we highlight the relevance of these results by displaying a significant number of human orthologous genes to the core set of mouse CDX2-responsive genes exhibiting an altered expression along with CDX2 in human malignancies.
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Affiliation(s)
- Victor Gourain
- Karlsruhe Institute of Technology, Institute of Biological and Chemical Systems, Karlsruhe, Germany
| | - Isabelle Duluc
- Université de Strasbourg, Inserm, IRFAC / UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France
| | - Claire Domon-Dell
- Université de Strasbourg, Inserm, IRFAC / UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France
| | - Jean-Noël Freund
- Université de Strasbourg, Inserm, IRFAC / UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France
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16
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Chen ACH, Huang W, Fong SW, Chan C, Lee KC, Yeung WSB, Lee YL. Hyperglycemia Altered DNA Methylation Status and Impaired Pancreatic Differentiation from Embryonic Stem Cells. Int J Mol Sci 2021; 22:ijms221910729. [PMID: 34639069 PMCID: PMC8509790 DOI: 10.3390/ijms221910729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
The prevalence of type 2 diabetes (T2D) is rapidly increasing across the globe. Fetal exposure to maternal diabetes was correlated with higher prevalence of impaired glucose tolerance and T2D later in life. Previous studies showed aberrant DNA methylation patterns in pancreas of T2D patients. However, the underlying mechanisms remained largely unknown. We utilized human embryonic stem cells (hESC) as the in vitro model for studying the effects of hyperglycemia on DNA methylome and early pancreatic differentiation. Culture in hyperglycemic conditions disturbed the pancreatic lineage potential of hESC, leading to the downregulation of expression of pancreatic markers PDX1, NKX6-1 and NKX6-2 after in vitro differentiation. Genome-wide DNA methylome profiling revealed over 2000 differentially methylated CpG sites in hESC cultured in hyperglycemic condition when compared with those in control glucose condition. Gene ontology analysis also revealed that the hypermethylated genes were enriched in cell fate commitment. Among them, NKX6-2 was validated and its hypermethylation status was maintained upon differentiation into pancreatic progenitor cells. We also established mouse ESC lines at both physiological glucose level (PG-mESC) and conventional hyperglycemia glucose level (HG-mESC). Concordantly, DNA methylome analysis revealed the enrichment of hypermethylated genes related to cell differentiation in HG-mESC, including Nkx6-1. Our results suggested that hyperglycemia dysregulated the epigenome at early fetal development, possibly leading to impaired pancreatic development.
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Affiliation(s)
- Andy Chun Hang Chen
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong, Shenzhen Hospital, Shenzhen 518000, China;
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong; (W.H.); (S.W.F.); (C.C.); (K.C.L.)
| | - Wen Huang
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong; (W.H.); (S.W.F.); (C.C.); (K.C.L.)
| | - Sze Wan Fong
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong; (W.H.); (S.W.F.); (C.C.); (K.C.L.)
| | - Chris Chan
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong; (W.H.); (S.W.F.); (C.C.); (K.C.L.)
| | - Kai Chuen Lee
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong; (W.H.); (S.W.F.); (C.C.); (K.C.L.)
| | - William Shu Biu Yeung
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong, Shenzhen Hospital, Shenzhen 518000, China;
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong; (W.H.); (S.W.F.); (C.C.); (K.C.L.)
- Correspondence: (W.S.B.Y.); (Y.L.L.)
| | - Yin Lau Lee
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong, Shenzhen Hospital, Shenzhen 518000, China;
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong; (W.H.); (S.W.F.); (C.C.); (K.C.L.)
- Correspondence: (W.S.B.Y.); (Y.L.L.)
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17
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Yu Q, Kilik U, Holloway EM, Tsai YH, Harmel C, Wu A, Wu JH, Czerwinski M, Childs CJ, He Z, Capeling MM, Huang S, Glass IA, Higgins PDR, Treutlein B, Spence JR, Camp JG. Charting human development using a multi-endodermal organ atlas and organoid models. Cell 2021; 184:3281-3298.e22. [PMID: 34019796 PMCID: PMC8208823 DOI: 10.1016/j.cell.2021.04.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 12/11/2022]
Abstract
Organs are composed of diverse cell types that traverse transient states during organogenesis. To interrogate this diversity during human development, we generate a single-cell transcriptome atlas from multiple developing endodermal organs of the respiratory and gastrointestinal tract. We illuminate cell states, transcription factors, and organ-specific epithelial stem cell and mesenchyme interactions across lineages. We implement the atlas as a high-dimensional search space to benchmark human pluripotent stem cell (hPSC)-derived intestinal organoids (HIOs) under multiple culture conditions. We show that HIOs recapitulate reference cell states and use HIOs to reconstruct the molecular dynamics of intestinal epithelium and mesenchyme emergence. We show that the mesenchyme-derived niche cue NRG1 enhances intestinal stem cell maturation in vitro and that the homeobox transcription factor CDX2 is required for regionalization of intestinal epithelium and mesenchyme in humans. This work combines cell atlases and organoid technologies to understand how human organ development is orchestrated.
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Affiliation(s)
- Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Umut Kilik
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Christoph Harmel
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael Czerwinski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charlie J Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ian A Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Peter D R Higgins
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland.
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18
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Tata A, Chow RD, Tata PR. Epithelial cell plasticity: breaking boundaries and changing landscapes. EMBO Rep 2021; 22:e51921. [PMID: 34096150 DOI: 10.15252/embr.202051921] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
Epithelial tissues respond to a wide variety of environmental and genotoxic stresses. As an adaptive mechanism, cells can deviate from their natural paths to acquire new identities, both within and across lineages. Under extreme conditions, epithelial tissues can utilize "shape-shifting" mechanisms whereby they alter their form and function at a tissue-wide scale. Mounting evidence suggests that in order to acquire these alternate tissue identities, cells follow a core set of "tissue logic" principles based on developmental paradigms. Here, we review the terminology and the concepts that have been put forward to describe cell plasticity. We also provide insights into various cell intrinsic and extrinsic factors, including genetic mutations, inflammation, microbiota, and therapeutic agents that contribute to cell plasticity. Additionally, we discuss recent studies that have sought to decode the "syntax" of plasticity-i.e., the cellular and molecular principles through which cells acquire new identities in both homeostatic and malignant epithelial tissues-and how these processes can be manipulated for developing novel cancer therapeutics.
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Affiliation(s)
- Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Ryan D Chow
- Department of Genetics, Systems Biology Institute, Medical Scientist Training Program, Yale University School of Medicine, New Haven, CT, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.,Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.,Regeneration Next, Duke University, Durham, NC, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
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19
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Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium. Nat Rev Gastroenterol Hepatol 2021; 18:7-23. [PMID: 33024279 PMCID: PMC7997278 DOI: 10.1038/s41575-020-00357-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/12/2020] [Indexed: 12/19/2022]
Abstract
The intestinal epithelium serves the unique and critical function of harvesting dietary nutrients, while simultaneously acting as a cellular barrier separating tissues from the luminal environment and gut microbial ecosystem. Two salient features of the intestinal epithelium enable it to perform these complex functions. First, cells within the intestinal epithelium achieve a wide range of specialized identities, including different cell types and distinct anterior-posterior patterning along the intestine. Second, intestinal epithelial cells are sensitive and responsive to the dynamic milieu of dietary nutrients, xenobiotics and microorganisms encountered in the intestinal luminal environment. These diverse identities and responsiveness of intestinal epithelial cells are achieved in part through the differential transcription of genes encoded in their shared genome. Here, we review insights from mice and other vertebrate models into the transcriptional regulatory mechanisms underlying intestinal epithelial identity and microbial responsiveness, including DNA methylation, chromatin accessibility, histone modifications and transcription factors. These studies are revealing that most transcription factors involved in intestinal epithelial identity also respond to changes in the microbiota, raising both opportunities and challenges to discern the underlying integrative transcriptional regulatory networks.
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20
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Saller J, Al Diffalha S, Neill K, Bhaskar RA, Oliveri C, Boulware D, Levine H, Kalvaria I, Corbett FS, Khazanchi A, Klapman J, Coppola D. CDX-2 Expression in Esophageal Biopsies Without Goblet Cell Intestinal Metaplasia May Be Predictive of Barrett's Esophagus. Dig Dis Sci 2020; 65:1992-1998. [PMID: 31691172 PMCID: PMC7771382 DOI: 10.1007/s10620-019-05914-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 10/20/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND CDX-2 is a nuclear homeobox transcription factor not normally expressed in esophageal and gastric epithelia, reported to highlight intestinal metaplasia (IM) in the esophagus. Pathological absence of goblet cells at initial screening via hematoxylin and eosin (HE) and alcian blue (AB) staining results in patient exclusion from surveillance programs. AIMS This study aimed to determine whether non-goblet cell IM, as defined by CDX-2 positivity, can be considered to be a precursor to Barrett's esophagus (BE). METHODS This study received IRB approval (17,284). Patients with gastroesophageal reflux disease (n = 181) who underwent upper-gastrointestinal endoscopy with biopsies of the distal esophagus to rule out BE using HE/AB staining and CDX-2 immunostaining were followed for 3 years. Initial and follow-up staining results were evaluated for age/sex. RESULTS Differences between development of goblet cell IM in CDX-2-negative and CDX-2-positive groups were evaluated. A Kaplan-Meier curve showed that, out of the 134 patients initially positive for CDX-2, 25 (18.7%) had developed goblet cell IM after 2 years and 106 (79.1%) after 3 years. Conversely, of the 47 patients initially negative for CDX-2, 8 (17.9%) developed goblet cell IM after 24 months and only 11 (23.8%) after 40 to 45 months (P = .049; age-adjusted Cox proportional hazard regression model). CONCLUSION In cases that are initially AB negative and CDX-2 positive, CDX-2 was demonstrated to have a potential prognostic utility for early detection of progression to BE. CDX-2 expression is significantly predictive for risk of goblet cell IM development 40 to 45 months after initial biopsy.
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Affiliation(s)
- James Saller
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Sameer Al Diffalha
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Kevin Neill
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Rahill A Bhaskar
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - David Boulware
- Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Isaac Kalvaria
- Florida Digestive Health Specialists, Lakewood Ranch, FL, USA
| | - F Scott Corbett
- Florida Digestive Health Specialists, Lakewood Ranch, FL, USA
| | - Arun Khazanchi
- Florida Digestive Health Specialists, Lakewood Ranch, FL, USA
| | - Jason Klapman
- Endoscopy, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Domenico Coppola
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
- Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA.
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21
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Gadaleta RM, Garcia-Irigoyen O, Cariello M, Scialpi N, Peres C, Vetrano S, Fiorino G, Danese S, Ko B, Luo J, Porru E, Roda A, Sabbà C, Moschetta A. Fibroblast Growth Factor 19 modulates intestinal microbiota and inflammation in presence of Farnesoid X Receptor. EBioMedicine 2020; 54:102719. [PMID: 32259714 PMCID: PMC7136604 DOI: 10.1016/j.ebiom.2020.102719] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Disruption of bile acid (BA) homeostasis plays a key role in intestinal inflammation. The gut-liver axis is the main site for the regulation of BA synthesis and BA pool size via the combined action of the nuclear Farnesoid X Receptor (FXR) and the enterokine Fibroblast Growth Factor 19 (FGF19). Increasing evidence have linked derangement of BA metabolism with dysbiosis and mucosal inflammation. Thus, here we aimed to investigate the potential action of an FGF19 analogue on intestinal microbiota and inflammation. METHODS A novel engineered non-tumorigenic variant of the FGF19 protein, M52-WO 2016/0168219 was generated. WT and FXRnull mice were injected with AAV-FGF19-M52 or the control AAV-GFP and subjected to Sodium Dextran Sulphate-induced colitis. FINDINGS FGF19-M52 reduced BA synthesis and pool size, modulated its composition and protected mice from intestinal inflammation. These events were coupled with preservation of the intestinal epithelial barrier integrity, inhibition of inflammatory immune response and modulation of microbiota composition. Interestingly, FGF19-M52-driven systemic and local anti-inflammatory activity was completely abolished in Farnesoid X Receptor (FXR)null mice, thus underscoring the need of FXR to guarantee enterocytes' fitness and complement FGF19 anti-inflammatory activity. To provide a translational perspective, we also show that circulating FGF19 levels are reduced in patients with Crohn's disease. INTERPRETATION Reactivation of the FXR-FGF19 axis in a murine model of intestinal inflammation could bona fide provide positive changes in BA metabolism with consequent reduction of intestinal inflammation and modulation of microbiota. These results point to the therapeutic potential of FGF19 in the treatment of intestinal inflammation with concomitant derangement of BA homeostasis. FUNDING A. Moschetta is funded by MIUR-PRIN 2017 <- 2017J3E2W2; Italian Association for Cancer Research (AIRC, IG 23239); Interreg V-A Greece-Italy 2014-2020-SILVER WELLBEING, MIS5003627; HDHL-INTIMIC EuJPI-FATMAL; MIUR PON "R&I" 2014-2020-ARS01_01220. No money has been paid by NGM Biopharmaceuticals or any other agency to write this article.
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Affiliation(s)
- Raffaella Maria Gadaleta
- Department of Interdisciplinary Medicine, "Aldo Moro" University, Piazza Giulio Cesare 11, 70124 Bari, Italy; National Institute for Biostructures and Biosystems, Via delle Medaglie d'Oro 135, 00136 Rome, Italy
| | - Oihane Garcia-Irigoyen
- Department of Interdisciplinary Medicine, "Aldo Moro" University, Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Marica Cariello
- Department of Interdisciplinary Medicine, "Aldo Moro" University, Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Natasha Scialpi
- National Institute for Biostructures and Biosystems, Via delle Medaglie d'Oro 135, 00136 Rome, Italy
| | - Claudia Peres
- National Institute for Biostructures and Biosystems, Via delle Medaglie d'Oro 135, 00136 Rome, Italy
| | - Stefania Vetrano
- Department of Biomedical Sciences, Humanitas University, Via Alessandro Manzoni, 56, 20089 Rozzano, Milan, Italy; Inflammatory Bowel Disease Center, Humanitas Cancer Center, via Rita Levi Montalcini 4, 20090 Milan, Italy
| | - Gionatha Fiorino
- Inflammatory Bowel Disease Center, Humanitas Cancer Center, via Rita Levi Montalcini 4, 20090 Milan, Italy
| | - Silvio Danese
- Department of Biomedical Sciences, Humanitas University, Via Alessandro Manzoni, 56, 20089 Rozzano, Milan, Italy; Inflammatory Bowel Disease Center, Humanitas Cancer Center, via Rita Levi Montalcini 4, 20090 Milan, Italy
| | - Brian Ko
- NGM Biopharmaceuticals Inc., 333 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Jian Luo
- NGM Biopharmaceuticals Inc., 333 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Emanuele Porru
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum, University of Bologna, Via Selmi, 2, 40126 Bologna, Italy
| | - Aldo Roda
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum, University of Bologna, Via Selmi, 2, 40126 Bologna, Italy
| | - Carlo Sabbà
- Department of Interdisciplinary Medicine, "Aldo Moro" University, Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Antonio Moschetta
- Department of Interdisciplinary Medicine, "Aldo Moro" University, Piazza Giulio Cesare 11, 70124 Bari, Italy; National Cancer Center, IRCCS Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco, 65, 70124 Bari, Italy.
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Cdx2 Animal Models Reveal Developmental Origins of Cancers. Genes (Basel) 2019; 10:genes10110928. [PMID: 31739541 PMCID: PMC6895827 DOI: 10.3390/genes10110928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022] Open
Abstract
The Cdx2 homeobox gene is important in assigning positional identity during the finely orchestrated process of embryogenesis. In adults, regenerative responses to tissues damage can require a replay of these same developmental pathways. Errors in reassigning positional identity during regeneration can cause metaplasias-normal tissue arising in an abnormal location-and this in turn, is a well-recognized cancer risk factor. In animal models, a gain of Cdx2 function can elicit a posterior shift in tissue identity, modeling intestinal-type metaplasias of the esophagus (Barrett's esophagus) and stomach. Conversely, loss of Cdx2 function can elicit an anterior shift in tissue identity, inducing serrated-type lesions expressing gastric markers in the colon. These metaplasias are major risk factors for the later development of esophageal, stomach and colon cancer. Leukemia, another cancer in which Cdx2 is ectopically expressed, may have mechanistic parallels with epithelial cancers in terms of stress-induced reprogramming. This review will address how animal models have refined our understanding of the role of Cdx2 in these common human cancers.
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Severe head dysgenesis resulting from imbalance between anterior and posterior ontogenetic programs. Cell Death Dis 2019; 10:812. [PMID: 31649239 PMCID: PMC6813351 DOI: 10.1038/s41419-019-2040-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/27/2019] [Accepted: 10/03/2019] [Indexed: 12/16/2022]
Abstract
Head dysgenesis is a major cause of fetal demise and craniofacial malformation. Although mutations in genes of the head ontogenetic program have been reported, many cases remain unexplained. Head dysgenesis has also been related to trisomy or amplification of the chromosomal region overlapping the CDX2 homeobox gene, a master element of the trunk ontogenetic program. Hence, we investigated the repercussion on head morphogenesis of the imbalance between the head and trunk ontogenetic programs, by means of ectopic rostral expression of CDX2 at gastrulation. This caused severe malformations affecting the forebrain and optic structures, and also the frontonasal process associated with defects in neural crest cells colonization. These malformations are the result of the downregulation of genes of the head program together with the abnormal induction of trunk program genes. Together, these data indicate that the imbalance between the anterior and posterior ontogenetic programs in embryos is a new possible cause of head dysgenesis during human development, linked to defects in setting up anterior neuroectodermal structures.
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24
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Yovchev MI, Lee EJ, Rodriguez‐Silva W, Locker J, Oertel M. Biliary Obstruction Promotes Multilineage Differentiation of Hepatic Stem Cells. Hepatol Commun 2019; 3:1137-1150. [PMID: 31388633 PMCID: PMC6672331 DOI: 10.1002/hep4.1367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/23/2019] [Indexed: 12/17/2022] Open
Abstract
Because of their high regenerative potential, stem cells are an ideal resource for development of therapies that replace injured tissue mass and restore function in patients with end-stage liver diseases. Using a rat model of bile duct ligation (BDL) and biliary fibrosis, we investigated cell engraftment, liver repopulation, and ectopic tissue formation after intrasplenic transplantation of epithelial stem/progenitor cells. Fetal liver cells were infused into the spleens of Fisher 344 rats with progressing biliary fibrosis induced by common BDL or rats without BDL. Cell delivery was well tolerated. After migration to the liver, donor-derived stem/progenitor cells engrafted, differentiated into hepatocytes and cholangiocytes, and formed large cell clusters at 2 months in BDL rats but not controls. Substantial numbers of donor cells were also detected at the splenic injection site where they generated hepatic and nonhepatic tissue. Transplanted cells differentiated into phenotypes other than hepato/cholangiocytic cells only in rats that underwent BDL. Quantitative reverse-transcription polymerase chain reaction analyses demonstrated marked up-regulation of tissue-specific genes of nonhepatic endodermal lineages (e.g., caudal type homeobox 2 [Cdx2], pancreatic and duodenal homeobox 1 [Pdx1], keratin 13 [CK-13]), confirmed by immunohistochemistry. Conclusion: BDL and its induced fibrosis promote liver repopulation by ectopically transplanted fetal liver-derived cells. These cell fractions contain multipotent stem cells that colonize the spleen of BDL rats and differentiate into multiple gastrointestinal tissues, including liver, pancreas, intestine, and esophagus. The splenic microenvironment, therefore, represents an ideal niche to assess the differentiation of these stem cells, while BDL provides a stimulus that induces their differentiation.
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Affiliation(s)
- Mladen I. Yovchev
- Department of Pathology, Division of Experimental PathologyUniversity of PittsburghPittsburghPA
| | - Edward J. Lee
- Department of Pathology, Division of Experimental PathologyUniversity of PittsburghPittsburghPA
| | | | - Joseph Locker
- Department of Pathology, Division of Experimental PathologyUniversity of PittsburghPittsburghPA
- Pittsburgh Liver Research CenterUniversity of PittsburghPittsburghPA
| | - Michael Oertel
- Department of Pathology, Division of Experimental PathologyUniversity of PittsburghPittsburghPA
- Pittsburgh Liver Research CenterUniversity of PittsburghPittsburghPA
- McGowan Institute for Regenerative MedicineUniversity of PittsburghPittsburghPA
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25
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Generation of Human iPSC-Derived Intestinal Epithelial Cell Monolayers by CDX2 Transduction. Cell Mol Gastroenterol Hepatol 2019; 8:513-526. [PMID: 31228606 PMCID: PMC6722387 DOI: 10.1016/j.jcmgh.2019.06.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS To develop an effective and safe orally administered drug, it is important to predict its intestinal absorption rate, intestinal first-pass effect, and drug-drug interactions of orally administered drugs. However, there is no existing model to comprehensively predict the intestinal pharmacokinetics and drug-response of orally administered drugs. In this study, we attempted to generate homogenous and functional intestinal epithelial cells from human induced pluripotent stem (iPS) cells for pharmaceutical research. METHODS We generated almost-homogenous Villin- and zonula occludens-1 (ZO1)-positive intestinal epithelial cells by caudal-related homeobox transcription factor 2 (CDX2) transduction into human iPS cell-derived intestinal progenitor cells. RESULTS The drug absorption rates in human iPS cell-derived intestinal epithelial cell monolayers (iPS-IECM) were highly correlated with those in humans (R2=0.91). The expression levels of cytochrome P450 (CYP) 3A4, a dominant drug-metabolizing enzyme in the small intestine, in human iPS-IECM were similar to those in human small intestine in vivo. In addition, intestinal availability in human iPS-IECM (the fraction passing the gut wall: Fg=0.73) was more similar to that in the human small intestine in vivo (Fg=0.57) than to that in Caco-2 cells (Fg=0.99), a human colorectal adenocarcinoma cell line. Moreover, the drug-drug interaction and drug-food interaction could be observed by using our human iPS-IECM in the presence of an inducer and inhibitor of CYP3A4, i.e., rifampicin and grape fruit juice, respectively. CONCLUSION Taking these results together, we succeeded in generating the human iPS-IECM that can be applied to various intestinal pharmacokinetics and drug-response tests of orally administered drugs.
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26
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Li XG, Zhu M, Chen MX, Fan HB, Fu HL, Zhou JY, Zhai ZY, Gao CQ, Yan HC, Wang XQ. Acute exposure to deoxynivalenol inhibits porcine enteroid activity via suppression of the Wnt/β-catenin pathway. Toxicol Lett 2019; 305:19-31. [DOI: 10.1016/j.toxlet.2019.01.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 12/06/2018] [Accepted: 01/18/2019] [Indexed: 12/21/2022]
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27
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Foley TE, Hess B, Savory JGA, Ringuette R, Lohnes D. Role of Cdx factors in early mesodermal fate decisions. Development 2019; 146:146/7/dev170498. [PMID: 30936115 DOI: 10.1242/dev.170498] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 03/01/2019] [Indexed: 12/30/2022]
Abstract
Murine cardiac and hematopoietic progenitors are derived from Mesp1+ mesoderm. Cdx function impacts both yolk sac hematopoiesis and cardiogenesis in zebrafish, suggesting that Cdx family members regulate early mesoderm cell fate decisions. We found that Cdx2 occupies a number of transcription factor loci during embryogenesis, including key regulators of both cardiac and blood development, and that Cdx function is required for normal expression of the cardiogenic transcription factors Nkx2-5 and Tbx5 Furthermore, Cdx and Brg1, an ATPase subunit of the SWI/SNF chromatin remodeling complex, co-occupy a number of loci, suggesting that Cdx family members regulate target gene expression through alterations in chromatin architecture. Consistent with this, we demonstrate loss of Brg1 occupancy and altered chromatin structure at several cardiogenic genes in Cdx-null mutants. Finally, we provide evidence for an onset of Cdx2 expression at E6.5 coinciding with egression of cardiac progenitors from the primitive streak. Together, these findings suggest that Cdx functions in multi-potential mesoderm to direct early cell fate decisions through transcriptional regulation of several novel target genes, and provide further insight into a potential epigenetic mechanism by which Cdx influences target gene expression.
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Affiliation(s)
- Tanya E Foley
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Bradley Hess
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Joanne G A Savory
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Randy Ringuette
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - David Lohnes
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
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28
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Tong K, Pellón-Cárdenas O, Sirihorachai VR, Warder BN, Kothari OA, Perekatt AO, Fokas EE, Fullem RL, Zhou A, Thackray JK, Tran H, Zhang L, Xing J, Verzi MP. Degree of Tissue Differentiation Dictates Susceptibility to BRAF-Driven Colorectal Cancer. Cell Rep 2019; 21:3833-3845. [PMID: 29281831 DOI: 10.1016/j.celrep.2017.11.104] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/09/2017] [Accepted: 11/29/2017] [Indexed: 02/07/2023] Open
Abstract
Oncogenic mutations in BRAF are believed to initiate serrated colorectal cancers; however, the mechanisms of BRAF-driven colon cancer are unclear. We find that oncogenic BRAF paradoxically suppresses stem cell renewal and instead promotes differentiation. Correspondingly, tumor formation is inefficient in BRAF-driven mouse models of colon cancer. By reducing levels of differentiation via genetic manipulation of either of two distinct differentiation-promoting factors (Smad4 or Cdx2), stem cell activity is restored in BRAFV600E intestines, and the oncogenic capacity of BRAFV600E is amplified. In human patients, we observe that reduced levels of differentiation in normal tissue is associated with increased susceptibility to serrated colon tumors. Together, these findings help resolve the conditions necessary for BRAF-driven colon cancer initiation. Additionally, our results predict that genetic and/or environmental factors that reduce tissue differentiation will increase susceptibility to serrated colon cancer. These findings offer an opportunity to identify susceptible individuals by assessing their tissue-differentiation status.
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Affiliation(s)
- Kevin Tong
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Oscar Pellón-Cárdenas
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Veerin R Sirihorachai
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Bailey N Warder
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Om A Kothari
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Ansu O Perekatt
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Emily E Fokas
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Robert L Fullem
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Anbo Zhou
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Joshua K Thackray
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Hiep Tran
- Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Lanjing Zhang
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA; Department of Pathology, University Medical Center of Princeton, Plainsboro, NJ 08536, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Human Genetics Institute of New Jersey (HGINJ), 145 Bevier Road, Piscataway Township, NJ 08854, USA; Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA.
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Kumar N, Tsai YH, Chen L, Zhou A, Banerjee KK, Saxena M, Huang S, Toke NH, Xing J, Shivdasani RA, Spence JR, Verzi MP. The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development. Development 2019; 146:dev172189. [PMID: 30745430 PMCID: PMC6432663 DOI: 10.1242/dev.172189] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/30/2019] [Indexed: 12/11/2022]
Abstract
Lineage-restricted transcription factors, such as the intestine-specifying factor CDX2, often have dual requirements across developmental time. Embryonic loss of CDX2 triggers homeotic transformation of intestinal fate, whereas adult-onset loss compromises crucial physiological functions but preserves intestinal identity. It is unclear how such diverse requirements are executed across the developmental continuum. Using primary and engineered human tissues, mouse genetics, and a multi-omics approach, we demonstrate that divergent CDX2 loss-of-function phenotypes in embryonic versus adult intestines correspond to divergent CDX2 chromatin-binding profiles in embryonic versus adult stages. CDX2 binds and activates distinct target genes in developing versus adult mouse and human intestinal cells. We find that temporal shifts in chromatin accessibility correspond to these context-specific CDX2 activities. Thus, CDX2 is not sufficient to activate a mature intestinal program; rather, CDX2 responds to its environment, targeting stage-specific genes to contribute to either intestinal patterning or mature intestinal function. This study provides insights into the mechanisms through which lineage-specific regulatory factors achieve divergent functions over developmental time.
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Affiliation(s)
- Namit Kumar
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lei Chen
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Anbo Zhou
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Kushal K Banerjee
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Madhurima Saxena
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Sha Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natalie H Toke
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Jinchuan Xing
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Jason R Spence
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Michael P Verzi
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
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30
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Ihara S, Hirata Y, Hikiba Y, Yamashita A, Tsuboi M, Hata M, Konishi M, Suzuki N, Sakitani K, Kinoshita H, Hayakawa Y, Nakagawa H, Ijichi H, Tateishi K, Koike K. Adhesive Interactions between Mononuclear Phagocytes and Intestinal Epithelium Perturb Normal Epithelial Differentiation and Serve as a Therapeutic Target in Inflammatory Bowel Disease. J Crohns Colitis 2018; 12:1219-1231. [PMID: 29917067 DOI: 10.1093/ecco-jcc/jjy088] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Disturbance of intestinal homeostasis is associated with the development of inflammatory bowel disease [IBD], and TGF-β signalling impairment in mononuclear phagocytes [MPs] causes murine colitis with goblet cell depletion. Here, we examined an organoid-MP co-culture system to study the role of MPs in intestinal epithelial differentiation and homeostasis. METHODS Intestinal organoids were co-cultured with lamina propria leukocytes and bone marrow-derived dendritic cells [BMDCs] from CD11c-cre Tgfbr2fl/fl mice. Organoid-MP adhesive interactions were evaluated by microscopy, RT-PCR, and flow cytometry. Murine colitis models (dextran sodium sulphate [DSS], CD11c-cre Tgfbr2fl/fl, T-cell-transfer) were used for histological and immunohistochemical analysis. Anti-E-cadherin antibody treatment or CD11c+-cell-specific CDH1 gene deletion were performed for E-cadherin neutralization or knockout. Colonic biopsies from patients with ulcerative colitis were analysed by flow cytometry. RESULTS Intestinal organoids co-cultured with CD11c+ lamina propria leukocytes or BMDCs from CD11c-cre Tgfbr2fl/fl mice showed morphological changes and goblet cell depletion with Notch signal activation, analogous to CD11c-cre Tgfbr2fl/fl colitis. E-cadherin was upregulated in CD11c+ MPs, especially CX3CR1+CCR2+ monocytes, of CD11c-cre Tgfbr2fl/fl mice. E-cadherin-mediated BMDC adhesion promoted Notch activation and cystic changes in organoids. Anti-E-cadherin antibody treatment attenuated colitis in CD11c-cre Tgfbr2fl/fl and T-cell-transferred mice. In addition, E-cadherin deletion in CD11c+ cells attenuated colitis in both CD11c-cre Tgfbr2fl/fl and DSS-treated mice. In patients with ulcerative colitis, E-cadherin expressed by intestinal CD11c+ leukocytes was enhanced compared with that in healthy controls. CONCLUSIONS E-cadherin-mediated MP-epithelium adhesion is associated with the development of colitis, and blocking these adhesions may have therapeutic potential for IBD.
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Affiliation(s)
- Sozaburo Ihara
- Division of Gastroenterology, The Institute for Adult Diseases, Asahi Life Foundation, Tokyo, Japan.,Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Hirata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Advanced Genome Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yohko Hikiba
- Division of Gastroenterology, The Institute for Adult Diseases, Asahi Life Foundation, Tokyo, Japan
| | - Aya Yamashita
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mayo Tsuboi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahiro Hata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mitsuru Konishi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobumi Suzuki
- Division of Gastroenterology, The Institute for Adult Diseases, Asahi Life Foundation, Tokyo, Japan
| | - Kosuke Sakitani
- Division of Gastroenterology, The Institute for Adult Diseases, Asahi Life Foundation, Tokyo, Japan
| | - Hiroto Kinoshita
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideaki Ijichi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keisuke Tateishi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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31
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Banerjee KK, Saxena M, Kumar N, Chen L, Cavazza A, Toke NH, O'Neill NK, Madha S, Jadhav U, Verzi MP, Shivdasani RA. Enhancer, transcriptional, and cell fate plasticity precedes intestinal determination during endoderm development. Genes Dev 2018; 32:1430-1442. [PMID: 30366903 PMCID: PMC6217732 DOI: 10.1101/gad.318832.118] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
After acquiring competence for selected cell fates, embryonic primordia may remain plastic for variable periods before tissue identity is irrevocably determined. Banerjee et al. show that the midgut endoderm is primed for heterologous cell fates and that transcription factors act on a background of shifting chromatin access to determine intestinal at the expense of foregut identity. After acquiring competence for selected cell fates, embryonic primordia may remain plastic for variable periods before tissue identity is irrevocably determined (commitment). We investigated the chromatin basis for these developmental milestones in mouse endoderm, a tissue with recognizable rostro–caudal patterning and transcription factor (TF)-dependent interim plasticity. Foregut-specific enhancers are as accessible and active in early midgut as in foregut endoderm, and intestinal enhancers and identity are established only after ectopic cis-regulatory elements are decommissioned. Depletion of the intestinal TF CDX2 before this cis element transition stabilizes foregut enhancers, reinforces ectopic transcriptional programs, and hence imposes foregut identities on the midgut. Later in development, as the window of chromatin plasticity elapses, CDX2 depletion weakens intestinal, without strengthening foregut, enhancers. Thus, midgut endoderm is primed for heterologous cell fates, and TFs act on a background of shifting chromatin access to determine intestinal at the expense of foregut identity. Similar principles likely govern other fate commitments.
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Affiliation(s)
- Kushal K Banerjee
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Madhurima Saxena
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Namit Kumar
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Lei Chen
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Alessia Cavazza
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Natalie H Toke
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Nicholas K O'Neill
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Shariq Madha
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Unmesh Jadhav
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA.,Cancer Institute of New Jersey, Piscataway, New Jersey 08854, USA.,Human Genetics Institute of New Jersey, Piscataway, New Jersey 08854, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02139, USA
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32
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Chromatin de-condensation by switching substrate elasticity. Sci Rep 2018; 8:12655. [PMID: 30140058 PMCID: PMC6107547 DOI: 10.1038/s41598-018-31023-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023] Open
Abstract
Mechanical properties of the cellular environment are known to influence cell fate. Chromatin de-condensation appears as an early event in cell reprogramming. Whereas the ratio of euchromatin versus heterochromatin can be increased chemically, we report herein for the first time that the ratio can also be increased by purely changing the mechanical properties of the microenvironment by successive 24 h-contact of the cells on a soft substrate alternated with relocation and growth for 7 days on a hard substrate. An initial contact with soft substrate caused massive SW480 cancer cell death by necrosis, whereas approximately 7% of the cells did survived exhibiting a high level of condensed chromatin (21% heterochromatin). However, four consecutive hard/soft cycles elicited a strong chromatin de-condensation (6% heterochromatin) correlating with an increase of cellular survival (approximately 90%). Furthermore, cell survival appeared to be reversible, indicative of an adaptive process rather than an irreversible gene mutation(s). This adaptation process is associated with modifications in gene expression patterns. A completely new approach for chromatin de-condensation, based only on mechanical properties of the microenvironment, without any drug mediation is presented.
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33
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Abstract
Chronic injury and inflammation in the esophagus can cause a change in cellular differentiation known as metaplasia. Most commonly, the differentiation changes manifest as Barrett's esophagus (BE), characterized by the normal stratified squamous epithelium converting into a cuboidal-columnar, glandular morphology. BE cells can phenotypically resemble specific normal cell types of the stomach or intestine, or they can have overlapping phenotypes in disorganized admixtures. The stomach can also undergo metaplasia characterized by aberrant gastric or intestinal differentiation patterns. In both organs, it has been argued that metaplasia may represent a recapitulation of the embryonic or juvenile gastrointestinal tract, as cells access a developmental progenitor genetic program that can help repair damaged tissue. Here, we review the normal development of esophagus and stomach, and describe how BE represents an intermixing of cells resembling gastric pseudopyloric (SPEM) and intestinal metaplasia. We discuss a cellular process recently termed "paligenosis" that governs how mature, differentiated cells can revert to a proliferating progenitor state in metaplasia. We discuss the "Cyclical Hit" theory in which paligenosis might be involved in the increased risk of metaplasia for progression to cancer. However, somatic mutations might occur in proliferative phases and then be warehoused upon redifferentiation. Through years of chronic injury and many rounds of paligenosis and dedifferentiation, eventually a cell with a mutation that prevents dedifferentiation may arise and clonally expand fueling stable metaplasia and potentially thereafter acquiring additional mutations and progressing to dysplasia and cancer.
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Affiliation(s)
- Ramon U Jin
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason C Mills
- Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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34
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Goldenring JR. Pyloric metaplasia, pseudopyloric metaplasia, ulcer-associated cell lineage and spasmolytic polypeptide-expressing metaplasia: reparative lineages in the gastrointestinal mucosa. J Pathol 2018; 245:132-137. [PMID: 29508389 DOI: 10.1002/path.5066] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 12/16/2022]
Abstract
The gastrointestinal mucosae provide a critical barrier between the external and internal milieu. Thus, damage to the mucosa requires an immediate response to provide appropriate wound closure and healing. Metaplastic lineages with phenotypes similar to the mucous glands of the distal stomach or Brunner's glands have been associated with various injurious scenarios in the stomach, small bowel, and colon. These lineages have been assigned various names including pyloric metaplasia, pseudopyloric metaplasia, ulcer-associated cell lineage (UACL), and spasmolytic polypeptide-expressing metaplasia (SPEM). A re-examination of the literature on these various forms of mucous cell metaplasia suggests that pyloric-type mucosal gland lineages may provide a ubiquitous response to mucosal injury throughout the gastrointestinal tract as well as in the pancreas, esophagus, and other mucosal surfaces. While the cellular origin of these putative reparative lineages likely varies in different regions of the gut, their final phenotypes may converge on a pyloric-type gland dedicated to mucous secretion. In addition to their healing properties in the setting of acute injury, these pyloric-type lineages may also represent precursors to neoplastic transitions in the face of chronic inflammatory influences. Further investigations are needed to determine how discrete molecular profiles relate to the origin and function of pyloric-type metaplasias previously described by histological characteristics in multiple epithelial mucosal systems in the setting of acute and chronic damage. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- James R Goldenring
- Section of Surgical Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA.,Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Vanderbilt Ingram Cancer Center, Nashville, TN, USA.,Nashville VA Medical Center, Nashville, TN, USA
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35
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Thompson CA, DeLaForest A, Battle MA. Patterning the gastrointestinal epithelium to confer regional-specific functions. Dev Biol 2018; 435:97-108. [PMID: 29339095 PMCID: PMC6615902 DOI: 10.1016/j.ydbio.2018.01.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/01/2018] [Accepted: 01/10/2018] [Indexed: 12/12/2022]
Abstract
The gastrointestinal (GI) tract, in simplest terms, can be described as an epithelial-lined muscular tube extending along the cephalocaudal axis from the oral cavity to the anus. Although the general architecture of the GI tract organs is conserved from end to end, the presence of different epithelial tissue structures and unique epithelial cell types within each organ enables each to perform the distinct digestive functions required for efficient nutrient assimilation. Spatiotemporal regulation of signaling pathways and downstream transcription factors controls GI epithelial morphogenesis during development to confer essential regional-specific epithelial structures and functions. Here, we discuss the fundamental functions of each GI tract organ and summarize the diversity of epithelial structures present along the cephalocaudal axis of the GI tract. Next, we discuss findings, primarily from genetic mouse models, that have defined the roles of key transcription factors during epithelial morphogenesis, including p63, SOX2, SOX15, GATA4, GATA6, HNF4A, and HNF4G. Additionally, we examine how the Hedgehog, WNT, and BMP signaling pathways contribute to defining unique epithelial features along the cephalocaudal axis of the GI tract. Lastly, we examine the molecular mechanisms controlling regionalized cytodifferentiation of organ-specific epithelial cell types within the GI tract, concentrating on the stomach and small intestine. The delineation of GI epithelial patterning mechanisms in mice has provided fundamental knowledge to guide the development and refinement of three-dimensional GI organotypic culture models such as those derived from directed differentiation of human pluripotent stem cells and those derived directly from human tissue samples. Continued examination of these pathways will undoubtedly provide vital insights into the mechanisms of GI development and disease and may afford new avenues for innovative tissue engineering and personalized medicine approaches to treating GI diseases.
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Affiliation(s)
- Cayla A Thompson
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Ann DeLaForest
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Michele A Battle
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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36
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Chen BJ, Zeng S, Xie R, Hu CJ, Wang SM, Wu YY, Xiao YF, Yang SM. hTERT promotes gastric intestinal metaplasia by upregulating CDX2 via NF-κB signaling pathway. Oncotarget 2018; 8:26969-26978. [PMID: 28460480 PMCID: PMC5432311 DOI: 10.18632/oncotarget.15926] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/20/2017] [Indexed: 12/17/2022] Open
Abstract
Background hTERT has been reported involved in the proliferation and metastasis of gastric cancer, but the role of hTERT in gastric intestinal metaplasia, a premalignant lesion of the gastric mucosa was unknown. The aim of the present study was to investigate the role of hTERT in GIM and the effect of hTERT on CDX2 expression in gastric cells. Results Experiments showed that expression of hTERT was significantly higher in GIM than in normal gastric mucosa. Moreover, hTERT increased the KLF4 level via NF-κB during GIM. Furthermore, KLF4 is involved in the up-regulation of CDX2 induced by hTERT, and hTERT can interact with p50, thereby increasing the level of CDX2. Materials and Methods Immunohistochemistry was used to detect the expression of hTERT in gastric intestinal metaplasia tissue. Then, effect of hTERT on the expression of CDX2 was detected by qRT-PCR, WB and dual luciferase experiment. The role of p65 and p50 in the regulation of CDX2 were further detected by WB, CO-IP and ChIP. Conclusions We may conclude that hTERT promotes GIM by up-regulating CDX2 via NF-κB signaling pathway.
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Affiliation(s)
- Bai-Jun Chen
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China.,Department of Gastroenterology, The First Affiliated Hospital, Chengdu Medical College, Chengdu, PR China
| | - Shuo Zeng
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
| | - Rui Xie
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
| | - Chang-Jiang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
| | - Su-Ming Wang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
| | - Yu-Yun Wu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
| | - Yu-Feng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
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37
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Lourenço FC, Winton DJ. Metaplastic Cdx2-depleted cells can be very disruptive neighbors. J Exp Med 2018; 215:725-727. [PMID: 29440363 PMCID: PMC5839770 DOI: 10.1084/jem.20180215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In this issue of JEM, Balbinot et al. (https://doi.org/10.1084/jem.20170934) describe an original mechanism where Cdx2 inactivation regulates intestinal metaplastic to neoplastic transition in a paracrine fashion. Surprisingly, the target cells are neighboring "normal" Cdx2-positive cells.
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Affiliation(s)
- Filipe C Lourenço
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England, UK
| | - Douglas J Winton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England, UK
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38
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Balbinot C, Armant O, Elarouci N, Marisa L, Martin E, De Clara E, Onea A, Deschamps J, Beck F, Freund JN, Duluc I. The Cdx2 homeobox gene suppresses intestinal tumorigenesis through non-cell-autonomous mechanisms. J Exp Med 2018; 215:911-926. [PMID: 29439001 PMCID: PMC5839756 DOI: 10.1084/jem.20170934] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/13/2017] [Accepted: 01/18/2018] [Indexed: 12/16/2022] Open
Abstract
Balbinot et al. show that intestinal epithelial cells depleted in the homeobox gene Cdx2 acquire an imperfect gastric-type metaplastic phenotype that, through changes in the microenvironment, induces the tumorigenic evolution of adjacent Cdx2-intact cells without themselves becoming cancerous. Developmental genes contribute to cancer, as reported for the homeobox gene Cdx2 playing a tumor suppressor role in the gut. In this study, we show that human colon cancers exhibiting the highest reduction in CDX2 expression belong to the serrated subtype with the worst evolution. In mice, mosaic knockout of Cdx2 in the adult intestinal epithelium induces the formation of imperfect gastric-type metaplastic lesions. The metaplastic knockout cells do not spontaneously become tumorigenic. However, they induce profound modifications of the microenvironment that facilitate the tumorigenic evolution of adjacent Cdx2-intact tumor-prone cells at the surface of the lesions through NF-κB activation, induction of inducible nitric oxide synthase, and stochastic loss of function of Apc. This study presents a novel paradigm in that metaplastic cells, generally considered as precancerous, can induce tumorigenesis from neighboring nonmetaplastic cells without themselves becoming cancerous. It unveils the novel property of non–cell-autonomous tumor suppressor gene for the Cdx2 gene in the gut.
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Affiliation(s)
- Camille Balbinot
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, IRFAC UMR-S1113, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Olivier Armant
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Karlsruhe, Germany
| | - Nabila Elarouci
- Cartes d'Identité des Tumeurs Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Laetitia Marisa
- Cartes d'Identité des Tumeurs Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Elisabeth Martin
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, IRFAC UMR-S1113, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Etienne De Clara
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, IRFAC UMR-S1113, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Alina Onea
- Département de Pathologie, Centre Hospitalier Universitaire de Strasbourg, Strasbourg, France
| | - Jacqueline Deschamps
- Developmental Biology and Stem Cell Research, Hubrecht Institute, Utrecht, Netherlands
| | - Felix Beck
- Barts and The London School of Medicine and Dentistry, London, England, UK
| | - Jean-Noël Freund
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, IRFAC UMR-S1113, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Isabelle Duluc
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, IRFAC UMR-S1113, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
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39
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Saxena M, Roman AKS, O'Neill NK, Sulahian R, Jadhav U, Shivdasani RA. Transcription factor-dependent 'anti-repressive' mammalian enhancers exclude H3K27me3 from extended genomic domains. Genes Dev 2018; 31:2391-2404. [PMID: 29321178 PMCID: PMC5795785 DOI: 10.1101/gad.308536.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/08/2017] [Indexed: 11/25/2022]
Abstract
Compacted chromatin and nucleosomes are known barriers to gene expression; the nature and relative importance of other transcriptional constraints remain unclear, especially at distant enhancers. Polycomb repressor complex 2 (PRC2) places the histone mark H3K27me3 predominantly at promoters, where its silencing activity is well documented. In adult tissues, enhancers lack H3K27me3, and it is unknown whether intergenic H3K27me3 deposits affect nearby genes. In primary intestinal villus cells, we identified hundreds of tissue-restricted enhancers that require the transcription factor (TF) CDX2 to prevent the incursion of H3K27me3 from adjoining areas of elevated basal marking into large well-demarcated genome domains. Similarly, GATA1-dependent enhancers exclude H3K27me3 from extended regions in erythroid blood cells. Excess intergenic H3K27me3 in both TF-deficient tissues is associated with extreme mRNA deficits, which are significantly rescued in intestinal cells lacking PRC2. Explaining these observations, enhancers show TF-dependent binding of the H3K27 demethylase KDM6A. Thus, in diverse cell types, certain genome regions far from promoters accumulate H3K27me3, and optimal gene expression depends on enhancers clearing this repressive mark. These findings reveal new "anti-repressive" function for hundreds of tissue-specific enhancers.
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Affiliation(s)
- Madhurima Saxena
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Adrianna K San Roman
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Nicholas K O'Neill
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Rita Sulahian
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Unmesh Jadhav
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02139, USA
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40
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Li XG, Xu GF, Zhai ZY, Gao CQ, Yan HC, Xi QY, Guan WT, Wang SB, Wang XQ. CDX2 increases SLC7A7 expression and proliferation of pig intestinal epithelial cells. Oncotarget 2017; 7:30597-609. [PMID: 27121315 PMCID: PMC5058704 DOI: 10.18632/oncotarget.8894] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/31/2016] [Indexed: 12/14/2022] Open
Abstract
Nutrient absorption mediated by nutrient transporters expressed in the intestinal epithelium supplies substrates to support intestinal processes, including epithelial cell proliferation. We evaluated the role of Caudal type homeobox 2 (CDX2), an intestine-specific transcription factor, in the proliferation of pig intestinal epithelial cells (IPEC-1) and searched for novel intestinal nutrient transporter genes activated by CDX2. Our cloned pig CDX2 cDNA contains a “homeobox” DNA binding motif, suggesting it is a transcriptional activator. CDX2 overexpression in IPEC-1 cells increased cell proliferation, the percentage of cells in S/G2 phase, and the abundance of transcripts of the cell cycle-related genes Cyclin A2; Cyclin B; Cyclin D2; proliferating cell nuclear antigen; and cell cycle cyclin-dependent kinases 1, 2 and 4, as well as the predicted CDX2 target genes SLC1A1, SLC5A1 and SLC7A7. In addition, luciferase reporter and chromatin immunoprecipitation assays revealed that CDX2 binds directly to the SLC7A7 promoter. This is the first report of CDX2 function in pig intestinal epithelial cells and identifies SLC7A7 as a novel CDX2 target gene. Our findings show that nutrient transporters are activated during CDX2-induced proliferation of normal intestinal epithelial cells.
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Affiliation(s)
- Xiang-Guang Li
- College of Animal Science, South China Agricultural University/National Engineering Research Center for Breeding Swine Industry, Guangzhou 510642, China
| | - Gao-Feng Xu
- College of Animal Science, South China Agricultural University/National Engineering Research Center for Breeding Swine Industry, Guangzhou 510642, China
| | - Zhen-Ya Zhai
- College of Animal Science, South China Agricultural University/National Engineering Research Center for Breeding Swine Industry, Guangzhou 510642, China
| | - Chun-Qi Gao
- College of Animal Science, South China Agricultural University/National Engineering Research Center for Breeding Swine Industry, Guangzhou 510642, China
| | - Hui-Chao Yan
- College of Animal Science, South China Agricultural University/National Engineering Research Center for Breeding Swine Industry, Guangzhou 510642, China
| | - Qian-Yun Xi
- College of Animal Science, South China Agricultural University/National Engineering Research Center for Breeding Swine Industry, Guangzhou 510642, China
| | - Wu-Tai Guan
- College of Animal Science, South China Agricultural University/National Engineering Research Center for Breeding Swine Industry, Guangzhou 510642, China
| | - Song-Bo Wang
- College of Animal Science, South China Agricultural University/National Engineering Research Center for Breeding Swine Industry, Guangzhou 510642, China
| | - Xiu-Qi Wang
- College of Animal Science, South China Agricultural University/National Engineering Research Center for Breeding Swine Industry, Guangzhou 510642, China
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41
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Fan HB, Zhai ZY, Li XG, Gao CQ, Yan HC, Chen ZS, Wang XQ. CDX2 Stimulates the Proliferation of Porcine Intestinal Epithelial Cells by Activating the mTORC1 and Wnt/β-Catenin Signaling Pathways. Int J Mol Sci 2017; 18:ijms18112447. [PMID: 29156556 PMCID: PMC5713414 DOI: 10.3390/ijms18112447] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/06/2017] [Accepted: 11/16/2017] [Indexed: 12/13/2022] Open
Abstract
Caudal type homeobox 2 (CDX2) is expressed in intestinal epithelial cells and plays a role in gut development and homeostasis by regulating cell proliferation. However, whether CDX2 cooperates with the mammalian target of rapamycin complex 1 (mTORC1) and Wnt/β-catenin signaling pathways to stimulate cell proliferation remains unknown. The objective of this study was to investigate the effect of CDX2 on the proliferation of porcine jejunum epithelial cells (IPEC-J2) and the correlation between CDX2, the mTORC1 and Wnt/β-catenin signaling pathways. CDX2 overexpression and knockdown cell culture models were established to explore the regulation of CDX2 on both pathways. Pathway-specific antagonists were used to verify the effects. The results showed that CDX2 overexpression increased IPEC-J2 cell proliferation and activated both the mTORC1 and Wnt/β-catenin pathways, and that CDX2 knockdown decreased cell proliferation and inhibited both pathways. Furthermore, the mTORC1 and Wnt/β-catenin pathway-specific antagonist rapamycin and XAV939 (3,5,7,8-tetrahydro-2-[4-(trifluoromethyl)]-4H -thiopyrano[4,3-d]pyrimidin-4-one) both suppressed the proliferation of IPEC-J2 cells overexpressing CDX2, and that the combination of rapamycin and XAV939 had an additive effect. Regardless of whether the cells were treated with rapamycin or XAV939 alone or in combination, both mTORC1 and Wnt/β-catenin pathways were down-regulated, accompanied by a decrease in CDX2 expression. Taken together, our data indicate that CDX2 stimulates porcine intestinal epithelial cell proliferation by activating the mTORC1 and Wnt/β-catenin signaling pathways.
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Affiliation(s)
- Hong-Bo Fan
- College of Animal Science/Guangdong Provincial Key Laboratory of Animal Nutrition Regulation/National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
| | - Zhen-Ya Zhai
- College of Animal Science/Guangdong Provincial Key Laboratory of Animal Nutrition Regulation/National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
| | - Xiang-Guang Li
- College of Animal Science/Guangdong Provincial Key Laboratory of Animal Nutrition Regulation/National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
| | - Chun-Qi Gao
- College of Animal Science/Guangdong Provincial Key Laboratory of Animal Nutrition Regulation/National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
| | - Hui-Chao Yan
- College of Animal Science/Guangdong Provincial Key Laboratory of Animal Nutrition Regulation/National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Science, College of Pharmacy and Health Science, St. John's University, Queens, NY 11439, USA.
| | - Xiu-Qi Wang
- College of Animal Science/Guangdong Provincial Key Laboratory of Animal Nutrition Regulation/National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
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Balbinot C, Vanier M, Armant O, Nair A, Penichon J, Soret C, Martin E, Saandi T, Reimund JM, Deschamps J, Beck F, Domon-Dell C, Gross I, Duluc I, Freund JN. Fine-tuning and autoregulation of the intestinal determinant and tumor suppressor homeobox gene CDX2 by alternative splicing. Cell Death Differ 2017; 24:2173-2186. [PMID: 28862703 DOI: 10.1038/cdd.2017.140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/23/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022] Open
Abstract
On the basis of phylogenetic analyses, we uncovered a variant of the CDX2 homeobox gene, a major regulator of the development and homeostasis of the gut epithelium, also involved in cancer. This variant, miniCDX2, is generated by alternative splicing coupled to alternative translation initiation, and contains the DNA-binding homeodomain but is devoid of transactivation domain. It is predominantly expressed in crypt cells, whereas the CDX2 protein is present in crypt cells but also in differentiated villous cells. Functional studies revealed a dominant-negative effect exerted by miniCDX2 on the transcriptional activity of CDX2, and conversely similar effects regarding several transcription-independent functions of CDX2. In addition, a regulatory role played by the CDX2 and miniCDX2 homeoproteins on their pre-mRNA splicing is displayed, through interactions with splicing factors. Overexpression of miniCDX2 in the duodenal Brunner glands leads to the expansion of the territory of these glands and ultimately to brunneroma. As a whole, this study characterized a new and original variant of the CDX2 homeobox gene. The production of this variant represents not only a novel level of regulation of this gene, but also a novel way to fine-tune its biological activity through the versatile functions exerted by the truncated variant compared to the full-length homeoprotein. This study highlights the relevance of generating protein diversity through alternative splicing in the gut and its diseases.
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Affiliation(s)
- Camille Balbinot
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Marie Vanier
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Olivier Armant
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Postfach 3640, Karlsruhe 76021, Germany
| | - Asmaa Nair
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Julien Penichon
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Christine Soret
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Elisabeth Martin
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Thoueiba Saandi
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jean-Marie Reimund
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jacqueline Deschamps
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands
| | - Felix Beck
- Barts and The London School of Medicine and Dentistry, London E1 2ES, UK
| | - Claire Domon-Dell
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Isabelle Gross
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Isabelle Duluc
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jean-Noël Freund
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
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43
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Maoz N, Buganim Y. Moving towards totipotency without a single miR-acle. Cell Res 2017; 27:600-601. [PMID: 28281537 PMCID: PMC5520849 DOI: 10.1038/cr.2017.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Totipotency is the ability of a single cell to form an entire embryo, including extraembryonic tissues, an ability we have yet to recapitalize, in vitro. In a recent paper published in Science, Choi et al. showed that pluripotent stem cells lacking microRNA miR-34a, have an expanded cell fate potential allowing differentiation into not only embryonic but also extraembryonic lineages.
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Affiliation(s)
- Noam Maoz
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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44
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Platet N, Hinkel I, Richert L, Murdamoothoo D, Moufok-Sadoun A, Vanier M, Lavalle P, Gaiddon C, Vautier D, Freund JN, Gross I. The tumor suppressor CDX2 opposes pro-metastatic biomechanical modifications of colon cancer cells through organization of the actin cytoskeleton. Cancer Lett 2017; 386:57-64. [DOI: 10.1016/j.canlet.2016.10.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 02/07/2023]
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45
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Ketogenesis contributes to intestinal cell differentiation. Cell Death Differ 2016; 24:458-468. [PMID: 27935584 DOI: 10.1038/cdd.2016.142] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/18/2016] [Accepted: 11/04/2016] [Indexed: 01/01/2023] Open
Abstract
The intestinal epithelium undergoes a continual process of proliferation, differentiation and apoptosis. Previously, we have shown that the PI3K/Akt/mTOR pathway has a critical role in intestinal homeostasis. However, the downstream targets mediating the effects of mTOR in intestinal cells are not known. Here, we show that the ketone body β-hydroxybutyrate (βHB), an endogenous inhibitor of histone deacetylases (HDACs) induces intestinal cell differentiation as noted by the increased expression of differentiation markers (Mucin2 (MUC2), lysozyme, IAP, sucrase-isomaltase, KRT20, villin, Caudal-related homeobox transcription factor 2 (CDX2) and p21Waf1). Conversely, knockdown of the ketogenic mitochondrial enzyme hydroxymethylglutaryl CoA synthase 2 (HMGCS2) attenuated spontaneous differentiation in the human colon cancer cell line Caco-2. Overexpression of HMGCS2, which we found is localized specifically in the more differentiated portions of the intestinal mucosa, increased the expression of CDX2, thus further suggesting the contributory role of HMGCS2 in intestinal differentiation. In addition, mice fed a ketogenic diet demonstrated increased differentiation of intestinal cells as noted by an increase in the enterocyte, goblet and Paneth cell lineages. Moreover, we showed that either knockdown of mTOR or inhibition of mTORC1 with rapamycin increases the expression of HMGCS2 in intestinal cells in vitro and in vivo, suggesting a possible cross-talk between mTOR and HMGCS2/βHB signaling in intestinal cells. In contrast, treatment of intestinal cells with βHB or feeding mice with a ketogenic diet inhibits mTOR signaling in intestinal cells. Together, we provide evidence showing that HMGCS2/βHB contributes to intestinal cell differentiation. Our results suggest that mTOR acts cooperatively with HMGCS2/βHB to maintain intestinal homeostasis.
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46
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Cdx and T Brachyury Co-activate Growth Signaling in the Embryonic Axial Progenitor Niche. Cell Rep 2016; 17:3165-3177. [DOI: 10.1016/j.celrep.2016.11.069] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/26/2016] [Accepted: 11/18/2016] [Indexed: 12/30/2022] Open
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47
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Shang Y, Pan Q, Chen L, Ye J, Zhong X, Li X, Meng L, Guo J, Tian Y, He Y, Chen W, Peng Z, Wang R. Achaete scute-like 2 suppresses CDX2 expression and inhibits intestinal neoplastic epithelial cell differentiation. Oncotarget 2016; 6:30993-1006. [PMID: 26307678 PMCID: PMC4741583 DOI: 10.18632/oncotarget.5206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 08/13/2015] [Indexed: 12/30/2022] Open
Abstract
The role of Achaete scute-like 2 (Ascl2) in colorectal cancer (CRC) cell differentiation is unknown. LS174T, HT-29 and Caco-2 cells have high Ascl2 expression, while Lovo and SW480 cells have low Ascl2 expression. LS174T and HT-29 cells with Ascl2 knockdown were transfected with caudal type homeobox 2 (CDX2) promoter constructs and used for luciferase assays and chromatin immunoprecipitation (ChIP) assays. Ascl2 knockdown promoted differentiation of CRC cells into a goblet cell phenotype, as determined by increased expression of MUC2, TFF3, and CDX2. Ascl2 knockdown activated CDX2 expression through a transcriptional mechanism via direct binding of Ascl2 to the proximal E-box of the CDX2 promoter. Ascl2 over-expression in Lovo and SW480 cells inhibited a goblet cell phenotype, as determined by reduced CDX2 and MUC2 expression. Inverse correlations between Ascl2 and CDX2, and Ascl2 and MUC2 mRNA levels, as well as Ascl2 and CDX2 protein levels were observed in CRC cancerous samples. This study demonstrates CDX2 repression by Ascl2 and highlights a role for Ascl2 in CRC cell differentiation. These findings suggest that the Ascl2/CDX2 axis may serve as a potential therapeutic target in colorectal cancer.
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Affiliation(s)
- Yangyang Shang
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Qiong Pan
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Lei Chen
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Jun Ye
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Xiaoli Zhong
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Xiaohuan Li
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Linkuan Meng
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Jin Guo
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Yin Tian
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Yonghong He
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Wensheng Chen
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Zhihong Peng
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Rongquan Wang
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
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Abstract
The stomach, an organ derived from foregut endoderm, secretes acid and enzymes and plays a key role in digestion. During development, mesenchymal-epithelial interactions drive stomach specification, patterning, differentiation and growth through selected signaling pathways and transcription factors. After birth, the gastric epithelium is maintained by the activity of stem cells. Developmental signals are aberrantly activated and stem cell functions are disrupted in gastric cancer and other disorders. Therefore, a better understanding of stomach development and stem cells can inform approaches to treating these conditions. This Review highlights the molecular mechanisms of stomach development and discusses recent findings regarding stomach stem cells and organoid cultures, and their roles in investigating disease mechanisms.
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Affiliation(s)
- Tae-Hee Kim
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Ramesh A Shivdasani
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
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49
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Hayakawa Y, Sethi N, Sepulveda AR, Bass AJ, Wang TC. Oesophageal adenocarcinoma and gastric cancer: should we mind the gap? Nat Rev Cancer 2016; 16:305-18. [PMID: 27112208 DOI: 10.1038/nrc.2016.24] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Over recent decades we have witnessed a shift in the anatomical distribution of gastric cancer (GC), which increasingly originates from the proximal stomach near the junction with the oesophagus. In parallel, there has been a dramatic rise in the incidence of oesophageal adenocarcinoma (OAC) in the lower oesophagus, which is associated with antecedent Barrett oesophagus (BO). In this context, there has been uncertainty regarding the characterization of adenocarcinomas spanning the area from the lower oesophagus to the distal stomach. Most relevant to this discussion is the distinction, if any, between OAC and intestinal-type GC of the proximal stomach. It is therefore timely to review our current understanding of OAC and intestinal-type GC, integrating advances from cell-of-origin studies and comprehensive genomic alteration analyses, ultimately enabling better insight into the relationship between these two cancers.
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Affiliation(s)
- Yoku Hayakawa
- Division of Digestive and Liver Diseases and Herbert Irving Cancer Research Center, Columbia University College of Physicians and Surgeons, 1130 St Nicholas Avenue, New York, New York 10032, USA
| | - Nilay Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Antonia R Sepulveda
- Division of Clinical Pathology and Cell Biology, Department of Pathology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Timothy C Wang
- Division of Digestive and Liver Diseases and Herbert Irving Cancer Research Center, Columbia University College of Physicians and Surgeons, 1130 St Nicholas Avenue, New York, New York 10032, USA
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50
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Soret C, Martin E, Duluc I, Dantzer F, Vanier M, Gross I, Freund JN, Domon-Dell C. Distinct mechanisms for opposite functions of homeoproteins Cdx2 and HoxB7 in double-strand break DNA repair in colon cancer cells. Cancer Lett 2016; 374:208-15. [PMID: 26902420 DOI: 10.1016/j.canlet.2016.02.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 01/08/2023]
Abstract
Homeobox genes, involved in embryonic development and tissues homeostasis in adults, are often deregulated in cancer, but their relevance in pathology is far from being fully elucidated. In colon cancers, we report that the homeoproteins HoxB7 and Cdx2 exhibit different heterogeneous patterns, Cdx2 being localized in moderately altered neoplasic glands in contrast to HoxB7 which predominates in poorly-differentiated areas; they are coexpressed in few cancer cells. In human colon cancer cells, both homeoproteins interact with the DNA repair factor KU70/80, but functional studies reveal opposite effects: HoxB7 stimulates DNA repair and cell survival upon etoposide treatment, whereas Cdx2 inhibits both processes. The stimulatory effect of HoxB7 on DNA repair requires the transactivation domain linked to the homeodomain involved in the interaction with KU70/80, whereas the transactivation domain of Cdx2 is dispensable for its inhibitory function, which instead needs the homeodomain to interact with KU70/80 and the C-terminal domain. Thus, HoxB7 and Cdx2 respectively use transcription-dependent and -independent mechanisms to stimulate and inhibit DNA repair. In addition, in cells co-expressing both homeoproteins, Cdx2 lessens DNA repair activity through a novel mechanism of inhibition of the transcriptional function of HoxB7, whereby Cdx2 forms a molecular complex with HoxB7 and prevents it to recognize its target in the chromatin. These results point out the complex interplay between the DSB DNA repair activity and the homeoproteins HoxB7 and Cdx2 in colon cancer cells, making the balance between these factors a determinant and a potential indicator of the efficacy of genotoxic drugs.
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Affiliation(s)
- Christine Soret
- INSERM UMR_S1113, 3 avenue Molière, 67200 Strasbourg, France; Université de Strasbourg, Faculté de Médecine, FMTS, 67081 Strasbourg, France
| | - Elisabeth Martin
- INSERM UMR_S1113, 3 avenue Molière, 67200 Strasbourg, France; Université de Strasbourg, Faculté de Médecine, FMTS, 67081 Strasbourg, France
| | - Isabelle Duluc
- INSERM UMR_S1113, 3 avenue Molière, 67200 Strasbourg, France; Université de Strasbourg, Faculté de Médecine, FMTS, 67081 Strasbourg, France
| | - Françoise Dantzer
- Université de Strasbourg, Faculté de Médecine, FMTS, 67081 Strasbourg, France; CNRS UMR7242, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, 67412 Illkirch, France
| | - Marie Vanier
- INSERM UMR_S1113, 3 avenue Molière, 67200 Strasbourg, France; Université de Strasbourg, Faculté de Médecine, FMTS, 67081 Strasbourg, France
| | - Isabelle Gross
- INSERM UMR_S1113, 3 avenue Molière, 67200 Strasbourg, France; Université de Strasbourg, Faculté de Médecine, FMTS, 67081 Strasbourg, France
| | - Jean-Noël Freund
- INSERM UMR_S1113, 3 avenue Molière, 67200 Strasbourg, France; Université de Strasbourg, Faculté de Médecine, FMTS, 67081 Strasbourg, France
| | - Claire Domon-Dell
- INSERM UMR_S1113, 3 avenue Molière, 67200 Strasbourg, France; Université de Strasbourg, Faculté de Médecine, FMTS, 67081 Strasbourg, France.
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