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Li X, Zhu G, Zhao B. Chromatin remodeling in tissue stem cell fate determination. CELL REGENERATION (LONDON, ENGLAND) 2024; 13:18. [PMID: 39348027 PMCID: PMC11442411 DOI: 10.1186/s13619-024-00203-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 09/22/2024] [Indexed: 10/01/2024]
Abstract
Tissue stem cells (TSCs), which reside in specialized tissues, constitute the major cell sources for tissue homeostasis and regeneration, and the contribution of transcriptional or epigenetic regulation of distinct biological processes in TSCs has been discussed in the past few decades. Meanwhile, ATP-dependent chromatin remodelers use the energy from ATP hydrolysis to remodel nucleosomes, thereby affecting chromatin dynamics and the regulation of gene expression programs in each cell type. However, the role of chromatin remodelers in tissue stem cell fate determination is less well understood. In this review, we systematically discuss recent advances in epigenetic control by chromatin remodelers of hematopoietic stem cells, intestinal epithelial stem cells, neural stem cells, and skin stem cells in their fate determination and highlight the importance of their essential role in tissue homeostasis, development, and regeneration. Moreover, the exploration of the molecular and cellular mechanisms of TSCs is crucial for advancing our understanding of tissue maintenance and for the discovery of novel therapeutic targets.
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Affiliation(s)
- Xinyang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Z Lab, bioGenous BIOTECH, Shanghai, 200438, China
| | - Gaoxiang Zhu
- School of Basic Medical Sciences, Jiangxi Medical College, The First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330031, China
| | - Bing Zhao
- School of Basic Medical Sciences, Jiangxi Medical College, The First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330031, China.
- Z Lab, bioGenous BIOTECH, Shanghai, 200438, China.
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2
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Dennison TW, Edgar RD, Payne F, Nayak KM, Ross ADB, Cenier A, Glemas C, Giachero F, Foster AR, Harris R, Kraiczy J, Salvestrini C, Stavrou G, Torrente F, Brook K, Trayers C, Elmentaite R, Youssef G, Tél B, Winton DJ, Skoufou-Papoutsaki N, Adler S, Bufler P, Azabdaftari A, Jenke A, G N, Thomas N, Miele E, Al-Mohammad A, Guarda G, Kugathasan S, Venkateswaran S, Clatworthy MR, Castro-Dopico T, Suchanek O, Strisciuglio C, Gasparetto M, Lee S, Xu X, Bello E, Han N, Zerbino DR, Teichmann SA, Nys J, Heuschkel R, Perrone F, Zilbauer M. Patient-derived organoid biobank identifies epigenetic dysregulation of intestinal epithelial MHC-I as a novel mechanism in severe Crohn's Disease. Gut 2024; 73:1464-1477. [PMID: 38857990 PMCID: PMC11347221 DOI: 10.1136/gutjnl-2024-332043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024]
Abstract
OBJECTIVE Epigenetic mechanisms, including DNA methylation (DNAm), have been proposed to play a key role in Crohn's disease (CD) pathogenesis. However, the specific cell types and pathways affected as well as their potential impact on disease phenotype and outcome remain unknown. We set out to investigate the role of intestinal epithelial DNAm in CD pathogenesis. DESIGN We generated 312 intestinal epithelial organoids (IEOs) from mucosal biopsies of 168 patients with CD (n=72), UC (n=23) and healthy controls (n=73). We performed genome-wide molecular profiling including DNAm, bulk as well as single-cell RNA sequencing. Organoids were subjected to gene editing and the functional consequences of DNAm changes evaluated using an organoid-lymphocyte coculture and a nucleotide-binding oligomerisation domain, leucine-rich repeat and CARD domain containing 5 (NLRC5) dextran sulphate sodium (DSS) colitis knock-out mouse model. RESULTS We identified highly stable, CD-associated loss of DNAm at major histocompatibility complex (MHC) class 1 loci including NLRC5 and cognate gene upregulation. Single-cell RNA sequencing of primary mucosal tissue and IEOs confirmed the role of NLRC5 as transcriptional transactivator in the intestinal epithelium. Increased mucosal MHC-I and NLRC5 expression in adult and paediatric patients with CD was validated in additional cohorts and the functional role of MHC-I highlighted by demonstrating a relative protection from DSS-mediated mucosal inflammation in NLRC5-deficient mice. MHC-I DNAm in IEOs showed a significant correlation with CD disease phenotype and outcomes. Application of machine learning approaches enabled the development of a disease prognostic epigenetic molecular signature. CONCLUSIONS Our study has identified epigenetically regulated intestinal epithelial MHC-I as a novel mechanism in CD pathogenesis.
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Affiliation(s)
- Thomas W Dennison
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Rachel D Edgar
- European Bioinformatics Institute, Cambridge, Cambridgeshire, UK
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Felicity Payne
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Komal M Nayak
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Alexander D B Ross
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- University Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Aurelie Cenier
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Technische Universität München, ZIEL - Institute for Food & Health, Freising, Germany
| | - Claire Glemas
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Federica Giachero
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - April R Foster
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Rebecca Harris
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Camilla Salvestrini
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Georgia Stavrou
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Franco Torrente
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Kimberley Brook
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Claire Trayers
- Department of Paediatric and Perinatal Pathology, Cambridge University Hospitals (CUH), Addenbrooke's Hospital, Cambridge, UK
| | | | - Gehad Youssef
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Bálint Tél
- Pediatric Center, MTA Center of Excellence, Semmelweis University, Budapest, Hungary
| | - Douglas James Winton
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Nefeli Skoufou-Papoutsaki
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Sam Adler
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Philip Bufler
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Aline Azabdaftari
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Jenke
- Department of Neonatology and General Pediatrics, Children's Hospital Kassel, Kassel, Germany
- Clinical Molecular Genetics and Epigenetics, Centre for Biomedical Education and Research (ZBAF), HELIOS University Hospital Wuppertal, Witten/Herdecke University, Wuppertal, Germany
| | - Natasha G
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Natasha Thomas
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Erasmo Miele
- Department of Translational Medical Science, Section of Pediatrics, University of Naples "Federico II", Naples, Italy
| | | | - Greta Guarda
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine (IRB), Università della Svizzera italiana, Bellinzona, Switzerland
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, GA, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Tomas Castro-Dopico
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ondrej Suchanek
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Caterina Strisciuglio
- Department of Woman, Child ad General and Specialistic Surgery, University of Campania " Vanvitelli", Naples, Italy
| | - Marco Gasparetto
- Norfolk and Norwich University Hospital, Jenny Lind Children's Hospital, Norwich, UK
| | - Seokjun Lee
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Xingze Xu
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Erica Bello
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Daniel R Zerbino
- European Bioinformatics Institute, Cambridge, Cambridgeshire, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
- Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
- Dept Physics/Cavendish Laboratory, Theory of Condensed Matter, JJ Thomson Ave, Cambridge, UK
| | - Josquin Nys
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Francesca Perrone
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Matthias Zilbauer
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
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3
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Vemuri K, Kumar S, Chen L, Verzi MP. Dynamic RNA polymerase II occupancy drives differentiation of the intestine under the direction of HNF4. Cell Rep 2024; 43:114242. [PMID: 38768033 PMCID: PMC11264335 DOI: 10.1016/j.celrep.2024.114242] [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: 11/08/2023] [Revised: 04/03/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024] Open
Abstract
Terminal differentiation requires massive restructuring of the transcriptome. During intestinal differentiation, the expression patterns of nearly 4,000 genes are altered as cells transition from progenitor cells in crypts to differentiated cells in villi. We identify dynamic occupancy of RNA polymerase II (Pol II) to gene promoters as the primary driver of transcriptomic shifts during intestinal differentiation in vivo. Changes in enhancer-promoter looping interactions accompany dynamic Pol II occupancy and are dependent upon HNF4, a pro-differentiation transcription factor. Using genetic loss-of-function, chromatin immunoprecipitation sequencing (ChIP-seq), and immunoprecipitation (IP) mass spectrometry, we demonstrate that HNF4 collaborates with chromatin remodelers and loop-stabilizing proteins and facilitates Pol II occupancy at hundreds of genes pivotal to differentiation. We also explore alternate mechanisms that drive differentiation gene expression and find that pause-release of Pol II and post-transcriptional mRNA stability regulate smaller subsets of differentially expressed genes. These studies provide insights into the mechanisms of differentiation in renewing adult tissue.
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Affiliation(s)
- Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Sneha Kumar
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ 08901, USA; NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI, Piscataway, NJ 08854, USA.
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4
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Larue AEM, Atlasi Y. The epigenetic landscape in intestinal stem cells and its deregulation in colorectal cancer. Stem Cells 2024; 42:509-525. [PMID: 38597726 PMCID: PMC11177158 DOI: 10.1093/stmcls/sxae027] [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: 10/08/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Epigenetic mechanisms play a pivotal role in controlling gene expression and cellular plasticity in both normal physiology and pathophysiological conditions. These mechanisms are particularly important in the regulation of stem cell self-renewal and differentiation, both in embryonic development and within adult tissues. A prime example of this finely tuned epigenetic control is observed in the gastrointestinal lining, where the small intestine undergoes renewal approximately every 3-5 days. How various epigenetic mechanisms modulate chromatin functions in intestinal stem cells (ISCs) is currently an active area of research. In this review, we discuss the main epigenetic mechanisms that control ISC differentiation under normal homeostasis. Furthermore, we explore the dysregulation of these mechanisms in the context of colorectal cancer (CRC) development. By outlining the main epigenetic mechanisms contributing to CRC, we highlight the recent therapeutics development and future directions for colorectal cancer research.
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Affiliation(s)
- Axelle E M Larue
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, United Kingdom
| | - Yaser Atlasi
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, United Kingdom
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5
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Devailly G, Fève K, Saci S, Sarry J, Valière S, Lluch J, Bouchez O, Ravon L, Billon Y, Gilbert H, Riquet J, Beaumont M, Demars J. Divergent selection for feed efficiency in pigs altered the duodenum transcriptomic response to feed intake and its DNA methylation profiles. Physiol Genomics 2024; 56:397-408. [PMID: 38497119 DOI: 10.1152/physiolgenomics.00123.2023] [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: 10/20/2023] [Revised: 03/01/2024] [Accepted: 03/10/2024] [Indexed: 03/19/2024] Open
Abstract
Feed efficiency is a trait of interest in pigs as it contributes to lowering the ecological and economical costs of pig production. A divergent genetic selection experiment from a Large White pig population was performed for 10 generations, leading to pig lines with relatively low- (LRFI) and high- (HRFI) residual feed intake (RFI). Feeding behavior and metabolic differences have been previously reported between the two lines. We hypothesized that part of these differences could be related to differential sensing and absorption of nutrients in the proximal intestine. We investigated the duodenum transcriptome and DNA methylation profiles comparing overnight fasting with ad libitum feeding in LRFI and HRFI pigs (n = 24). We identified 1,106 differentially expressed genes between the two lines, notably affecting pathways of the transmembrane transport activity and related to mitosis or chromosome separation. The LRFI line showed a greater transcriptomic response to feed intake than the HRFI line. Feed intake affected genes from both anabolic and catabolic pathways in the pig duodenum, such as rRNA production and autophagy. Several nutrient transporter and tight junction genes were differentially expressed between lines and/or by short-term feed intake. We also identified 409 differentially methylated regions in the duodenum mucosa between the two lines, while this epigenetic mark was less affected by feeding. Our findings highlighted that the genetic selection for feed efficiency in pigs changed the transcriptome profiles of the duodenum, and notably its response to feed intake, suggesting key roles for this proximal gut segment in mechanisms underlying feed efficiency.NEW & NOTEWORTHY The duodenum is a key organ for the hunger/satiety loop and nutrient sensing. We investigated how the duodenum transcriptome and DNA methylation profiles are affected by feed intakes in pigs. We observed thousands of changes in gene expression levels between overnight-fasted and fed pigs in high-feed efficiency pig lines, but almost none in the related low-feed efficiency pig line.
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Affiliation(s)
| | - Katia Fève
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Safia Saci
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Julien Sarry
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Sophie Valière
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Jérôme Lluch
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Laure Ravon
- Pig Phenotyping and Innovative Breeding Facility, GenESI, UE1372, INRAE, Surgères, France
| | - Yvon Billon
- Pig Phenotyping and Innovative Breeding Facility, GenESI, UE1372, INRAE, Surgères, France
| | - Hélène Gilbert
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Juliette Riquet
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Martin Beaumont
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
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6
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Krumpolec P, Kodada D, Hadžega D, Petrovič O, Babišová K, Dosedla E, Turcsányiová Z, Minárik G. Changes in DNA methylation associated with a specific mode of delivery: a pilot study. Front Med (Lausanne) 2024; 11:1291429. [PMID: 38314203 PMCID: PMC10835804 DOI: 10.3389/fmed.2024.1291429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024] Open
Abstract
Background The mode of delivery represents an epigenetic factor with potential to affect further development of the individual by multiple mechanisms. DNA methylation may be one of them, representing a major epigenetic mechanism involving direct chemical modification of the individual's DNA. This pilot study aims to examine whether a specific mode of delivery induces changes of DNA methylation by comparing the umbilical cord blood and peripheral blood of the newborns. Methods Blood samples from infants born by vaginal delivery and caesarean section were analysed to prepare the Methylseq library according to NEBNext enzymatic Methyl-seq Methylation Library Preparation Kit with further generation of target-enriched DNA libraries using the Twist Human Methylome Panel. DNA methylation status was determined using Illumina next-generation sequencing (NGS). Results We identified 168 differentially methylated regions in umbilical cord blood samples and 157 regions in peripheral blood samples. These were associated with 59 common biological, metabolic and signalling pathways for umbilical cord and peripheral blood samples. Conclusion Caesarean section is likely to represent an important epigenetic factor with the potential to induce changes in the genome that could play an important role in development of a broad spectrum of disorders. Our results could contribute to the elucidation of how epigenetic factors, such as a specific mode of delivery, could have adverse impact on health of an individual later in their life.
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Affiliation(s)
| | - Dominik Kodada
- Medirex Group Academy n.o., Nitra, Slovakia
- Department of Clinical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | | | | | | | - Erik Dosedla
- Department of Gynaecology and Obstetrics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Zuzana Turcsányiová
- Department of Gynaecology and Obstetrics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
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7
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Zhou Y, Zhang Y, Peng M, Zhang Y, Li C, Shu L, Hu Y, Su J, Xu J. scDMV: a zero-one inflated beta mixture model for DNA methylation variability with scBS-seq data. Bioinformatics 2024; 40:btad772. [PMID: 38141207 PMCID: PMC10786675 DOI: 10.1093/bioinformatics/btad772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/11/2023] [Accepted: 12/22/2023] [Indexed: 12/25/2023] Open
Abstract
MOTIVATION The utilization of single-cell bisulfite sequencing (scBS-seq) methods allows for precise analysis of DNA methylation patterns at the individual cell level, enabling the identification of rare populations, revealing cell-specific epigenetic changes, and improving differential methylation analysis. Nonetheless, the presence of sparse data and an overabundance of zeros and ones, attributed to limited sequencing depth and coverage, frequently results in reduced precision accuracy during the process of differential methylation detection using scBS-seq. Consequently, there is a pressing demand for an innovative differential methylation analysis approach that effectively tackles these data characteristics and enhances recognition accuracy. RESULTS We propose a novel beta mixture approach called scDMV for analyzing methylation differences in single-cell bisulfite sequencing data, which effectively handles excess zeros and ones and accommodates low-input sequencing. Our extensive simulation studies demonstrate that the scDMV approach outperforms several alternative methods in terms of sensitivity, precision, and controlling the false positive rate. Moreover, in real data applications, we observe that scDMV exhibits higher precision and sensitivity in identifying differentially methylated regions, even with low-input samples. In addition, scDMV reveals important information for GO enrichment analysis with single-cell whole-genome sequencing data that are often overlooked by other methods. AVAILABILITY AND IMPLEMENTATION The scDMV method, along with a comprehensive tutorial, can be accessed as an R package on the following GitHub repository: https://github.com/PLX-m/scDMV.
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Affiliation(s)
- Yan Zhou
- School of Mathematical Sciences, Institute of Statistical Sciences, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Shenzhen University, Shenzhen, China
| | - Ying Zhang
- School of Mathematical Sciences, Institute of Statistical Sciences, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Shenzhen University, Shenzhen, China
| | - Minjiao Peng
- School of Mathematics and Statistics and KLAS, Northeast Normal University, Changchun, China
| | - Yaru Zhang
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Chenghao Li
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Lianjie Shu
- Faculty of Business Administration, University of Macau, Macau, China
| | - Yaohua Hu
- School of Mathematical Sciences, Institute of Statistical Sciences, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Shenzhen University, Shenzhen, China
| | - Jianzhong Su
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jinfeng Xu
- Department of Biostatistics, City University of Hong Kong, Tat Chee Avenue, Hong Kong, China
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8
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Vemuri K, Kumar S, Chen L, Verzi MP. Dynamic RNA Polymerase II Recruitment Drives Differentiation of the Intestine under the direction of HNF4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566322. [PMID: 37986803 PMCID: PMC10659318 DOI: 10.1101/2023.11.08.566322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Terminal differentiation requires a massive restructuring of the transcriptome. During intestinal differentiation, the expression patterns of nearly 4000 genes are altered as cells transition from progenitor cells in crypts to differentiated cells in villi. We identified dynamic recruitment of RNA Polymerase II (Pol II) to gene promoters as the primary driver of transcriptomic shifts during intestinal differentiation in vivo. Changes in enhancer-promoter looping interactions accompany dynamic Pol II recruitment and are dependent upon HNF4, a pro-differentiation transcription factor. Using genetic loss-of- function, ChIP-seq and IP mass spectrometry, we demonstrate that HNF4 collaborates with chromatin remodelers and loop-stabilizing proteins and facilitates Pol II recruitment at hundreds of genes pivotal to differentiation. We also explore alternate mechanisms which drive differentiation gene expression and find pause-release of Pol II and post- transcriptional mRNA stability regulate smaller subsets of differentially expressed genes. These studies provide insights into the mechanisms of differentiation in a renewing adult tissue.
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Affiliation(s)
- Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Sneha Kumar
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ 08901, USA
- NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI Piscataway, NJ 08854, USA
- Lead Contact
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9
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Sun M, Tan Z, Lin K, Li X, Zhu J, Zhan L, Zheng H. Advanced Progression for the Heterogeneity and Homeostasis of Intestinal Stem Cells. Stem Cell Rev Rep 2023; 19:2109-2119. [PMID: 37351833 DOI: 10.1007/s12015-023-10578-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2023] [Indexed: 06/24/2023]
Abstract
Current understanding of the leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5) in intestinal stem cells (ISCs) is well established, however, the implications of ISC heterogeneity and homeostasis are poorly understood. Prior studies have provided important evidence for the association between heterogeneity of ISC pools with pathogenesis and therapeutic response of malignant disease. Leveraging the advantages of organoids and single cell RNA sequencing (scRNA-seq), glandular development has been simulated and cell heterogeneity has been clarified. Based on this research, several potential ISCs were identified, such as LGR5 + p27 + quiescent ISCs, LGR5 + Mex3a + slowly proliferating stem cells, and CLU + reverse stem cells. We also illustrated major factors responsible for ISC homeostasis including metabolism-related (LKB1, TGR5, HMGCS2), inflammation-related (IFB-b, IFN2, TNF), and Wnt signaling-related (CREPT, Mex3a, MTG16) factors. ISCs play complex roles in intestinal tumorigenesis, chemoresistance and occasional relapse of colon cancer, which bear discussion. In this review, we focus on novel technical challenges in ISCs fate drawing upon recent research with the goals of clarifying our understanding of complex ISCs, elucidating the integrated intestinal crypt niche, and creating new opportunities for therapeutic development.
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Affiliation(s)
- Minqiong Sun
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui, China
| | - Zhenya Tan
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui, China
| | - Keqiong Lin
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui, China
| | - Xiaofei Li
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui, China
| | - Jicheng Zhu
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui, China
| | - Li Zhan
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui, China
| | - Hong Zheng
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui, China.
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10
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Nguyen JD, Llamas J, Shi T, Crump JG, Groves AK, Segil N. DNA methylation in the mouse cochlea promotes maturation of supporting cells and contributes to the failure of hair cell regeneration. Proc Natl Acad Sci U S A 2023; 120:e2300839120. [PMID: 37549271 PMCID: PMC10438394 DOI: 10.1073/pnas.2300839120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/11/2023] [Indexed: 08/09/2023] Open
Abstract
Mammalian hair cells do not functionally regenerate in adulthood but can regenerate at embryonic and neonatal stages in mice by direct transdifferentiation of neighboring supporting cells into new hair cells. Previous work showed loss of transdifferentiation potential of supporting cells is in part due to H3K4me1 enhancer decommissioning of the hair cell gene regulatory network during the first postnatal week. However, inhibiting this decommissioning only partially preserves transdifferentiation potential. Therefore, we explored other repressive epigenetic modifications that may be responsible for this loss of plasticity. We find supporting cells progressively accumulate DNA methylation at promoters of developmentally regulated hair cell genes. Specifically, DNA methylation overlaps with binding sites of Atoh1, a key transcription factor for hair cell fate. We further show that DNA hypermethylation replaces H3K27me3-mediated repression of hair cell genes in mature supporting cells, and is accompanied by progressive loss of chromatin accessibility, suggestive of facultative heterochromatin formation. Another subset of hair cell loci is hypermethylated in supporting cells, but not in hair cells. Ten-eleven translocation (TET) enzyme-mediated demethylation of these hypermethylated sites is necessary for neonatal supporting cells to transdifferentiate into hair cells. We also observe changes in chromatin accessibility of supporting cell subtypes at the single-cell level with increasing age: Gene programs promoting sensory epithelium development loses chromatin accessibility, in favor of gene programs that promote physiological maturation and function of the cochlea. We also find chromatin accessibility is partially recovered in a chronically deafened mouse model, which holds promise for future translational efforts in hearing restoration.
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Affiliation(s)
- John D. Nguyen
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at the University of Southern California, Los Angeles, CA90033
| | - Juan Llamas
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at the University of Southern California, Los Angeles, CA90033
- Caruso Department of Otolaryngology-Head and Neck Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, CA90033
| | - Tuo Shi
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at the University of Southern California, Los Angeles, CA90033
- Caruso Department of Otolaryngology-Head and Neck Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, CA90033
| | - J. Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at the University of Southern California, Los Angeles, CA90033
| | - Andrew K. Groves
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
- Department of Neuroscience, Baylor College of Medicine, Houston, TX77030
| | - Neil Segil
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology at the University of Southern California, Los Angeles, CA90033
- Caruso Department of Otolaryngology-Head and Neck Surgery, Keck School of Medicine of the University of Southern California, Los Angeles, CA90033
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11
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Ansari I, Solé-Boldo L, Ridnik M, Gutekunst J, Gilliam O, Korshko M, Liwinski T, Jickeli B, Weinberg-Corem N, Shoshkes-Carmel M, Pikarsky E, Elinav E, Lyko F, Bergman Y. TET2 and TET3 loss disrupts small intestine differentiation and homeostasis. Nat Commun 2023; 14:4005. [PMID: 37414790 PMCID: PMC10326054 DOI: 10.1038/s41467-023-39512-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
TET2/3 play a well-known role in epigenetic regulation and mouse development. However, their function in cellular differentiation and tissue homeostasis remains poorly understood. Here we show that ablation of TET2/3 in intestinal epithelial cells results in a murine phenotype characterized by a severe homeostasis imbalance in the small intestine. Tet2/3-deleted mice show a pronounced loss of mature Paneth cells as well as fewer Tuft and more Enteroendocrine cells. Further results show major changes in DNA methylation at putative enhancers, which are associated with cell fate-determining transcription factors and functional effector genes. Notably, pharmacological inhibition of DNA methylation partially rescues the methylation and cellular defects. TET2/3 loss also alters the microbiome, predisposing the intestine to inflammation under homeostatic conditions and acute inflammation-induced death. Together, our results uncover previously unrecognized critical roles for DNA demethylation, possibly occurring subsequently to chromatin opening during intestinal development, culminating in the establishment of normal intestinal crypts.
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Affiliation(s)
- Ihab Ansari
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Llorenç Solé-Boldo
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Meshi Ridnik
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Oliver Gilliam
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Maria Korshko
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Timur Liwinski
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- University Psychiatric Clinics Basel, Clinic for Adults, University of Basel, Basel, Switzerland
| | - Birgit Jickeli
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Noa Weinberg-Corem
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Michal Shoshkes-Carmel
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eli Pikarsky
- The Lautenberg Center for Immunology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eran Elinav
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
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12
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Ghorbaninejad M, Asadzadeh-Aghdaei H, Baharvand H, Meyfour A. Intestinal organoids: A versatile platform for modeling gastrointestinal diseases and monitoring epigenetic alterations. Life Sci 2023; 319:121506. [PMID: 36858311 DOI: 10.1016/j.lfs.2023.121506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 03/03/2023]
Abstract
Considering the significant limitations of conventional 2D cell cultures and tissue in vitro models, creating intestinal organoids has burgeoned as an ideal option to recapitulate the heterogeneity of the native intestinal epithelium. Intestinal organoids can be developed from either tissue-resident adult stem cells (ADSs) or pluripotent stem cells (PSCs) in both forms induced PSCs and embryonic stem cells. Here, we review current advances in the development of intestinal organoids that have led to a better recapitulation of the complexity, physiology, morphology, function, and microenvironment of the intestine. We discuss current applications of intestinal organoids with an emphasis on disease modeling. In particular, we point out recent studies on SARS-CoV-2 infection in human intestinal organoids. We also discuss the less explored application of intestinal organoids in epigenetics by highlighting the role of epigenetic modifications in intestinal development, homeostasis, and diseases, and subsequently the power of organoids in mirroring the regulatory role of epigenetic mechanisms in these conditions and introducing novel predictive/diagnostic biomarkers. Finally, we propose 3D organoid models to evaluate the effects of novel epigenetic drugs (epi-drugs) on the treatment of GI diseases where epigenetic mechanisms play a key role in disease development and progression, particularly in colorectal cancer treatment and epigenetically acquired drug resistance.
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Affiliation(s)
- Mahsa Ghorbaninejad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - 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
| | - Hossein Baharvand
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran; Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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13
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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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14
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Liu Y, Sun X, Zhong W, Li B. B-scaling: A novel nonparametric data fusion method. Ann Appl Stat 2022. [DOI: 10.1214/21-aoas1537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Yiwen Liu
- Department of Epidemiology and Biostatistics, University of Arizona
| | - Xiaoxiao Sun
- Department of Epidemiology and Biostatistics, University of Arizona
| | | | - Bing Li
- Department of Statistics, Pennsylvania State University
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15
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Tao C, Liu J, Li Z, Lai P, Zhang S, Qu J, Tang Y, Liu A, Zou Z, Bai X, Li J. DNMT1 is a negative regulator of osteogenesis. Biol Open 2022; 11:274589. [PMID: 35238333 PMCID: PMC8905718 DOI: 10.1242/bio.058534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 12/10/2021] [Indexed: 11/21/2022] Open
Abstract
The role and underlying mechanisms of DNA methylation in osteogenesis/chondrogenesis remain poorly understood. We here reveal DNA methyltransferase 1 (DNMT1), which is responsible for copying DNA methylation onto the newly synthesized DNA strand after DNA replication, is overexpressed in sponge bone of people and mice with senile osteoporosis and required for suppression of osteoblast (OB) differentiation of mesenchymal stem cells (MSCs) and osteoprogenitors. Depletion of DNMT1 results in demethylation at the promoters of key osteogenic genes such as RORA and Fgfr2, and consequent upregulation of their transcription in vitro. Mechanistically, DNMT1 binds exactly to the promoters of these genes and are responsible for their 5-mc methylation. Conversely, simultaneous depletion of RORA or Fgfr2 blunts the effects of DNMT1 silencing on OB differentiation, suggesting RORA or Fgfr2 may be crucial for modulating osteogenic differentiation downstream of DNMT1. Collectively, these results reveal DNMT1 as a key repressor of OB differentiation and bone formation while providing us a new rationale for specific inhibition of DNMT1 as a potential therapeutic strategy to treat age-related bone loss. Summary: DNMT1 is overexpressed in sponge bone of people and mice with senile osteoporosis and required for suppression of osteoblast (OB) differentiation of mesenchymal stem cells (MSCs) and osteoprogenitors.
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Affiliation(s)
- Chen Tao
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jia Liu
- Department of Orthopedics, Affliated hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Ziqi Li
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Pinglin Lai
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Academy of Orthopedics, Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Sheng Zhang
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiankun Qu
- Department of Surgery, Tan Cheng County Maternal and Child Health Care Hospital, Linyi, Shandong 276100, China
| | - Yujin Tang
- Department of Orthopedics, Affliated hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Anling Liu
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhipeng Zou
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaochun Bai
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Academy of Orthopedics, Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Jianwei Li
- Division of Orthopaedics and Traumatology, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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16
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Holubekova V, Kolkova Z, Kasubova I, Samec M, Mazurakova A, Koklesova L, Kubatka P, Rokos T, Kozubik E, Biringer K, Kudela E. Interaction of cervical microbiome with epigenome of epithelial cells: Significance of inflammation to primary healthcare. Biomol Concepts 2022; 13:61-80. [PMID: 35245973 DOI: 10.1515/bmc-2022-0005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
One pillar of the predictive, preventive, and personalized medicine framework strategies is the female health. The evaluation of women's lifestyle and dietary habits in context with genetic and modifiable risk factors may reflect the prevention of cervical cancer before the occurrence of clinical symptoms and prediction of cervical lesion behavior. The main aim of this review is to analyze publications in the field of precision medicine that allow the use of research knowledge of cervical microbiome, epigenetic modifications, and inflammation in potential application in clinical practice. Personalized approach in evaluating patient's risk of future development of cervical abnormality should consider the biomarkers of the local microenvironment characterized by the microbial composition, epigenetic pattern of cervical epithelium, and presence of chronic inflammation. Novel sequencing techniques enable a more detailed characterization of actual state in cervical epithelium. Better understanding of all changes in multiomics level enables a better assessment of disease prognosis and selects the eligible targeted therapy in personalized medicine. Restoring of healthy vaginal microflora and reversing the outbreak of cervical abnormality can be also achieved by dietary habits as well as uptake of prebiotics, probiotics, synbiotics, microbial transplantation, and others.
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Affiliation(s)
- Veronika Holubekova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Zuzana Kolkova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Ivana Kasubova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Marek Samec
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Alena Mazurakova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Lenka Koklesova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Tomas Rokos
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Erik Kozubik
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Kamil Biringer
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Erik Kudela
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
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17
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Besaratinia A, Caceres A, Tommasi S. DNA Hydroxymethylation in Smoking-Associated Cancers. Int J Mol Sci 2022; 23:2657. [PMID: 35269796 PMCID: PMC8910185 DOI: 10.3390/ijms23052657] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 02/01/2023] Open
Abstract
5-hydroxymethylcytosine (5-hmC) was first detected in mammalian DNA five decades ago. However, it did not take center stage in the field of epigenetics until 2009, when ten-eleven translocation 1 (TET1) was found to oxidize 5-methylcytosine to 5-hmC, thus offering a long-awaited mechanism for active DNA demethylation. Since then, a remarkable body of research has implicated DNA hydroxymethylation in pluripotency, differentiation, neural system development, aging, and pathogenesis of numerous diseases, especially cancer. Here, we focus on DNA hydroxymethylation in smoking-associated carcinogenesis to highlight the diagnostic, therapeutic, and prognostic potentials of this epigenetic mark. We describe the significance of 5-hmC in DNA demethylation, the importance of substrates and cofactors in TET-mediated DNA hydroxymethylation, the regulation of TETs and related genes (isocitrate dehydrogenases, fumarate hydratase, and succinate dehydrogenase), the cell-type dependency and genomic distribution of 5-hmC, and the functional role of 5-hmC in the epigenetic regulation of transcription. We showcase examples of studies on three major smoking-associated cancers, including lung, bladder, and colorectal cancers, to summarize the current state of knowledge, outstanding questions, and future direction in the field.
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Affiliation(s)
- Ahmad Besaratinia
- Department of Population & Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA; (A.C.); (S.T.)
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18
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Edgar RD, Perrone F, Foster AR, Payne F, Lewis S, Nayak KM, Kraiczy J, Cenier A, Torrente F, Salvestrini C, Heuschkel R, Hensel KO, Harris R, Jones DL, Zerbino DR, Zilbauer M. Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids. Cell Mol Gastroenterol Hepatol 2022; 14:1295-1310. [PMID: 36038072 PMCID: PMC9703134 DOI: 10.1016/j.jcmgh.2022.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Human intestinal epithelial organoids (IEOs) are a powerful tool to model major aspects of intestinal development, health, and diseases because patient-derived cultures retain many features found in vivo. A necessary aspect of the organoid model is the requirement to expand cultures in vitro through several rounds of passaging. This is of concern because the passaging of cells has been shown to affect cell morphology, ploidy, and function. METHODS Here, we analyzed 173 human IEO lines derived from the small and large bowel and examined the effect of culture duration on DNA methylation (DNAm). Furthermore, we tested the potential impact of DNAm changes on gene expression and cellular function. RESULTS Our analyses show a reproducible effect of culture duration on DNAm in a large discovery cohort as well as 2 publicly available validation cohorts generated in different laboratories. Although methylation changes were seen in only approximately 8% of tested cytosine-phosphate-guanine dinucleotides (CpGs) and global cellular function remained stable, a subset of methylation changes correlated with altered gene expression at baseline as well as in response to inflammatory cytokine exposure and withdrawal of Wnt agonists. Importantly, epigenetic changes were found to be enriched in genomic regions associated with colonic cancer and distant to the site of replication, indicating similarities to malignant transformation. CONCLUSIONS Our study shows distinct culture-associated epigenetic changes in mucosa-derived human IEOs, some of which appear to impact gene transcriptomic and cellular function. These findings highlight the need for future studies in this area and the importance of considering passage number as a potentially confounding factor.
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Affiliation(s)
- Rachel D Edgar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Francesca Perrone
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - April R Foster
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - Felicity Payne
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Sophia Lewis
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California
| | - Komal M Nayak
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Aurélie Cenier
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Franco Torrente
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Camilla Salvestrini
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Kai O Hensel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Witten/Herdecke University, Department of Paediatrics, Helios Medical Centre Wuppertal, Children's Hospital, Wuppertal, Germany
| | - Rebecca Harris
- Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - D Leanne Jones
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California; Department of Anatomy and Medicine, Division of Geriatrics, University of California, San Francisco, San Francisco, California; Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, California
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
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19
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Abstract
The intestinal tract is the entry gate for nutrients and symbiotic organisms, being in constant contact with external environment. DNA methylation is one of the keys to how environmental conditions, diet and nutritional status included, shape functionality in the gut and systemically. This review aims to summarise findings on the importance of methylation to gut development, differentiation and function. Evidence to date on how external factors such as diet, dietary supplements, nutritional status and microbiota modifications modulate intestinal function through DNA methylation is also presented.
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20
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Meyer AR, Brown ME, McGrath PS, Dempsey PJ. Injury-Induced Cellular Plasticity Drives Intestinal Regeneration. Cell Mol Gastroenterol Hepatol 2021; 13:843-856. [PMID: 34915204 PMCID: PMC8803615 DOI: 10.1016/j.jcmgh.2021.12.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022]
Abstract
The epithelial lining of the intestine, particularly the stem cell compartment, is affected by harsh conditions in the luminal environment and also is susceptible to genotoxic agents such as radiation and chemotherapy. Therefore, the ability for intestinal epithelial cells to revert to a stem cell state is an important physiological damage response to regenerate the intestinal epithelium at sites of mucosal injury. Many signaling networks involved in maintaining the stem cell niche are activated as part of the damage response to promote cellular plasticity and regeneration. The relative contribution of each cell type and signaling pathway is a critical area of ongoing research, likely dependent on the nature of injury as well as the regional specification within the intestine. Here, we review the current understanding of the multicellular cooperation to restore the intestinal epithelium after damage.
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Affiliation(s)
| | | | | | - Peter J. Dempsey
- Correspondence Address correspondence to: Peter J. Dempsey, PhD, Section of Developmental Biology, Department of Pediatrics, University of Colorado School of Medicine, 1775 Aurora Court, Barbara Davis Center, M20–3306, Aurora, Colorado 80045. fax: (303) 724-6538.
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21
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Beck MA, Fischer H, Grabner LM, Groffics T, Winter M, Tangermann S, Meischel T, Zaussinger‐Haas B, Wagner P, Fischer C, Folie C, Arand J, Schöfer C, Ramsahoye B, Lagger S, Machat G, Eisenwort G, Schneider S, Podhornik A, Kothmayer M, Reichart U, Glösmann M, Tamir I, Mildner M, Sheibani‐Tezerji R, Kenner L, Petzelbauer P, Egger G, Sibilia M, Ablasser A, Seiser C. DNA hypomethylation leads to cGAS-induced autoinflammation in the epidermis. EMBO J 2021; 40:e108234. [PMID: 34586646 PMCID: PMC8591534 DOI: 10.15252/embj.2021108234] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 08/28/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a fundamental epigenetic modification, important across biological processes. The maintenance methyltransferase DNMT1 is essential for lineage differentiation during development, but its functions in tissue homeostasis are incompletely understood. We show that epidermis-specific DNMT1 deletion severely disrupts epidermal structure and homeostasis, initiating a massive innate immune response and infiltration of immune cells. Mechanistically, DNA hypomethylation in keratinocytes triggered transposon derepression, mitotic defects, and formation of micronuclei. DNA release into the cytosol of DNMT1-deficient keratinocytes activated signaling through cGAS and STING, thus triggering inflammation. Our findings show that disruption of a key epigenetic mark directly impacts immune and tissue homeostasis, and potentially impacts our understanding of autoinflammatory diseases and cancer immunotherapy.
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22
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Liu S, Yin P, Xu J, Dotts AJ, Kujawa SA, Coon V JS, Zhao H, Dai Y, Bulun SE. Progesterone receptor-DNA methylation crosstalk regulates depletion of uterine leiomyoma stem cells: A potential therapeutic target. Stem Cell Reports 2021; 16:2099-2106. [PMID: 34388365 PMCID: PMC8452515 DOI: 10.1016/j.stemcr.2021.07.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 01/12/2023] Open
Abstract
Uterine leiomyoma (LM) is the most common tumor in women. Via its receptor (PGR) expressed in differentiated LM cells, progesterone stimulates paracrine signaling that induces proliferation of PGR-deficient LM stem cells (LSCs). Antiprogestins shrink LM but tumors regrow after treatment cessation possibly due to persisting LSCs. Using sorted primary LM cell populations, we found that the PGR gene locus and its target cistrome are hypermethylated in LSCs, inhibiting the expression of genes critical for progesterone-induced LSC differentiation. PGR knockdown shifted the transcriptome of total LM cells toward LSCs and increased global DNA methylation by regulating TET methylcytosine dioxygenases. DNA methylation inhibitor 5'-Aza activated PGR signaling, stimulated LSC differentiation, and synergized with antiprogestin to reduce tumor size in vivo. Taken together, targeting the feedback loop between DNA methylation and progesterone signaling may accelerate the depletion of LSCs through rapid differentiation and sensitize LM to antiprogestin therapy, thus preventing tumor regrowth.
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Affiliation(s)
- Shimeng Liu
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ping Yin
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jingting Xu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Ariel J Dotts
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Stacy A Kujawa
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - John S Coon V
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hong Zhao
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yang Dai
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Serdar E Bulun
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Prentice Women's Hospital, 250 E. Superior Street, Chicago, IL 60611, USA.
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23
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Sotthibundhu A, Muangchan P, Phonchai R, Promjantuek W, Chaicharoenaudomrung N, Kunhorm P, Noisa P. Autophagy Promoted Neural Differentiation of Human Placenta-derived Mesenchymal Stem Cells. In Vivo 2021; 35:2609-2620. [PMID: 34410948 DOI: 10.21873/invivo.12543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND/AIM Human placenta-derived mesenchymal stem cells (hPMSCs) are multipotent and possess neurogenicity. Numerous studies have shown that Notch inhibition and DNA demethylation promote neural differentiation. Here, we investigated the modulation of autophagy during neural differentiation of hPMSCs, induced by DAPT and 5-Azacytidine. MATERIALS AND METHODS hPMSCs were treated with DAPT to induce neural differentiation, and the autophagy regulating molecules were used to assess the impact of autophagy on neural differentiation. RESULTS The hPMSCs presented with typical mesenchymal stem cell phenotypes, in which the majority of cells expressed CD73, CD90 and CD105. hPMSCs were multipotent, capable of differentiating into mesodermal cells. After treatment with DAPT, hPMSCs upregulated the expression of neuronal genes including SOX2, Nestin, and βIII-tubulin, and the autophagy genes LC3I/II and Beclin. These genes were further increased when 5-Azacytidine was co-supplemented in the culture medium. The inhibition of autophagy by chloroquine impeded the neural differentiation of hPMSCs, marked by the downregulation of βIII-tubulin, while the activation of autophagy by valproic acid (VPA) instigated the emergence of βIII-tubulin-positive cells. CONCLUSION During the differentiation process, autophagy was modulated, implying that autophagy could play a significant role during the differentiation of these cells. The blockage and stimulation of autophagy could either hinder or induce the formation of neural-like cells, respectively. Therefore, the refinement of autophagic activity at an appropriate level might improve the efficiency of stem cell differentiation.
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Affiliation(s)
- Areechun Sotthibundhu
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
| | - Pattamon Muangchan
- Laboratory of Cell-Based Assays and Innovations, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Ruchee Phonchai
- Laboratory of Cell-Based Assays and Innovations, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Wilasinee Promjantuek
- Laboratory of Cell-Based Assays and Innovations, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Nipha Chaicharoenaudomrung
- Laboratory of Cell-Based Assays and Innovations, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Phongsakorn Kunhorm
- Laboratory of Cell-Based Assays and Innovations, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Parinya Noisa
- Laboratory of Cell-Based Assays and Innovations, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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24
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Planques A, Kerner P, Ferry L, Grunau C, Gazave E, Vervoort M. DNA methylation atlas and machinery in the developing and regenerating annelid Platynereis dumerilii. BMC Biol 2021; 19:148. [PMID: 34340707 PMCID: PMC8330077 DOI: 10.1186/s12915-021-01074-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/16/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Methylation of cytosines in DNA (5mC methylation) is a major epigenetic modification that modulates gene expression and constitutes the basis for mechanisms regulating multiple aspects of embryonic development and cell reprogramming in vertebrates. In mammals, 5mC methylation of promoter regions is linked to transcriptional repression. Transcription regulation by 5mC methylation notably involves the nucleosome remodeling and deacetylase complex (NuRD complex) which bridges DNA methylation and histone modifications. However, less is known about regulatory mechanisms involving 5mC methylation and their function in non-vertebrate animals. In this paper, we study 5mC methylation in the marine annelid worm Platynereis dumerilii, an emerging evolutionary and developmental biology model capable of regenerating the posterior part of its body post-amputation. RESULTS Using in silico and experimental approaches, we show that P. dumerilii displays a high level of DNA methylation comparable to that of mammalian somatic cells. 5mC methylation in P. dumerilii is dynamic along the life cycle of the animal and markedly decreases at the transition between larval to post-larval stages. We identify a full repertoire of mainly single-copy genes encoding the machinery associated with 5mC methylation or members of the NuRD complex in P. dumerilii and show that this repertoire is close to the one inferred for the last common ancestor of bilaterians. These genes are dynamically expressed during P. dumerilii development and regeneration. Treatment with the DNA hypomethylating agent Decitabine impairs P. dumerilii larval development and regeneration and has long-term effects on post-regenerative growth. CONCLUSIONS Our data reveal high levels of 5mC methylation in the annelid P. dumerilii, highlighting that this feature is not specific to vertebrates in the bilaterian clade. Analysis of DNA methylation levels and machinery gene expression during development and regeneration, as well as the use of a chemical inhibitor of DNA methylation, suggest an involvement of 5mC methylation in P. dumerilii development and regeneration. We also present data indicating that P. dumerilii constitutes a promising model to study biological roles and mechanisms of DNA methylation in non-vertebrate bilaterians and to provide new knowledge about evolution of the functions of this key epigenetic modification in bilaterian animals.
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Affiliation(s)
- Anabelle Planques
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Pierre Kerner
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Laure Ferry
- Université de Paris, CNRS, Epigenetics and Cell Fate, F-75006, Paris, France
| | - Christoph Grunau
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, F-66860, Perpignan, France
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.
| | - Michel Vervoort
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.
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25
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Lorzadeh A, Romero-Wolf M, Goel A, Jadhav U. Epigenetic Regulation of Intestinal Stem Cells and Disease: A Balancing Act of DNA and Histone Methylation. Gastroenterology 2021; 160:2267-2282. [PMID: 33775639 PMCID: PMC8169626 DOI: 10.1053/j.gastro.2021.03.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 02/08/2023]
Abstract
Genetic mutations or regulatory failures underlie cellular malfunction in many diseases, including colorectal cancer and inflammatory bowel diseases. However, mutational defects alone fail to explain the complexity of such disorders. Epigenetic regulation-control of gene action through chemical and structural changes of chromatin-provides a platform to integrate multiple extracellular inputs and prepares the cellular genome for appropriate gene expression responses. Coregulation by polycomb repressive complex 2-mediated trimethylation of lysine 27 on histone 3 and DNA methylation has emerged as one of the most influential epigenetic controls in colorectal cancer and many other diseases, but molecular details remain inadequate. Here we review the molecular interplay of these epigenetic features in relation to gastrointestinal development, homeostasis, and disease biology. We discuss other epigenetic mechanisms pertinent to the balance of trimethylation of lysine 27 on histone 3 and DNA methylation and their actions in gastrointestinal cancers. We also review the current molecular understanding of chromatin control in the pathogenesis of inflammatory bowel diseases.
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Affiliation(s)
- Alireza Lorzadeh
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Maile Romero-Wolf
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Unmesh Jadhav
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.
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26
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Petrillo F, Iervolino A, Angrisano T, Jelen S, Costanzo V, D’Acierno M, Cheng L, Wu Q, Guerriero I, Mazzarella MC, De Falco A, D’Angelo F, Ceccarelli M, Caraglia M, Capasso G, Fenton RA, Trepiccione F. Dysregulation of Principal Cell miRNAs Facilitates Epigenetic Regulation of AQP2 and Results in Nephrogenic Diabetes Insipidus. J Am Soc Nephrol 2021; 32:1339-1354. [PMID: 33727367 PMCID: PMC8259636 DOI: 10.1681/asn.2020010031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/02/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs), formed by cleavage of pre-microRNA by the endoribonuclease Dicer, are critical modulators of cell function by post-transcriptionally regulating gene expression. METHODS Selective ablation of Dicer in AQP2-expressing cells (DicerAQP2Cre+ mice) was used to investigate the role of miRNAs in the kidney collecting duct of mice. RESULTS The mice had severe polyuria and nephrogenic diabetes insipidus, potentially due to greatly reduced AQP2 and AQP4 levels. Although epithelial sodium channel levels were decreased in cortex and increased in inner medulla, amiloride-sensitive sodium reabsorption was equivalent in DicerAQP2Cre+ mice and controls. Small-RNA sequencing and proteomic analysis revealed 31 and 178 significantly regulated miRNAs and proteins, respectively. Integrated bioinformatic analysis of the miRNAome and proteome suggested alterations in the epigenetic machinery and various transcription factors regulating AQP2 expression in DicerAQP2Cre+ mice. The expression profile and function of three miRNAs (miR-7688-5p, miR-8114, and miR-409-3p) whose predicted targets were involved in epigenetic control (Phf2, Kdm5c, and Kdm4a) or transcriptional regulation (GATA3, GATA2, and ELF3) of AQP2 were validated. Luciferase assays could not demonstrate direct interaction of AQP2 or the three potential transcription factors with miR-7688-5p, miR-8114, and miR-409-3p. However, transfection of respective miRNA mimics reduced AQP2 expression. Chromatin immunoprecipitation assays demonstrated decreased Phf2 and significantly increased Kdm5c interactions at the Aqp2 gene promoter in DicerAQP2Cre+ mice, resulting in decreased RNA Pol II association. CONCLUSIONS Novel evidence indicates miRNA-mediated epigenetic regulation of AQP2 expression.
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Affiliation(s)
- Federica Petrillo
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Anna Iervolino
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | - Tiziana Angrisano
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Sabina Jelen
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | - Vincenzo Costanzo
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | | | - Lei Cheng
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Qi Wu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Ilaria Guerriero
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | | | - Alfonso De Falco
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | - Fulvio D’Angelo
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | - Michele Ceccarelli
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy,Department of Electrical Engineering and Information Technology (DIETI) University of Naples “Federico II”, Naples, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Giovambattista Capasso
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy,Department of Translational Medical Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Francesco Trepiccione
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy,Department of Translational Medical Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
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27
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Ayuso M, Irwin R, Walsh C, Van Cruchten S, Van Ginneken C. Low birth weight female piglets show altered intestinal development, gene expression, and epigenetic changes at key developmental loci. FASEB J 2021; 35:e21522. [PMID: 33734504 DOI: 10.1096/fj.202002587r] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/15/2021] [Accepted: 02/26/2021] [Indexed: 12/15/2022]
Abstract
Intestinal development is compromised in low birth weight (LBW) pigs, negatively impacting their growth, health, and resilience. We investigated the molecular mechanisms of the altered intestinal maturation observed in neonatal and juvenile LBW female piglets by comparing the changes in intestinal morphology, gene expression, and methylation in LBW versus normal birth weight (NBW) female piglets. A total of 16 LBW/NBW sibling pairs were sacrificed at 0 hours, 8 hours, 10 days, and 8 weeks of age. The gastrointestinal tract was weighed, measured, and the small intestine was sampled for histomorphology, gene expression, and methylation analyses. Impaired intestinal development, with shorter villi and shallower crypts, was observed in LBW female piglets. The expression of intestinal development markers (ALPI and OLFM) rapidly peaked after birth in NBW but not in LBW female piglets. The lower expression of genes involved in nutrient digestion (ANPEP and SI) and barrier function (OCLN and CLDN4) in LBW, together with their delayed development of intestinal villi and crypts could help to explain the compromised health and growth potential of LBW female piglets. The changes in methylation observed in LBW in key regulators of intestinal development (OLFM4 and FZD5) suggest long-term effects of BW on intestinal gene expression, development, and function. Accordingly, experimental demethylation induced in IPEC-J2 cells led to increased expression of intestinal genes (MGA, DPP4, and GLUT2). Overall, we have identified the alterations in transcription or epigenetic marking at a number of genes critical to intestinal development, which may contribute to both the short- and long-term failure of LBW female piglets to thrive.
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Affiliation(s)
- Miriam Ayuso
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Rachelle Irwin
- School of Biomedical Sciences, Ulster University, Coleraine, UK
| | - Colum Walsh
- School of Biomedical Sciences, Ulster University, Coleraine, UK
| | - Steven Van Cruchten
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Chris Van Ginneken
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
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28
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Reilly BM, Luger T, Park S, Lio CWJ, González-Avalos E, Wheeler EC, Lee M, Williamson L, Tanaka T, Diep D, Zhang K, Huang Y, Rao A, Bejar R. 5-Azacytidine Transiently Restores Dysregulated Erythroid Differentiation Gene Expression in TET2-Deficient Erythroleukemia Cells. Mol Cancer Res 2021; 19:451-464. [PMID: 33172974 PMCID: PMC7925369 DOI: 10.1158/1541-7786.mcr-20-0453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/05/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022]
Abstract
DNA methyltransferase inhibitors (DNMTI) like 5-Azacytidine (5-Aza) are the only disease-modifying drugs approved for the treatment of higher-risk myelodysplastic syndromes (MDS), however less than 50% of patients respond, and there are no predictors of response with clinical utility. Somatic mutations in the DNA methylation regulating gene tet-methylcytosine dioxygenase 2 (TET2) are associated with response to DNMTIs, however the mechanisms responsible for this association remain unknown. Using bisulfite padlock probes, mRNA sequencing, and hydroxymethylcytosine pull-down sequencing at several time points throughout 5-Aza treatment, we show that TET2 loss particularly influences DNA methylation (5mC) and hydroxymethylation (5hmC) patterns at erythroid gene enhancers and is associated with downregulation of erythroid gene expression in the human erythroleukemia cell line TF-1. 5-Aza disproportionately induces expression of these down-regulated genes in TET2KO cells and this effect is related to dynamic 5mC changes at erythroid gene enhancers after 5-Aza exposure. We identified differences in remethylation kinetics after 5-Aza exposure for several types of genomic regulatory elements, with distal enhancers exhibiting longer-lasting 5mC changes than other regions. This work highlights the role of 5mC and 5hmC dynamics at distal enhancers in regulating the expression of differentiation-associated gene signatures, and sheds light on how 5-Aza may be more effective in patients harboring TET2 mutations. IMPLICATIONS: TET2 loss in erythroleukemia cells induces hypermethylation and impaired expression of erythroid differentiation genes which can be specifically counteracted by 5-Azacytidine, providing a potential mechanism for the increased efficacy of 5-Aza in TET2-mutant patients with MDS. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/19/3/451/F1.large.jpg.
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Affiliation(s)
- Brian M Reilly
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California
- Moores Cancer Center, University of California San Diego, La Jolla, California
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California
| | - Timothy Luger
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Soo Park
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Chan-Wang Jerry Lio
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California
| | - Edahí González-Avalos
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California
| | - Emily C Wheeler
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California
| | - Minjung Lee
- Center for Epigenetics and Disease Prevention, Texas A&M University Health Science Center, Houston, Texas
| | - Laura Williamson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Tiffany Tanaka
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Dinh Diep
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Texas A&M University Health Science Center, Houston, Texas
| | - Anjana Rao
- Moores Cancer Center, University of California San Diego, La Jolla, California
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California
| | - Rafael Bejar
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California.
- Moores Cancer Center, University of California San Diego, La Jolla, California
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FoxA-dependent demethylation of DNA initiates epigenetic memory of cellular identity. Dev Cell 2021; 56:602-612.e4. [PMID: 33636105 DOI: 10.1016/j.devcel.2021.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/03/2020] [Accepted: 02/02/2021] [Indexed: 12/12/2022]
Abstract
Tissue-specific DNA methylation patterns are created by transcription factors that recruit methylation and demethylation enzymes to cis-regulatory elements. To date, it is not known whether transcription factors are needed to continuously maintain methylation profiles in development and mature tissues or whether they only establish these marks during organ development. We queried the role of the pioneer factor FoxA in generating hypomethylated DNA at liver enhancers. We discovered a set of FoxA-binding sites that undergo regional, FoxA-dependent demethylation during organ development. Conditional ablation of FoxA genes in the adult liver demonstrated that continued FoxA presence was not required to maintain the hypomethylated state, even when massive cell proliferation was induced. This study provides strong evidence for the stable, epigenetic nature of tissue-specific DNA methylation patterns directed by lineage-determining transcription factors during organ development.
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Hageman JH, Heinz MC, Kretzschmar K, van der Vaart J, Clevers H, Snippert HJG. Intestinal Regeneration: Regulation by the Microenvironment. Dev Cell 2021; 54:435-446. [PMID: 32841594 DOI: 10.1016/j.devcel.2020.07.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Accepted: 07/13/2020] [Indexed: 01/05/2023]
Abstract
Damage to the intestinal stem cell niche can result from mechanical stress, infections, chronic inflammation or cytotoxic therapies. Progenitor cells can compensate for insults to the stem cell population through dedifferentiation. The microenvironment modulates this regenerative response by influencing the activity of signaling pathways, including Wnt, Notch, and YAP/TAZ. For instance, mesenchymal cells and immune cells become more abundant after damage and secrete signaling molecules that promote the regenerative process. Furthermore, regeneration is influenced by the nutritional state, microbiome, and extracellular matrix. Here, we review how all these components cooperate to restore epithelial homeostasis in the intestine after injury.
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Affiliation(s)
- Joris H Hageman
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Maria C Heinz
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Kai Kretzschmar
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Mildred-Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Jelte van der Vaart
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands.
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Ostrop J, Zwiggelaar RT, Terndrup Pedersen M, Gerbe F, Bösl K, Lindholm HT, Díez-Sánchez A, Parmar N, Radetzki S, von Kries JP, Jay P, Jensen KB, Arrowsmith C, Oudhoff MJ. A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation. Front Cell Dev Biol 2021; 8:618552. [PMID: 33575256 PMCID: PMC7872100 DOI: 10.3389/fcell.2020.618552] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
Intestinal organoids are an excellent model to study epithelial biology. Yet, the selection of analytical tools to accurately quantify heterogeneous organoid cultures remains limited. Here, we developed a semi-automated organoid screening method, which we applied to a library of highly specific chemical probes to identify epigenetic regulators of intestinal epithelial biology. The role of epigenetic modifiers in adult stem cell systems, such as the intestinal epithelium, is still undefined. Based on this resource dataset, we identified several targets that affected epithelial cell differentiation, including HDACs, EP300/CREBBP, LSD1, and type I PRMTs, which were verified by complementary methods. For example, we show that inhibiting type I PRMTs, which leads enhanced epithelial differentiation, blocks the growth of adenoma but not normal organoid cultures. Thus, epigenetic probes are powerful tools to study intestinal epithelial biology and may have therapeutic potential.
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Affiliation(s)
- Jenny Ostrop
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Rosalie T. Zwiggelaar
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Marianne Terndrup Pedersen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - François Gerbe
- Cancer Biology Department, Institute of Functional Genomics, University of Montpellier, Montpellier, France
| | - Korbinian Bösl
- Department of Bioinformatics, Computational Biological Unit, University of Bergen, Bergen, Norway
| | - Håvard T. Lindholm
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Alberto Díez-Sánchez
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Naveen Parmar
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Silke Radetzki
- Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Jens Peter von Kries
- Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Philippe Jay
- Cancer Biology Department, Institute of Functional Genomics, University of Montpellier, Montpellier, France
| | - Kim B. Jensen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Menno J. Oudhoff
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
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Nair J, Maheshwari A. Epigenetics in Necrotizing Enterocolitis. Curr Pediatr Rev 2021; 17:172-184. [PMID: 33882811 DOI: 10.2174/1573396317666210421110608] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/14/2021] [Accepted: 02/26/2021] [Indexed: 11/22/2022]
Abstract
Epigenetic alterations in our genetic material can lead to heritable changes in the risk, clinical manifestations, course, and outcomes of many diseases. Understanding these epigenetic mechanisms can help in identifying potential therapeutic targets. This is especially important in necrotizing enterocolitis (NEC), where prenatal as well as postnatal factors impact susceptibility to this devastating condition, but our therapeutic options are limited. Developmental factors affecting intestinal structure and function, our immune system, gut microbiome, and postnatal enteral nutrition are all thought to play a prominent role in this disease. In this manuscript, we have reviewed the epigenetic mechanisms involved in NEC. These include key developmental changes in DNA methylation in the immature intestine, the role of long non-coding RNA (lncRNA) in maintaining intestinal barrier function, epigenetic influences of prenatal inflammation on immunological pathways in NEC pathogenesis such as Toll-Like Receptor 4 (TLR4) and epigenetic changes associated with enteral feeding causing upregulation of pro-inflammatory genes. We have assimilated research findings from our own laboratory with an extensive review of the literature utilizing key terms in multiple databases, including PubMed, EMBASE, and Science Direct.
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Affiliation(s)
- Jayasree Nair
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Akhil Maheshwari
- Department of Pediatrics, Johns Hopkins University, Baltimore, MA, United States
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33
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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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Abstract
The cardinal properties of adult tissue stem cells are self-renewal and the ability to generate diverse resident cell types. The daily losses of terminally differentiated intestinal, skin, and blood cells require "professional" stem cells to produce replacements. This occurs by continuous expansion of stem cells and their immediate progeny, followed by coordinated activation of divergent transcriptional programs to generate stable cells with diverse functions. Other tissues turn over slowly, if at all, and vary widely in strategies for facultative stem cell activity or interconversion among mature resident cell types (transdifferentiation). Cell fate potential is programmed in tissue-specific configurations of chromatin, which restrict the complement of available genes and cis-regulatory elements, hence allowing specific cell types to arise. Using as a model the transcriptional and chromatin basis of cell differentiation and dedifferentiation in intestinal crypts, we discuss here how self-renewing and other tissues execute homeostatic and injury-responsive stem cell activity.
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Affiliation(s)
- Madhurima Saxena
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; .,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Harvard University, Boston, Massachusetts 02215, USA.,Current affiliation: Translational Medicine, Bristol-Myers-Squibb, Cambridge, Massachusetts 02142, USA;
| | - Ramesh A Shivdasani
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; .,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Harvard University, Boston, Massachusetts 02215, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
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35
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Rispal J, Escaffit F, Trouche D. Chromatin Dynamics in Intestinal Epithelial Homeostasis: A Paradigm of Cell Fate Determination versus Cell Plasticity. Stem Cell Rev Rep 2020; 16:1062-1080. [PMID: 33051755 PMCID: PMC7667136 DOI: 10.1007/s12015-020-10055-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2020] [Indexed: 12/12/2022]
Abstract
The rapid renewal of intestinal epithelium is mediated by a pool of stem cells, located at the bottom of crypts, giving rise to highly proliferative progenitor cells, which in turn differentiate during their migration along the villus. The equilibrium between renewal and differentiation is critical for establishment and maintenance of tissue homeostasis, and is regulated by signaling pathways (Wnt, Notch, Bmp…) and specific transcription factors (TCF4, CDX2…). Such regulation controls intestinal cell identities by modulating the cellular transcriptome. Recently, chromatin modification and dynamics have been identified as major actors linking signaling pathways and transcriptional regulation in the control of intestinal homeostasis. In this review, we synthesize the many facets of chromatin dynamics involved in controlling intestinal cell fate, such as stemness maintenance, progenitor identity, lineage choice and commitment, and terminal differentiation. In addition, we present recent data underlying the fundamental role of chromatin dynamics in intestinal cell plasticity. Indeed, this plasticity, which includes dedifferentiation processes or the response to environmental cues (like microbiota’s presence or food ingestion), is central for the organ’s physiology. Finally, we discuss the role of chromatin dynamics in the appearance and treatment of diseases caused by deficiencies in the aforementioned mechanisms, such as gastrointestinal cancer, inflammatory bowel disease or irritable bowel syndrome. Graphical abstract ![]()
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Affiliation(s)
- Jérémie Rispal
- LBCMCP, Centre of Integrative Biology (CBI), Université de Toulouse, CNRS, UPS, Toulouse, 31062, France
| | - Fabrice Escaffit
- LBCMCP, Centre of Integrative Biology (CBI), Université de Toulouse, CNRS, UPS, Toulouse, 31062, France.
| | - Didier Trouche
- LBCMCP, Centre of Integrative Biology (CBI), Université de Toulouse, CNRS, UPS, Toulouse, 31062, France
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36
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Liu S, Yin P, Xu J, Dotts AJ, Kujawa SA, Coon V JS, Zhao H, Shilatifard A, Dai Y, Bulun SE. Targeting DNA Methylation Depletes Uterine Leiomyoma Stem Cell-enriched Population by Stimulating Their Differentiation. Endocrinology 2020; 161:5894164. [PMID: 32812024 PMCID: PMC7497820 DOI: 10.1210/endocr/bqaa143] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/11/2020] [Indexed: 01/01/2023]
Abstract
Uterine leiomyoma (LM) is the most common tumor in women and can cause severe morbidity. Leiomyoma growth requires the maintenance and proliferation of a stem cell population. Dysregulated deoxyribonucleic acid (DNA) methylation has been reported in LM, but its role in LM stem cell regulation remains unclear. Here, we fluorescence-activated cell sorting (FACS)-sorted cells from human LM tissues into 3 populations: LM stem cell-like cells (LSC, 5%), LM intermediate cells (LIC, 7%), and differentiated LM cells (LDC, 88%), and we analyzed the transcriptome and epigenetic landscape of LM cells at different differentiation stages. Leiomyoma stem cell-like cells harbored a unique methylome, with 8862 differentially methylated regions compared to LIC and 9444 compared to LDC, most of which were hypermethylated. Consistent with global hypermethylation, transcript levels of TET1 and TET3 methylcytosine dioxygenases were lower in LSC. Integrative analyses revealed an inverse relationship between methylation and gene expression changes during LSC differentiation. In LSC, hypermethylation suppressed the genes important for myometrium- and LM-associated functions, including muscle contraction and hormone action, to maintain stemness. The hypomethylating drug, 5'-Aza, stimulated LSC differentiation, depleting the stem cell population and inhibiting tumor initiation. Our data suggest that DNA methylation maintains the pool of LSC, which is critical for the regeneration of LM tumors.
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Affiliation(s)
- Shimeng Liu
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ping Yin
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jingting Xu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
| | - Ariel J Dotts
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Stacy A Kujawa
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - John S Coon V
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Hong Zhao
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Yang Dai
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
| | - Serdar E Bulun
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Correspondence: Serdar E Bulun, MD, Prentice Women’s Hospital, 250 E. Superior Street, Chicago, IL 60611, USA.
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Abstract
Adult stem cells undergo both replicative and chronological aging in their niches, with catastrophic declines in regenerative potential with age. Due to repeated environmental insults during aging, the chromatin landscape of stem cells erodes, with changes in both DNA and histone modifications, accumulation of damage, and altered transcriptional response. A body of work has shown that altered chromatin is a driver of cell fate changes and a regulator of self-renewal in stem cells and therefore a prime target for juvenescence therapeutics. This review focuses on chromatin changes in stem cell aging and provides a composite view of both common and unique epigenetic themes apparent from the studies of multiple stem cell types.
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Affiliation(s)
- Changyou Shi
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Lin Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
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38
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Baulies A, Angelis N, Li VSW. Hallmarks of intestinal stem cells. Development 2020; 147:147/15/dev182675. [PMID: 32747330 DOI: 10.1242/dev.182675] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Intestinal stem cells (ISCs) are highly proliferative cells that fuel the continuous renewal of the intestinal epithelium. Understanding their regulatory mechanisms during tissue homeostasis is key to delineating their roles in development and regeneration, as well as diseases such as bowel cancer and inflammatory bowel disease. Previous studies of ISCs focused mainly on the position of these cells along the intestinal crypt and their capacity for multipotency. However, evidence increasingly suggests that ISCs also exist in distinct cellular states, which can be an acquired rather than a hardwired intrinsic property. In this Review, we summarise the recent findings into how ISC identity can be defined by proliferation state, signalling crosstalk, epigenetics and metabolism, and propose an update on the hallmarks of ISCs. We further discuss how these properties contribute to intestinal development and the dynamics of injury-induced regeneration.
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Affiliation(s)
- Anna Baulies
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nikolaos Angelis
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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39
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Verzi MP, Shivdasani RA. Epigenetic regulation of intestinal stem cell differentiation. Am J Physiol Gastrointest Liver Physiol 2020; 319:G189-G196. [PMID: 32628072 PMCID: PMC7500269 DOI: 10.1152/ajpgi.00084.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To fulfill the lifelong need to supply diverse epithelial cells, intestinal stem cells (ISCs) rely on executing accurate transcriptional programs. This review addresses the mechanisms that control those programs. Genes that define cell behaviors and identities are regulated principally through thousands of dispersed enhancers, each individually <1 kb long and positioned from a few to hundreds of kilobases away from transcription start sites, upstream or downstream from coding genes or within introns. Wnt, Notch, and other epithelial control signals feed into these cis-regulatory DNA elements, which are also common loci of polymorphisms and mutations that confer disease risk. Cell-specific gene activity requires promoters to interact with the correct combination of signal-responsive enhancers. We review the current state of knowledge in ISCs regarding active enhancers, the nucleosome modifications that may enable appropriate and hinder inappropriate enhancer-promoter contacts, and the roles of lineage-restricted transcription factors.
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Affiliation(s)
- Michael P. Verzi
- 1Department of Genetics, Rutgers, State University of New Jersey, Piscataway, New Jersey,2Cancer Institute of New Jersey and Human Genetics Institute of New Jersey, Piscataway, New Jersey
| | - Ramesh A. Shivdasani
- 3Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts,4Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts,5Harvard Stem Cell Institute, Cambridge, Massachusetts
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40
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dnmt1 function is required to maintain retinal stem cells within the ciliary marginal zone of the zebrafish eye. Sci Rep 2020; 10:11293. [PMID: 32647199 PMCID: PMC7347529 DOI: 10.1038/s41598-020-68016-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/15/2020] [Indexed: 12/22/2022] Open
Abstract
The ciliary marginal zone (CMZ) of the zebrafish retina contains a population of actively proliferating resident stem cells, which generate retinal neurons throughout life. The maintenance methyltransferase, dnmt1, is expressed within the CMZ. Loss of dnmt1 function results in gene misregulation and cell death in a variety of developmental contexts, however, its role in retinal stem cell (RSC) maintenance is currently unknown. Here, we demonstrate that zebrafish dnmt1s872 mutants possess severe defects in RSC maintenance within the CMZ. Using a combination of immunohistochemistry, in situ hybridization, and a transgenic reporter assay, our results demonstrate a requirement for dnmt1 activity in the regulation of RSC proliferation, gene expression and in the repression of endogenous retroelements (REs). Ultimately, cell death is elevated in the dnmt1−/− CMZ, but in a p53-independent manner. Using a transgenic reporter for RE transposition activity, we demonstrate increased transposition in the dnmt1−/− CMZ. Taken together our data identify a critical role for dnmt1 function in RSC maintenance in the vertebrate eye.
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41
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The Epigenetic Progenitor Origin of Cancer Reassessed: DNA Methylation Brings Balance to the Stem Force. EPIGENOMES 2020; 4:epigenomes4020008. [PMID: 34968242 PMCID: PMC8594692 DOI: 10.3390/epigenomes4020008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 12/17/2022] Open
Abstract
Cancer initiation and progression toward malignant stages occur as the results of accumulating genetic alterations and epigenetic dysregulation. During the last decade, the development of next generation sequencing (NGS) technologies and the increasing pan-genomic knowledge have revolutionized how we consider the evolving epigenetic landscapes during homeostasis and tumor progression. DNA methylation represents the best studied mark and is considered as a common mechanism of epigenetic regulation in normal homeostasis and cancer. A remarkable amount of work has recently started clarifying the central role played by DNA methylation dynamics on the maintenance of cell identity and on cell fate decisions during the different steps of normal development and tumor evolution. Importantly, a growing number of studies show that DNA methylation is key in the maintenance of adult stemness and in orchestrating commitment in multiple ways. Perturbations of the normal DNA methylation patterns impair the homeostatic balance and can lead to tumor initiation. Therefore, DNA methylation represents an interesting therapeutic target to recover homeostasis in tumor stem cells.
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42
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Serena C, Millan M, Ejarque M, Saera-Vila A, Maymó-Masip E, Núñez-Roa C, Monfort-Ferré D, Terrón-Puig M, Bautista M, Menacho M, Martí M, Espin E, Vendrell J, Fernández-Veledo S. Adipose stem cells from patients with Crohn's disease show a distinctive DNA methylation pattern. Clin Epigenetics 2020; 12:53. [PMID: 32252817 PMCID: PMC7137346 DOI: 10.1186/s13148-020-00843-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/24/2020] [Indexed: 12/22/2022] Open
Abstract
Background Crohn’s disease (CD) is characterized by persistent inflammation and ulceration of the small or large bowel, and expansion of mesenteric adipose tissue, termed creeping fat (CF). We previously demonstrated that human adipose-derived stem cells (hASCs) from CF of patients with CD exhibit dysfunctional phenotypes, including a pro-inflammatory profile, high phagocytic capacity, and weak immunosuppressive properties. Importantly, these phenotypes persist in patients in remission and are found in all adipose depots explored including subcutaneous fat. We hypothesized that changes in hASCs are a consequence of epigenetic modifications. Methods We applied epigenome-wide profiling with a methylation array (Illumina EPIC/850k array) and gene expression analysis to explore the impact of CD on the methylation signature of hASCs isolated from the subcutaneous fat of patients with CD and healthy controls (n = 7 and 5, respectively; cohort I). Differentially methylated positions (p value cutoff < 1 × 10−4 and ten or more DMPs per gene) and regions (inclusion threshold 0.2, p value cutoff < 1 × 10−2 and more than 2 DMRs per gene) were identified using dmpfinder and Bumphunter (minfi), respectively. Changes in the expression of differentially methylated genes in hASCs were validated in a second cohort (n = 10/10 inactive and active CD and 10 controls; including patients from cohort I) and also in peripheral blood mononuclear cells (PBMCs) of patients with active/inactive CD and of healthy controls (cohort III; n = 30 independent subjects). Results We found a distinct DNA methylation landscape in hASCs from patients with CD, leading to changes in the expression of differentially methylated genes involved in immune response, metabolic, cell differentiation, and development processes. Notably, the expression of several of these genes in hASCs and PBMCs such as tumor necrosis factor alpha (TNFA) and PR domain zinc finger protein 16 (PRDM16) were not restored to normal (healthy) levels after disease remission. Conclusions hASCs of patients with CD exhibit a unique DNA methylation and gene expression profile, but the expression of several genes are only partially restored in patients with inactive CD, both in hASCs and PBMCs. Understanding how CD shapes the functionality of hASCs is critical for investigating the complex pathophysiology of this disease, as well as for the success of cell-based therapies. Graphical abstract Human adipose-stem cells isolated from subcutaneous fat of patients with Crohn’s disease exhibit an altered DNA methylation pattern and gene expression profile compared with those isolated from healthy individuals, with immune system, cell differentiation, metabolic and development processes identified as the main pathways affected. Interestingly, the gene expression of several genes involved in these pathways is only partially restored to control levels in patients with inactive Crohn’s disease, both in human adipose-stem cells and peripheral blood mononuclear cells. Understanding how Crohn’s disease shapes the functionality of human adipose-stem cells is critical for investigating the complex pathophysiology of this disease, as well as for the success of cell-based therapies.
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Affiliation(s)
- Carolina Serena
- Institut d´Investigació Sanitària Pere Virgili, Hospital Universitari Joan XXIII, Dr Mallafré Guasch, 4, 43007, Tarragona, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28014, Madrid, Spain
| | - Monica Millan
- Colorectal Surgery Unit, Hospital Universitari Joan XXIII, 43007, Tarragona, Spain.,Colorectal Surgery Unit, Hospital Universitari La Fe, Valencia, Spain
| | - Miriam Ejarque
- Institut d´Investigació Sanitària Pere Virgili, Hospital Universitari Joan XXIII, Dr Mallafré Guasch, 4, 43007, Tarragona, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28014, Madrid, Spain
| | - Alfonso Saera-Vila
- Institut d´Investigació Sanitària Pere Virgili, Hospital Universitari Joan XXIII, Dr Mallafré Guasch, 4, 43007, Tarragona, Spain
| | - Elsa Maymó-Masip
- Institut d´Investigació Sanitària Pere Virgili, Hospital Universitari Joan XXIII, Dr Mallafré Guasch, 4, 43007, Tarragona, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28014, Madrid, Spain
| | - Catalina Núñez-Roa
- Institut d´Investigació Sanitària Pere Virgili, Hospital Universitari Joan XXIII, Dr Mallafré Guasch, 4, 43007, Tarragona, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28014, Madrid, Spain
| | - Diandra Monfort-Ferré
- Institut d´Investigació Sanitària Pere Virgili, Hospital Universitari Joan XXIII, Dr Mallafré Guasch, 4, 43007, Tarragona, Spain
| | - Margarida Terrón-Puig
- Institut d´Investigació Sanitària Pere Virgili, Hospital Universitari Joan XXIII, Dr Mallafré Guasch, 4, 43007, Tarragona, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28014, Madrid, Spain
| | - Michelle Bautista
- Digestive Unit, Hospital Universitari Joan XXIII, 43007, Tarragona, Spain
| | - Margarita Menacho
- Digestive Unit, Hospital Universitari Joan XXIII, 43007, Tarragona, Spain
| | - Marc Martí
- Colorectal Surgery Unit, General Surgery Service, Hospital Valle de Hebron, Universitat Autonoma de Barcelona, 08035, Barcelona, Spain
| | - Eloy Espin
- Colorectal Surgery Unit, General Surgery Service, Hospital Valle de Hebron, Universitat Autonoma de Barcelona, 08035, Barcelona, Spain
| | - Joan Vendrell
- Institut d´Investigació Sanitària Pere Virgili, Hospital Universitari Joan XXIII, Dr Mallafré Guasch, 4, 43007, Tarragona, Spain. .,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28014, Madrid, Spain. .,Universitat Rovira i Virgili, Tarragona, Spain.
| | - Sonia Fernández-Veledo
- Institut d´Investigació Sanitària Pere Virgili, Hospital Universitari Joan XXIII, Dr Mallafré Guasch, 4, 43007, Tarragona, Spain. .,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28014, Madrid, Spain.
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Bruschi M, Garnier L, Cleroux E, Giordano A, Dumas M, Bardet AF, Kergrohen T, Quesada S, Cesses P, Weber M, Gerbe F, Jay P. Loss of Apc Rapidly Impairs DNA Methylation Programs and Cell Fate Decisions in Lgr5 + Intestinal Stem Cells. Cancer Res 2020; 80:2101-2113. [PMID: 32213541 DOI: 10.1158/0008-5472.can-19-2104] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/13/2020] [Accepted: 03/19/2020] [Indexed: 12/24/2022]
Abstract
Colorectal cancer initiation and progression result from the accumulation of genetic and epigenetic alterations. Although aberrant gene expression and DNA methylation profiles are considered hallmarks of colorectal cancer development, the precise timing at which these are produced during tumor establishment remains elusive. Here we investigated the early transcriptional and epigenetic changes induced by adenomatous polyposis coli (Apc) inactivation in intestinal crypts. Hyperactivation of the Wnt pathway via Apc inactivation in crypt base columnar intestinal stem cells (ISC) led to their rapid accumulation driven by an impaired molecular commitment to differentiation, which was associated with discrete alterations in DNA methylation. Importantly, inhibiting the enzymes responsible for de novo DNA methylation restored the responsiveness of Apc-deficient intestinal organoids to stimuli regulating the proliferation-to-differentiation transition in ISC. This work reveals that early DNA methylation changes play critical roles in the establishment of the impaired fate decision program consecutive to Apc loss of function. SIGNIFICANCE: This study demonstrates the functional impact of changes in DNA methylation to determine the colorectal cancer cell phenotype following loss of Apc function.
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Affiliation(s)
- Marco Bruschi
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Laure Garnier
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Elouan Cleroux
- UMR 7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, Illkirch, France
| | - Alicia Giordano
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Michael Dumas
- UMR 7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, Illkirch, France
| | - Anaïs F Bardet
- UMR 7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, Illkirch, France
| | - Thomas Kergrohen
- Département de Cancérologie de l'Enfant et de l'Adolescent, Institut de Cancérologie Gustave Roussy, Université Paris-Sud, Université Paris-Saclay, Villejuif Cedex, France
| | - Stanislas Quesada
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Pierre Cesses
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Michael Weber
- UMR 7242 Biotechnology and Cell Signaling, CNRS, University of Strasbourg, Illkirch, France
| | - François Gerbe
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France.
| | - Philippe Jay
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France.
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44
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Kuchay RAH. New insights into the molecular basis of lactase non-persistence/persistence: a brief review. Drug Discov Ther 2020; 14:1-7. [PMID: 32101819 DOI: 10.5582/ddt.2019.01079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Lactose, a disaccharide and main carbohydrate in milk, requires hydrolysis in the intestinal tract to release its monosaccharides galactose and glucose for use as energy source by enterocytes. This hydrolysis is catalyzed by the enzyme lactase, a β-galactosidase located in the brush border membrane of small intestinal enterocytes. In most mammals, lactase activity declines after the weaning, a condition known as lactase non-persistence (LNP). Lactase persistence (LP) is an autosomal dominant trait enabling the continued production of the enzyme lactase throughout adult life. Non-persistence or persistence of lactase expression into adult life being a polymorphic trait has been attributed to various single nucleotide polymorphisms in the enhancer region surrounding lactase gene (LCT). However, latest research has pointed to 'genetic-epigenetic interactions' as key to regulation of lactase expression. LNP and LP DNA haplotypes have demonstrated markedly different epigenetic aging as genetic factors contribute to gradual accumulation of epigenetic changes with age to affect lactase expression. This review will attempt to present an overview of latest insights into molecular basis of LNP/LP including the crucial role of 'genetic-epigenetic interactions' in regulating lactase expression.
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45
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Cheung K, Barter MJ, Falk J, Proctor CJ, Reynard LN, Young DA. Histone ChIP-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity. FASEB J 2020; 34:5317-5331. [PMID: 32058623 PMCID: PMC7187454 DOI: 10.1096/fj.201902061rr] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/27/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022]
Abstract
Epigenetic mechanisms are known to regulate gene expression during chondrogenesis. In this study, we have characterized the epigenome during the in vitro differentiation of human mesenchymal stem cells (hMSCs) into chondrocytes. Chromatin immunoprecipitation followed by next‐generation sequencing (ChIP‐seq) was used to assess a range of N‐terminal posttranscriptional modifications (marks) to histone H3 lysines (H3K4me3, H3K4me1, H3K27ac, H3K27me3, and H3K36me3) in both hMSCs and differentiated chondrocytes. Chromatin states were characterized using histone ChIP‐seq and cis‐regulatory elements were identified in chondrocytes. Chondrocyte enhancers were associated with chondrogenesis‐related gene ontology (GO) terms. In silico analysis and integration of DNA methylation data with chondrogenesis chromatin states revealed that enhancers marked by histone marks H3K4me1 and H3K27ac were de‐methylated during in vitro chondrogenesis. Similarity analysis between hMSC and chondrocyte chromatin states defined in this study with epigenomes of cell‐types defined by the Roadmap Epigenomics project revealed that enhancers are more distinct between cell‐types compared to other chromatin states. Motif analysis revealed that the transcription factor SOX9 is enriched in chondrocyte enhancers. Luciferase reporter assays confirmed that chondrocyte enhancers characterized in this study exhibited enhancer activity which may be modulated by DNA methylation and SOX9 overexpression. Altogether, these integrated data illustrate the cross‐talk between different epigenetic mechanisms during chondrocyte differentiation.
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Affiliation(s)
- Kathleen Cheung
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK.,Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew J Barter
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Julia Falk
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Carole J Proctor
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Louise N Reynard
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
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46
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The microbiota programs DNA methylation to control intestinal homeostasis and inflammation. Nat Microbiol 2020; 5:610-619. [PMID: 32015497 DOI: 10.1038/s41564-019-0659-3] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/11/2019] [Indexed: 12/12/2022]
Abstract
Although much research has been done on the diversity of the gut microbiome, little is known about how it influences intestinal homeostasis under normal and pathogenic conditions. Epigenetic mechanisms have recently been suggested to operate at the interface between the microbiota and the intestinal epithelium. We performed whole-genome bisulfite sequencing on conventionally raised and germ-free mice, and discovered that exposure to commensal microbiota induced localized DNA methylation changes at regulatory elements, which are TET2/3-dependent. This culminated in the activation of a set of 'early sentinel' response genes to maintain intestinal homeostasis. Furthermore, we demonstrated that exposure to the microbiota in dextran sodium sulfate-induced acute inflammation results in profound DNA methylation and chromatin accessibility changes at regulatory elements, leading to alterations in gene expression programs enriched in colitis- and colon-cancer-associated functions. Finally, by employing genetic interventions, we show that microbiota-induced epigenetic programming is necessary for proper intestinal homeostasis in vivo.
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Goto Y, Ibi M, Sato H, Tanaka J, Yasuhara R, Aota K, Azuma M, Fukada T, Mishima K, Irié T. PLAG1 enhances the stemness profiles of acinar cells in normal human salivary glands in a cell type-specific manner. J Oral Biosci 2020; 62:99-106. [PMID: 32007659 DOI: 10.1016/j.job.2020.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/27/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Details of the histogenesis of salivary gland tumors are largely unknown. The oncogenic role of PLAG1 in the salivary gland has been demonstrated in vivo. Herein, we demonstrate PLAG1 roles in the acinar and ductal cells of normal human salivary glands to clarify the early events that occur during the histogenesis of salivary gland tumors. METHODS Normal salivary gland cells with acinar and ductal phenotypes were transfected with PLAG1 plasmid DNA. Subsequently, PLAG1 overexpressed and mock cells were examined by cell proliferation, transwell migration, and salisphere formation assays. Differentiation and salivary and pluripotent stem cell marker expression levels were evaluated by quantitative reverse transcription-polymerase chain reaction and immunofluorescence. Alterations in transcriptional expressions were investigated via cap analysis of gene expression with gene-enrichment and functional annotation analysis. RESULTS PLAG1 promoted cell proliferation and transwell migration in the acinar and ductal cells, and markedly enhanced the stemness profiles and luminal cell-like profiles in acinar cells; the stemness profiles were partially increased in the ductal cells. CONCLUSION PLAG1 enhanced the stemness profiles in the acinar cells of normal human salivary glands in a cell type-specific manner. Thus, it may be involved in salivary gland tumorigenesis by increasing the stemness character of the normal salivary gland cells.
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Affiliation(s)
- Yuriko Goto
- Division of Anatomical and Cellular Pathology, Department of Pathology, Iwate Medical University, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate, 028-3694, Japan
| | - Miho Ibi
- Division of Anatomical and Cellular Pathology, Department of Pathology, Iwate Medical University, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate, 028-3694, Japan
| | - Hirotaka Sato
- Division of Anatomical and Cellular Pathology, Department of Pathology, Iwate Medical University, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate, 028-3694, Japan
| | - Junichi Tanaka
- Division of Pathology, Department of Oral Diagnostic Sciences, School of Dentistry, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Rika Yasuhara
- Division of Pathology, Department of Oral Diagnostic Sciences, School of Dentistry, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Keiko Aota
- Department of Oral Medicine, Tokushima University Graduate School of Biomedical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8504, Japan
| | - Masayuki Azuma
- Department of Oral Medicine, Tokushima University Graduate School of Biomedical Sciences, 3-18-15 Kuramoto-cho, Tokushima, 770-8504, Japan
| | - Toshiyuki Fukada
- Division of Pathology, Department of Oral Diagnostic Sciences, School of Dentistry, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan; Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamabouji, Yamashiro, Tokushima, 770-8055, Japan; RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kenji Mishima
- Division of Pathology, Department of Oral Diagnostic Sciences, School of Dentistry, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Tarou Irié
- Division of Anatomical and Cellular Pathology, Department of Pathology, Iwate Medical University, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate, 028-3694, Japan; Division of Pathology, Department of Oral Diagnostic Sciences, School of Dentistry, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan.
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48
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Liu YL, Guo SG, Xie CY, Niu K, De Jonge H, Wu X. Uridine inhibits the stemness of intestinal stem cells in 3D intestinal organoids and mice. RSC Adv 2020; 10:6377-6387. [PMID: 35496025 PMCID: PMC9049648 DOI: 10.1039/c9ra07742a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
The activity of intestinal stem cells (ISCs) is foremost in maintaining homeostasis and repair of intestines.
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Affiliation(s)
- Yi-Lin Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Region
- Institute of Subtropical Agriculture
- Chinese Academy of Sciences
- Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process
| | - Song-Ge Guo
- Key Laboratory of Agro-ecological Processes in Subtropical Region
- Institute of Subtropical Agriculture
- Chinese Academy of Sciences
- Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process
| | - Chun-yan Xie
- College of Resources and Environment
- College of Bioscience and Biotechnology
- Hunan Agricultural University
- Changsha
- China
| | - Kaimin Niu
- Institute of Biological Resources
- Jiangxi Academy of Sciences
- Nanchang 330096
- China
| | - Hugo De Jonge
- Department of Gastroenterology and Hepatology
- Erasmus MC University Medical Center
- Rotterdam
- Netherlands
| | - Xin Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region
- Institute of Subtropical Agriculture
- Chinese Academy of Sciences
- Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process
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49
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Ghazimoradi MH, Farivar S. The role of DNA demethylation in induction of stem cells. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 153:17-22. [PMID: 31901417 DOI: 10.1016/j.pbiomolbio.2019.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/27/2019] [Accepted: 12/31/2019] [Indexed: 01/03/2023]
Abstract
DNA methylation is an epigenetic factor, which plays important roles in embryo and many other diseases development. This factor determines gene expression, and when half of them have CpG islands, DNA methylation and its enzyme effectors have been under the vast studies. Whole genome DNA demethylation is a crucial step of embryogenesis and also cell fate determination in embryos. Therefore, demethylation agents were used as a tool for dedifferentiation and transdifferentiation. Although many of these efforts have been successful, but using this method gave us a vast spectral cell type which is confusing. In this article, we briefly reviewed DNA methylation, and its role in embryogenesis and gene expression. In addition to that, we introduce studies that used this action as a direct method in induction of stem cells and cell fate decision.
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Affiliation(s)
- Mohammad H Ghazimoradi
- Genetics, Stem Cells, Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983963113, Iran
| | - Shirin Farivar
- Genetics, Stem Cells, Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983963113, Iran.
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50
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Bormann F, Rodríguez-Paredes M, Lasitschka F, Edelmann D, Musch T, Benner A, Bergman Y, Dieter SM, Ball CR, Glimm H, Linhart HG, Lyko F. Cell-of-Origin DNA Methylation Signatures Are Maintained during Colorectal Carcinogenesis. Cell Rep 2019; 23:3407-3418. [PMID: 29898408 DOI: 10.1016/j.celrep.2018.05.045] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/16/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022] Open
Abstract
Colorectal adenomas are precursor lesions of colorectal cancers and represent clonal amplifications of single cells from colonic crypts. DNA methylation patterns specify cell-type identity during cellular differentiation and, therefore, provide opportunities for the molecular analysis of tumors. We have now analyzed DNA methylation patterns in colorectal adenomas and identified three biologically defined subclasses that describe different intestinal crypt differentiation stages. Importantly, colorectal carcinomas could be classified into the same methylation subtypes, reflecting their shared cell types of origin with adenomas. Further data analysis also revealed significantly reduced overall survival for one of the subtypes. Our results provide a concept for understanding the methylation patterns observed in colorectal cancer and provide opportunities for tumor subclassification and patient stratification.
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Affiliation(s)
- Felix Bormann
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Tanja Musch
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, 91120 Jerusalem, Israel
| | - Sebastian M Dieter
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Claudia R Ball
- Department of Translational Medical Oncology, NCT-Dresden and DKFZ Heidelberg, 01307 Dresden, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, NCT-Dresden and DKFZ Heidelberg, 01307 Dresden, Germany; University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Heinz G Linhart
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany; Klinik Lindau, 88131 Lindau, Germany; Department of Gastroenterology, University Hospital Freiburg, 79160 Freiburg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany.
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