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Luo Y, Feng X, Lang W, Xu W, Wang W, Mei C, Ye L, Zhu S, Wang L, Zhou X, Zeng H, Ma L, Ren Y, Jin J, Xu R, Huang G, Tong H. Ectopic expression of the transcription factor ONECUT3 drives a complex karyotype in myelodysplastic syndromes. J Clin Invest 2024; 134:e172468. [PMID: 38386414 PMCID: PMC11014670 DOI: 10.1172/jci172468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 02/20/2024] [Indexed: 02/24/2024] Open
Abstract
Chromosomal instability is a prominent biological feature of myelodysplastic syndromes (MDS), with over 50% of patients with MDS harboring chromosomal abnormalities or a complex karyotype (CK). Despite this observation, the mechanisms underlying mitotic and chromosomal defects in MDS remain elusive. In this study, we identified ectopic expression of the transcription factor ONECUT3, which is associated with CKs and poorer survival outcomes in MDS. ONECUT3-overexpressing cell models exhibited enrichment of several notable pathways, including signatures of sister chromosome exchange separation and mitotic nuclear division with the upregulation of INCENP and CDCA8 genes. Notably, dysregulation of chromosome passenger complex (CPC) accumulation, besides the cell equator and midbody, during mitotic phases consequently caused cytokinesis failure and defective chromosome segregation. Mechanistically, the homeobox (HOX) domain of ONECUT3, serving as the DNA binding domain, occupied the unique genomic regions of INCENP and CDCA8 and transcriptionally activated these 2 genes. We identified a lead compound, C5484617, that functionally targeted the HOX domain of ONECUT3, inhibiting its transcriptional activity on downstream genes, and synergistically resensitized MDS cells to hypomethylating agents. This study revealed that ONECUT3 promoted chromosomal instability by transcriptional activation of INCENP and CDCA8, suggesting potential prognostic and therapeutic roles for targeting high-risk MDS patients with a CK.
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Affiliation(s)
- Yingwan Luo
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaomin Feng
- Department of Cell Systems and Anatomy, Department of Pathology and Laboratory Medicine, UT Health San Antonio, Joe R. and Teresa Lozano Long School of Medicine, Mays Cancer Center at UT Health San Antonio, San Antonio, Texas, USA
| | - Wei Lang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Weihong Xu
- Stanford Genome Technology Center, Palo Alto, California, USA
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Nansha District, Guangzhou, China
| | - Wei Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chen Mei
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Li Ye
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shuanghong Zhu
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lu Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xinping Zhou
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huimin Zeng
- Department of Cell Systems and Anatomy, Department of Pathology and Laboratory Medicine, UT Health San Antonio, Joe R. and Teresa Lozano Long School of Medicine, Mays Cancer Center at UT Health San Antonio, San Antonio, Texas, USA
- Department of Pediatrics, Peking University People’s Hospital, Beijing, China
| | - Liya Ma
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanling Ren
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Rongzhen Xu
- Department of Hematology, The Second Affiliated Hospital, School of Medicine
| | - Gang Huang
- Department of Cell Systems and Anatomy, Department of Pathology and Laboratory Medicine, UT Health San Antonio, Joe R. and Teresa Lozano Long School of Medicine, Mays Cancer Center at UT Health San Antonio, San Antonio, Texas, USA
| | - Hongyan Tong
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Center, and
- Zhejiang Provincial Key Lab of Hematopoietic Malignancy, Zhejiang University, Hangzhou, Zhejiang, China
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Ganjali F, Asri N, Rostami-Nejad M, Hashemi M, Ainy E, Masotti A, Asadzadeh Aghdaei H. Expression analysis of IL-2, TBX21 and SOCS1 in peripheral blood cells of celiac disease patients reveals the diagnostic potential of IL-2. Mol Biol Rep 2023; 50:4841-4849. [PMID: 37039998 DOI: 10.1007/s11033-023-08394-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/17/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND Celiac disease (CD) is a chronic immune-mediated enteropathy and a cytokine network is involved in its pathogenesis. Interleukin-2 (IL-2) has a key role in the adaptive immune pathogenesis of CD and has been reported to be one of the earliest cytokines to be elicited after gluten exposure by CD patients. This study aimed at investigating the expression level of IL-2 and functionally related genes SOCS1 and TBX21 in active and treated CD patients compared to controls. METHODS AND RESULTS Peripheral blood (PB) samples were collected from 40 active CD (ACD), 100 treated CD, and 100 healthy subjects. RNA was extracted, cDNA was synthesized and mRNA expression levels of the desired genes were investigated by Real-time PCR. The gene-gene interaction network was also constructed by GeneMANIA. Our results showed a higher PB mRNA expression of IL-2 in ACD patients compared to controls (p = 0.001) and treated CD patients (p˂0.0001). The mRNA expression level of TBX21 was also significantly up-regulated in ACD patients compared to controls (P = 0.03). SOCS1 mRNA level did not differ between active and treated CD patients and controls (p˃0.05) but showed a significant correlation with the patient's aphthous stomatitis symptom (r = 0.37, p = 0.01). ROC curve analysis suggested that the use of IL-2 levels can reach a high specificity and sensitivity in discriminating active CD patients. CONCLUSIONS The PB level of IL-2 has the potential to be introduced as a diagnostic biomarker for CD. Larger cohort studies, including pediatric patients, are needed to achieve more insights in this regard.
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Affiliation(s)
- Fatemeh Ganjali
- Department of Cellular and molecular biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Nastaran Asri
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami-Nejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Science Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Elaheh Ainy
- Department of Vice Chancellor Research Affairs, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Andrea Masotti
- Bambino Gesù Children's Hospital-IRCCS, Research Laboratories, V.le San Paolo 15, 00146, Rome, Italy
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Luna Velez M, Neikes HK, Snabel RR, Quint Y, Qian C, Martens A, Veenstra G, Freeman MR, van Heeringen S, Vermeulen M. ONECUT2 regulates RANKL-dependent enterocyte and microfold cell differentiation in the small intestine; a multi-omics study. Nucleic Acids Res 2023; 51:1277-1296. [PMID: 36625255 PMCID: PMC9943655 DOI: 10.1093/nar/gkac1236] [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] [Received: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023] Open
Abstract
Microfold (M) cells reside in the intestinal epithelium of Peyer's patches (PP). Their unique ability to take up and transport antigens from the intestinal lumen to the underlying lymphoid tissue is key in the regulation of the gut-associated immune response. Here, we applied a multi-omics approach to investigate the molecular mechanisms that drive M cell differentiation in mouse small intestinal organoids. We generated a comprehensive profile of chromatin accessibility changes and transcription factor dynamics during in vitro M cell differentiation, allowing us to uncover numerous cell type-specific regulatory elements and associated transcription factors. By using single-cell RNA sequencing, we identified an enterocyte and M cell precursor population. We used our newly developed computational tool SCEPIA to link precursor cell-specific gene expression to transcription factor motif activity in cis-regulatory elements, uncovering high expression of and motif activity for the transcription factor ONECUT2. Subsequent in vitro and in vivo perturbation experiments revealed that ONECUT2 acts downstream of the RANK/RANKL signalling axis to support enterocyte differentiation, thereby restricting M cell lineage specification. This study sheds new light on the mechanism regulating cell fate balance in the PP, and it provides a powerful blueprint for investigation of cell fate switches in the intestinal epithelium.
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Affiliation(s)
- Maria V Luna Velez
- Department of Molecular Biology, Radboud University Nijmegen, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Nijmegen 6525 AJ, The Netherlands
| | - Hannah K Neikes
- Department of Molecular Biology, Radboud University Nijmegen, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Nijmegen 6525 AJ, The Netherlands
| | - Rebecca R Snabel
- Department of Molecular Developmental Biology, Radboud University Nijmegen, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 AJ, The Netherlands
| | - Yarah Quint
- Department of Molecular Biology, Radboud University Nijmegen, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Nijmegen 6525 AJ, The Netherlands
| | - Chen Qian
- Department of Surgery, Division of Cancer Biology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Aniek Martens
- Department of Molecular Biology, Radboud University Nijmegen, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Nijmegen 6525 AJ, The Netherlands
| | - Gert Jan C Veenstra
- Department of Molecular Developmental Biology, Radboud University Nijmegen, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 AJ, The Netherlands
| | - Michael R Freeman
- Department of Surgery, Division of Cancer Biology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Simon J van Heeringen
- Department of Molecular Developmental Biology, Radboud University Nijmegen, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 AJ, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Radboud University Nijmegen, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Nijmegen 6525 AJ, The Netherlands
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Kadkhoda S, Ghafouri-Fard S, Noorbakhsh F, Ravaei S, Darbeheshti F, Amoli MM, Taslimi R, Shakoori A. The importance of regulatory pathway mediated by Circ0001955 in colorectal cancer. Exp Mol Pathol 2022; 128:104819. [PMID: 35914612 DOI: 10.1016/j.yexmp.2022.104819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 04/10/2022] [Accepted: 07/22/2022] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Colorectal cancer (CRC) has become one of the most common cancers in recent years. Given the importance that non-coding RNAs have recently acquired in various diseases including cancers, we decided to design this study to evaluate the expression levels of circ0001955/miR-145-5p/ONECUT2 axis in CRC. METHODS After bioinformatics analysis of GEO datasets related to CRC, a putative circ0001955/ miR-145-5p/ ONECUT2 pathway was assumed. Then, the expression levels of these genes were measured in 50 CRC samples and adjacent tissues by qRT- PCR. Also, correlation coefficients, receiver operating characteristic (ROC) curves, and correlation between circ0001955 levels with clinicopathological parameters of patients were analyzed. RESULTS Circ0001955 and ONECUT2 were considerably up-regulated, while the expression level of miR-145-5p was decreased in CRC samples compared with adjacent tissues (p < 0.05). Moreover, statistically significant correlations were observed between expression levels of circ0001955, miR-145-5p, and ONECUT2. We did not find any significant correlation between circ0001955 expression and clinicopathological parameters. CONCLUSION Our study showed that circ0001955 is dysregulated in CRC. This finding can open a new window for researchers for a better understanding of the potential pathways involved in CRC pathogenesis and, consequently, to find new treatment pathways.
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Affiliation(s)
- Sepideh Kadkhoda
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Sima Ravaei
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzaneh Darbeheshti
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Medical Genetics Network (MeGeNe), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mahsa M Amoli
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular -Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Taslimi
- Department of Gastroenterology, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - Abbas Shakoori
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Department of Medical Genetics, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran.
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5
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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: 54] [Impact Index Per Article: 18.0] [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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Fawkner-Corbett D, Antanaviciute A, Parikh K, Jagielowicz M, Gerós AS, Gupta T, Ashley N, Khamis D, Fowler D, Morrissey E, Cunningham C, Johnson PRV, Koohy H, Simmons A. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell 2021; 184:810-826.e23. [PMID: 33406409 PMCID: PMC7864098 DOI: 10.1016/j.cell.2020.12.016] [Citation(s) in RCA: 216] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/10/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022]
Abstract
Development of the human intestine is not well understood. Here, we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis, and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe diverse functions for these including as vascular niche cells. We pinpoint the origins of Peyer’s patches and gut-associated lymphoid tissue (GALT) and describe location-specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders. We compile a publicly available online resource, spatio-temporal analysis resource of fetal intestinal development (STAR-FINDer), to facilitate further work. Multimodal atlas of human intestinal development maps 101 cell types onto tissue Charts developmental origins of diverse cellular compartments and their progenitors Functional diversity of fibroblasts in stem cell, vasculature, and GALT formation Resource applied to interrogate pathology of in utero intestinal diseases
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Affiliation(s)
- David Fawkner-Corbett
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK; Academic Paediatric Surgery Unit (APSU), Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Agne Antanaviciute
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Kaushal Parikh
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Marta Jagielowicz
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ana Sousa Gerós
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Tarun Gupta
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Neil Ashley
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Doran Khamis
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Darren Fowler
- Paediatric Pathology, Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Edward Morrissey
- MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Chris Cunningham
- Colorectal Surgery Department, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Paul R V Johnson
- Academic Paediatric Surgery Unit (APSU), Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Hashem Koohy
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
| | - Alison Simmons
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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7
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Yu J, Li D, Jiang H. Emerging role of ONECUT2 in tumors. Oncol Lett 2020; 20:328. [PMID: 33101497 DOI: 10.3892/ol.2020.12192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 08/21/2020] [Indexed: 12/24/2022] Open
Abstract
One cut domain family member 2 (ONECUT2), also termed OC-2, is a newly discovered member of the ONECUT transcription factor family. As a transcription factor, ONECUT2 can widely regulate protein expression associated with cell proliferation, migration, adhesion, differentiation and cell material metabolism. Recent studies have revealed that ONECUT2 is associated with tumor cell proliferation, angiogenesis and metastasis; it is also associated with epithelial-mesenchymal transition in cancer cells. The present review examines the distribution and expression of ONECUT2 in a variety of tumors, its oncogenic role in tumor progression and the possible mechanisms of regulation. Given the emerging role of ONECUT2 in the development and progression of tumors, ONECUT2 might be a promising target for tumor therapy.
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Affiliation(s)
- Jia Yu
- Department of Geriatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Dongyang Li
- Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Hua Jiang
- Department of Geriatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, P.R. China
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8
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Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection. THE CEREBELLUM 2019; 17:308-325. [PMID: 29307116 DOI: 10.1007/s12311-017-0912-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Laser-capture microdissection was used to isolate external germinal layer tissue from three developmental periods of mouse cerebellar development: embryonic days 13, 15, and 18. The cerebellar granule cell-enriched mRNA library was generated with next-generation sequencing using the Helicos technology. Our objective was to discover transcriptional regulators that could be important for the development of cerebellar granule cells-the most numerous neuron in the central nervous system. Through differential expression analysis, we have identified 82 differentially expressed transcription factors (TFs) from a total of 1311 differentially expressed genes. In addition, with TF-binding sequence analysis, we have identified 46 TF candidates that could be key regulators responsible for the variation in the granule cell transcriptome between developmental stages. Altogether, we identified 125 potential TFs (82 from differential expression analysis, 46 from motif analysis with 3 overlaps in the two sets). From this gene set, 37 TFs are considered novel due to the lack of previous knowledge about their roles in cerebellar development. The results from transcriptome-wide analyses were validated with existing online databases, qRT-PCR, and in situ hybridization. This study provides an initial insight into the TFs of cerebellar granule cells that might be important for development and provide valuable information for further functional studies on these transcriptional regulators.
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9
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Janeckova L, Kostovcikova K, Svec J, Stastna M, Strnad H, Kolar M, Hudcovic T, Stancikova J, Tureckova J, Baloghova N, Sloncova E, Galuskova K, Tlaskalova-Hogenova H, Korinek V. Unique Gene Expression Signatures in the Intestinal Mucosa and Organoids Derived from Germ-Free and Monoassociated Mice. Int J Mol Sci 2019; 20:ijms20071581. [PMID: 30934845 PMCID: PMC6480644 DOI: 10.3390/ijms20071581] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/18/2019] [Accepted: 03/26/2019] [Indexed: 12/19/2022] Open
Abstract
Commensal microbiota contribute to gut homeostasis by inducing transcription of mucosal genes. Analysis of the impact of various microbiota on intestinal tissue provides an important insight into the function of this organ. We used cDNA microarrays to determine the gene expression signature of mucosa isolated from the small intestine and colon of germ-free (GF) mice and animals monoassociated with two E. coli strains. The results were compared to the expression data obtained in conventionally reared (CR) mice. In addition, we analyzed gene expression in colon organoids derived from CR, GF, and monoassociated animals. The analysis revealed that the complete absence of intestinal microbiota mainly affected the mucosal immune system, which was not restored upon monoassociation. The most important expression changes observed in the colon mucosa indicated alterations in adipose tissue and lipid metabolism. In the comparison of differentially expressed genes in the mucosa or organoids obtained from GF and CR mice, only six genes were common for both types of samples. The results show that the increased expression of the angiopoietin-like 4 (Angptl4) gene encoding a secreted regulator of lipid metabolism indicates the GF status.
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Affiliation(s)
- Lucie Janeckova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Klara Kostovcikova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Jiri Svec
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
- Department of Radiotherapy and Oncology, Third Faculty of Medicine, Charles University, Prague, Srobarova 50, 100 34 Prague 10, Czech Republic.
| | - Monika Stastna
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Hynek Strnad
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Michal Kolar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Tomas Hudcovic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Jitka Stancikova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Jolana Tureckova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Nikol Baloghova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Eva Sloncova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Katerina Galuskova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Helena Tlaskalova-Hogenova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Vladimir Korinek
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
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10
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Nigmatullina L, Norkin M, Dzama MM, Messner B, Sayols S, Soshnikova N. Id2 controls specification of Lgr5 + intestinal stem cell progenitors during gut development. EMBO J 2017; 36:869-885. [PMID: 28077488 DOI: 10.15252/embj.201694959] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 11/09/2022] Open
Abstract
The adult intestinal stem cells (ISCs), their hierarchies, mechanisms of maintenance and differentiation have been extensively studied. However, when and how ISCs are established during embryogenesis remains unknown. We show here that the transcription regulator Id2 controls the specification of embryonic Lgr5+ progenitors in the developing murine small intestine. Cell fate mapping analysis revealed that Lgr5+ progenitors emerge at E13.5 in wild-type embryos and differ from the rest on the intestinal epithelium by a characteristic ISC signature. In the absence of Id2, the intestinal epithelium differentiates into Lgr5+ cells already at E9.5. Furthermore, the size of the Lgr5+ cell pool is significantly increased. We show that Id2 restricts the activity of the Wnt signalling pathway at early stages and prevents precocious differentiation of the embryonic intestinal epithelium. Id2-deficient embryonic epithelial cells cultured ex vivo strongly activate Wnt target genes as well as markers of neoplastic transformation and form fast growing undifferentiated spheroids. Furthermore, adult ISCs from Id2-deficient mice display a distinct transcriptional signature, supporting an essential role for Id2 in the correct specification of ISCs.
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11
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Huang CZ, Yu T, Chen QK. DNA Methylation Dynamics During Differentiation, Proliferation, and Tumorigenesis in the Intestinal Tract. Stem Cells Dev 2015; 24:2733-9. [PMID: 26413818 DOI: 10.1089/scd.2015.0235] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA methylation, an epigenetic control mechanism in mammals, is widely present in the intestinal tract during the differentiation and proliferation of epithelial cells. Cells in stem cell pools or villi have different patterns of DNA methylation. The process of DNA methylation is dynamic and occurs at many relevant regulatory elements during the rapid transition of stem cells into fully mature, differentiated epithelial cells. Changes in DNA methylation patterns most often take place in enhancer and promoter regions and are associated with transcription factor binding. During differentiation, enhancer regions associated with genes important to enterocyte differentiation are demethylated, activating gene expression. Abnormal patterns of DNA methylation during differentiation and proliferation in the intestinal tract can lead to the formation of aberrant crypt foci and destroy the barrier and absorptive functions of the intestinal epithelium. Accumulation of these epigenetic changes may even result in tumorigenesis. In the current review, we discuss recent findings on the association between DNA methylation and cell differentiation and proliferation in the small intestine and highlight the possible links between dysregulation of this process and tumorigenesis.
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Affiliation(s)
- Can-Ze Huang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , Guangzhou, Guangdong, People's Republic of China
| | - Tao Yu
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , Guangzhou, Guangdong, People's Republic of China
| | - Qi-Kui Chen
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , Guangzhou, Guangdong, People's Republic of China
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12
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A Gene Regulatory Network Cooperatively Controlled by Pdx1 and Sox9 Governs Lineage Allocation of Foregut Progenitor Cells. Cell Rep 2015; 13:326-36. [PMID: 26440894 DOI: 10.1016/j.celrep.2015.08.082] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/10/2015] [Accepted: 08/29/2015] [Indexed: 01/05/2023] Open
Abstract
The generation of pancreas, liver, and intestine from a common pool of progenitors in the foregut endoderm requires the establishment of organ boundaries. How dorsal foregut progenitors activate pancreatic genes and evade the intestinal lineage choice remains unclear. Here, we identify Pdx1 and Sox9 as cooperative inducers of a gene regulatory network that distinguishes the pancreatic from the intestinal lineage. Genetic studies demonstrate dual and cooperative functions for Pdx1 and Sox9 in pancreatic lineage induction and repression of the intestinal lineage choice. Pdx1 and Sox9 bind to regulatory sequences near pancreatic and intestinal differentiation genes and jointly regulate their expression, revealing direct cooperative roles for Pdx1 and Sox9 in gene activation and repression. Our study identifies Pdx1 and Sox9 as important regulators of a transcription factor network that initiates pancreatic fate and sheds light on the gene regulatory circuitry that governs the development of distinct organs from multi-lineage-competent foregut progenitors.
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13
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Wang X, Yamamoto Y, Wilson LH, Zhang T, Howitt BE, Farrow MA, Kern F, Ning G, Hong Y, Khor CC, Chevalier B, Bertrand D, Wu L, Nagarajan N, Sylvester FA, Hyams JS, Devers T, Bronson R, Lacy DB, Ho KY, Crum CP, McKeon F, Xian W. Cloning and variation of ground state intestinal stem cells. Nature 2015; 522:173-8. [PMID: 26040716 PMCID: PMC4853906 DOI: 10.1038/nature14484] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 04/14/2015] [Indexed: 12/18/2022]
Abstract
Stem cells of the gastrointestinal tract, pancreas, liver, and other columnar epithelia collectively resist cloning in their elemental states. Here we demonstrate the cloning and propagation of highly clonogenic, “ground state” stem cells of the human intestine and colon. We show that derived stem cell pedigrees sustain limited copy number and sequence variation despite extensive serial passaging and display exquisitely precise, cell-autonomous commitment to epithelial differentiation consistent with their origins along the intestinal tract. This developmentally patterned and epigenetically maintained commitment of stem cells likely enforces the functional specificity of the adult intestinal tract. Using clonally-derived colonic epithelia, we show that toxins A or B of the enteric pathogen C. difficile recapitulate the salient features of pseudomembranous colitis. The stability of the epigenetic commitment programs of these stem cells, coupled with their unlimited replicative expansion and maintained clonogenicity, suggests certain advantages for their use in disease modeling and regenerative medicine.
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Affiliation(s)
- Xia Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Yusuke Yamamoto
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Lane H Wilson
- 1] The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA [2] Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut 06032, USA
| | - Ting Zhang
- Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore
| | - Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02118, USA
| | - Melissa A Farrow
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Florian Kern
- Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore
| | - Gang Ning
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Yue Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Chiea Chuen Khor
- 1] Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore [2] Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore
| | - Benoit Chevalier
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Denis Bertrand
- Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore
| | - Lingyan Wu
- Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore
| | - Francisco A Sylvester
- Department of Pediatrics, Division of Gastroenterology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, Connecticut 06106, USA
| | - Thomas Devers
- Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut 06032, USA
| | - Roderick Bronson
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - D Borden Lacy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Khek Yu Ho
- Department of Medicine, National University of Singapore, 119228 Singapore
| | - Christopher P Crum
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02118, USA
| | - Frank McKeon
- 1] The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA [2] Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore [3] Department of Medicine, National University of Singapore, 119228 Singapore [4] Multiclonal Therapeutics, Inc., Farmington, Connecticut 06032, USA
| | - Wa Xian
- 1] The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA [2] Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut 06032, USA [3] Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02118, USA [4] Department of Medicine, National University of Singapore, 119228 Singapore [5] Multiclonal Therapeutics, Inc., Farmington, Connecticut 06032, USA
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14
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Onecut1 and Onecut2 transcription factors operate downstream of Pax6 to regulate horizontal cell development. Dev Biol 2015; 402:48-60. [PMID: 25794677 DOI: 10.1016/j.ydbio.2015.02.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 02/18/2015] [Accepted: 02/22/2015] [Indexed: 11/22/2022]
Abstract
Genetic studies of the last decades strongly indicated that generation of particular retinal cell types is governed by gene regulatory networks of transcription factors and their target genes. The paired and homeodomain transcription factor Pax6 plays a pivotal role in retinal development as its inactivation in the retinal progenitor cell population leads to abolished differentiation of all retinal cell types. However, until now, only a few transcription factors operating downstream of Pax6 responsible for generation of individual retinal cell types have been identified. In this study, we identified two transcription factors of the Onecut family, Onecut1 and Onecut2, as Pax6 downstream-acting factors. Onecut1 and Onecut2 were previously shown to be expressed in developing horizontal cells, retinal ganglion cells and cone photoreceptors; however, their role in differentiation of these cell types is poorly understood. In this study, we show that the horizontal cell genesis is severely disturbed in Onecut-deficient retinae. In single Onecut1 and Onecut2 mutants, the number of horizontal cells is dramatically reduced while horizontal cells are completely missing in the Onecut1/Onecut2 compound mutant. Analysis of genes involved in the horizontal cell genesis such as Foxn4, Ptf1a, Prox1 and Lim1 showed that although horizontal cells are initially formed, they are not maintained in Onecut-deficient retinae. Taken together, this study suggests the model in which Pax6 regulates the maintenance of horizontal cells through the activation of Onecut1 and Onecut2 transcription factors.
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15
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Farr RJ, Joglekar MV, Hardikar AA. Circulating microRNAs in Diabetes Progression: Discovery, Validation, and Research Translation. EXPERIENTIA SUPPLEMENTUM (2012) 2015; 106:215-244. [PMID: 26608206 DOI: 10.1007/978-3-0348-0955-9_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Diabetes, in all of its forms, is a disease state that demonstrates wide ranging pathological effects throughout the body. Until now, the only method of diagnosing and monitoring the progression of diabetes was through the measurement of blood glucose. Unfortunately, beta cell dysfunction initiates well before the clinical onset of diabetes, and so the development of an effective biomarker signature is of paramount importance to predict and monitor the progression of this disease. MicroRNAs (miRNAs/miRs) are small (18-22 nucleotide) noncoding (nc)RNAs that post-transcriptionally regulate endogenous gene expression by targeted inhibition or degradation of messenger (m)RNA. Recently, miRNAs have shown great promise as biomarkers as some exhibit differential expression in multiple disease states, including type 1 and type 2 diabetes (T1D/T2D). Furthermore, miRNAs are quite stable in circulation, resistant to freeze-thaw and pH-mediated degradation, and are relatively easy to detect using quantitative (q)PCR. Here, we discuss microRNAs that may form a diabetes biomarker signature. To identify these transcripts we outline miRNAs that play a central role in pancreas development and diabetes, as well as previously identified miRNAs with differential expression in individuals with T1D and T2D. Validation and refinement of a miRNA biomarker signature for diabetes would allow identification and intervention of individuals at risk of this disease, as well as stratification and monitoring of patients with established diabetes.
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Affiliation(s)
- Ryan J Farr
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Sydney Medical School, The University of Sydney, Level 6, Medical Foundation Building, 92-94 Parramatta Road, Camperdown, NSW, 2050, Australia
| | - Mugdha V Joglekar
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Sydney Medical School, The University of Sydney, Level 6, Medical Foundation Building, 92-94 Parramatta Road, Camperdown, NSW, 2050, Australia
| | - Anandwardhan A Hardikar
- Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Sydney Medical School, The University of Sydney, Level 6, Medical Foundation Building, 92-94 Parramatta Road, Camperdown, NSW, 2050, Australia.
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16
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Sheaffer KL, Kim R, Aoki R, Elliott EN, Schug J, Burger L, Schübeler D, Kaestner KH. DNA methylation is required for the control of stem cell differentiation in the small intestine. Genes Dev 2014; 28:652-64. [PMID: 24637118 PMCID: PMC3967052 DOI: 10.1101/gad.230318.113] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
There is a tight correlation between the epigenetic status of genes and expression changes during differentiation. Sheaffer et al. used acute deletion of Dnmt1 to reduce DNA methylation maintenance in the intestinal epithelium. This caused crypt expansion and decreased differentiation. DNA methylation was dynamic at enhancers during the rapid transition from stem to differentiated epithelial cells. These findings reveal that the loss of DNA methylation at intestinal stem cell gene enhancers causes inappropriate gene expression and delayed differentiation. The mammalian intestinal epithelium has a unique organization in which crypts harboring stem cells produce progenitors and finally clonal populations of differentiated cells. Remarkably, the epithelium is replaced every 3–5 d throughout adult life. Disrupted maintenance of the intricate balance of proliferation and differentiation leads to loss of epithelial integrity or barrier function or to cancer. There is a tight correlation between the epigenetic status of genes and expression changes during differentiation; however, the mechanism of how changes in DNA methylation direct gene expression and the progression from stem cells to their differentiated descendants is unclear. Using conditional gene ablation of the maintenance methyltransferase Dnmt1, we demonstrate that reducing DNA methylation causes intestinal crypt expansion in vivo. Determination of the base-resolution DNA methylome in intestinal stem cells and their differentiated descendants shows that DNA methylation is dynamic at enhancers, which are often associated with genes important for both stem cell maintenance and differentiation. We establish that the loss of DNA methylation at intestinal stem cell gene enhancers causes inappropriate gene expression and delayed differentiation.
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Affiliation(s)
- Karyn L Sheaffer
- Department of Genetics, Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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17
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Gubelmann C, Waszak SM, Isakova A, Holcombe W, Hens K, Iagovitina A, Feuz JD, Raghav SK, Simicevic J, Deplancke B. A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks. Mol Syst Biol 2013; 9:682. [PMID: 23917988 PMCID: PMC3779800 DOI: 10.1038/msb.2013.38] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 06/28/2013] [Indexed: 02/06/2023] Open
Abstract
The comprehensive mapping of gene promoters and enhancers has significantly improved our understanding of how the mammalian regulatory genome is organized. An important challenge is to elucidate how these regulatory elements contribute to gene expression by identifying their trans-regulatory inputs. Here, we present the generation of a mouse-specific transcription factor (TF) open-reading frame clone library and its implementation in yeast one-hybrid assays to enable large-scale protein-DNA interaction detection with mouse regulatory elements. Once specific interactions are identified, we then use a microfluidics-based method to validate and precisely map them within the respective DNA sequences. Using well-described regulatory elements as well as orphan enhancers, we show that this cross-platform pipeline characterizes known and uncovers many novel TF-DNA interactions. In addition, we provide evidence that several of these novel interactions are relevant in vivo and aid in elucidating the regulatory architecture of enhancers.
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Affiliation(s)
- Carine Gubelmann
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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18
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A CpG mutational hotspot in a ONECUT binding site accounts for the prevalent variant of hemophilia B Leyden. Am J Hum Genet 2013; 92:460-7. [PMID: 23472758 DOI: 10.1016/j.ajhg.2013.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 01/30/2013] [Accepted: 02/07/2013] [Indexed: 11/23/2022] Open
Abstract
Hemophilia B, or the "royal disease," arises from mutations in coagulation factor IX (F9). Mutations within the F9 promoter are associated with a remarkable hemophilia B subtype, termed hemophilia B Leyden, in which symptoms ameliorate after puberty. Mutations at the -5/-6 site (nucleotides -5 and -6 relative to the transcription start site, designated +1) account for the majority of Leyden cases and have been postulated to disrupt the binding of a transcriptional activator, the identity of which has remained elusive for more than 20 years. Here, we show that ONECUT transcription factors (ONECUT1 and ONECUT2) bind to the -5/-6 site. The various hemophilia B Leyden mutations that have been reported in this site inhibit ONECUT binding to varying degrees, which correlate well with their associated clinical severities. In addition, expression of F9 is crucially dependent on ONECUT factors in vivo, and as such, mice deficient in ONECUT1, ONECUT2, or both exhibit depleted levels of F9. Taken together, our findings establish ONECUT transcription factors as the missing hemophilia B Leyden regulators that operate through the -5/-6 site.
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19
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Wu F, Sapkota D, Li R, Mu X. Onecut 1 and Onecut 2 are potential regulators of mouse retinal development. J Comp Neurol 2012; 520:952-69. [PMID: 21830221 PMCID: PMC3898336 DOI: 10.1002/cne.22741] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Our current study focuses on the expression of two members of the onecut transcription factor family, Onecut1 (Oc1) and Onecut2 (Oc2), in the developing mouse retina. By immunofluorescence staining, we found that Oc1 and Oc2 had very similar expression patterns throughout retinal development. Both factors started to be expressed in the retina at around embryonic day (E) 11.5. At early stages (E11.5 and E12.5), they were expressed in both the neuroblast layer (NBL) and ganglion cell layer (GCL). As development progressed (from E14.5 to postnatal day [P] 0), expression diminished in the retinal progenitor cells and became more restricted to the GCL. By P5, Oc1 and Oc2 were expressed at very low levels in the GCL. By co-labeling with transcription factors known to be involved in retinal ganglion cell (RGC) development, we found that Oc1 and Oc2 had extensive overlap with Math5 in the NBL, and that they completely overlapped with Pou4f2 and Isl1 in the GCL, but only partially in the NBL. Co-labeling of Oc1 with cell cycle markers confirmed that Oc1 was expressed in both proliferating retinal progenitors and postmitotic retinal cells. In addition, we demonstrated that expression of Oc1 and Oc2 did not require Math5, Isl1, or Pou4f2. Thus, Oc1 and Oc2 may regulate the formation of RGCs in a pathway independent of Math5, Pou4f2, and Isl1. Furthermore, we showed that Oc1 and Oc2 were expressed in both developing and mature horizontal cells (HCs). Therefore the two factors may also function in the genesis and maintenance of HCs.
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Affiliation(s)
- Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, Developmental Genomics Group, University at Buffalo, Buffalo, New York 14203
| | - Darshan Sapkota
- Department of Ophthalmology/Ross Eye Institute, Developmental Genomics Group, University at Buffalo, Buffalo, New York 14203
- Department of Biochemistry, Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York 14203
| | - Renzhong Li
- Department of Ophthalmology/Ross Eye Institute, Developmental Genomics Group, University at Buffalo, Buffalo, New York 14203
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, Developmental Genomics Group, University at Buffalo, Buffalo, New York 14203
- Department of Biochemistry, Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York 14203
- State University of New York (SUNY) Eye Institute, University at Buffalo, Buffalo, New York 14203
- Cancer Center Support Grant (CCSG) Molecular Epidemiology and Functional Genomics (MEFG) Program, Roswell Park Cancer Institute, Buffalo, New York 14263
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