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Resource: A Cellular Developmental Taxonomy of the Bone Marrow Mesenchymal Stem Cell Population in Mice. Hemasphere 2023; 7:e823. [PMID: 36741354 PMCID: PMC9891453 DOI: 10.1097/hs9.0000000000000823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/29/2022] [Indexed: 02/03/2023] Open
Abstract
Mesenchymal stem cells (MSCs) play pivotal roles in tissue (re)generation. In the murine bone marrow, they are thought to reside within the Sca-1+ CD51+ bone marrow stromal cell population. Here, using scRNAseq, we aimed to delineate the cellularheterogeneity of this MSC-enriched population throughout development. At the fetal stage, the MSC population is relatively homogeneous with subsets predicted to contain stem/progenitor cells, based on transcriptional modeling and marker expression. These subsets decline in relative size throughout life, with postnatal emergence of specialized clusters, including hematopoietic stem/progenitor cell (HSPC) niches. In fetal development, these stromal HSPC niches are lacking, but subsets of endothelial cells express HSPC factors, suggesting that they may provide initial niches for emerging hematopoiesis. This cellular taxonomy of the MSC population upon development is anticipated to provide a resource aiding the prospective identification of cellular subsets and molecular mechanisms driving bone marrow (re)generation.
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Correa-Gallegos D, Jiang D, Rinkevich Y. Fibroblasts as confederates of the immune system. Immunol Rev 2021; 302:147-162. [PMID: 34036608 DOI: 10.1111/imr.12972] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 12/18/2022]
Abstract
Fibroblastic stromal cells are as diverse, in origin and function, as the niches they fashion in the mammalian body. This cellular variety impacts the spectrum of responses elicited by the immune system. Fibroblast influence on the immune system keeps evolving our perspective on fibroblast roles and functions beyond just a passive structural part of organs. This review discusses the foundations of fibroblastic stromal-immune crosstalk, under the scope of stromal heterogeneity as a basis for tissue-specific tutoring of the immune system. Focusing on the skin as a relevant immunological organ, we detail the complex interactions between distinct fibroblast populations and immune cells that occur during homeostasis, injury repair, scarring, and disease. We further review the relevance of fibroblastic stromal cell heterogeneity and how this heterogeneity is central to regulate the immune system from its inception during embryonic development into adulthood.
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Affiliation(s)
- Donovan Correa-Gallegos
- Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Helmholtz Zentrum München, Munich, Germany
| | - Dongsheng Jiang
- Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Helmholtz Zentrum München, Munich, Germany
| | - Yuval Rinkevich
- Institute of Regenerative Biology and Medicine, Helmholtz Zentrum München, Munich, Germany
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3
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Helbling PM, Piñeiro-Yáñez E, Gerosa R, Boettcher S, Al-Shahrour F, Manz MG, Nombela-Arrieta C. Global Transcriptomic Profiling of the Bone Marrow Stromal Microenvironment during Postnatal Development, Aging, and Inflammation. Cell Rep 2020; 29:3313-3330.e4. [PMID: 31801092 DOI: 10.1016/j.celrep.2019.11.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/03/2019] [Accepted: 10/31/2019] [Indexed: 12/22/2022] Open
Abstract
Bone marrow (BM) stromal cells provide the regulatory framework for hematopoiesis and contribute to developmental stage-specific niches, such as those preserving hematopoietic stem cells. Despite advances in our understanding of stromal function, little is known about the transcriptional changes that this compartment undergoes throughout lifespan and during adaptation to stress. Using RNA sequencing, we perform transcriptional analyses of four principal stromal subsets, namely CXCL12-abundant reticular, platelet-derived growth factor receptor (PDGFR)-α+Sca1+, sinusoidal, and arterial endothelial cells, from early postnatal, adult, and aged mice. Our data reveal (1) molecular fingerprints defining cell-specific anatomical and functional features, (2) a radical reprogramming of pro-hematopoietic, immune, and matrisomic transcriptional programs during the transition from juvenile stages to adulthood, and (3) the aging-driven progressive upregulation of pro-inflammatory gene expression in stroma. We further demonstrate that transcriptomic pathways elicited in vivo by prototypic microbial molecules are largely recapitulated during aging, thereby supporting the inflammatory basis of age-related adaptations of BM hematopoietic function.
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Affiliation(s)
- Patrick M Helbling
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, 8091 Zurich, Switzerland
| | - Elena Piñeiro-Yáñez
- Bioinformatics Unit, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Rahel Gerosa
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, 8091 Zurich, Switzerland
| | - Steffen Boettcher
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, 8091 Zurich, Switzerland
| | - Fátima Al-Shahrour
- Bioinformatics Unit, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, 8091 Zurich, Switzerland
| | - César Nombela-Arrieta
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, 8091 Zurich, Switzerland.
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Balistreri CR, Garagnani P, Madonna R, Vaiserman A, Melino G. Developmental programming of adult haematopoiesis system. Ageing Res Rev 2019; 54:100918. [PMID: 31226498 DOI: 10.1016/j.arr.2019.100918] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/15/2019] [Accepted: 06/17/2019] [Indexed: 12/15/2022]
Abstract
The Barker hypothesis of 'foetal origin of adult diseases' has led to emphasize the concept of 'developmental programming', based on the crucial role of epigenetic factors. Accordingly, it has been demonstrated that parental adversity (before conception and during pregnancy) and foetal factors (i.e., hypoxia, malnutrition and placental insufficiency) permanently modify the physiological systems of the progeny, predisposing them to premature ageing and chronic disease during adulthood. Thus, an altered functionality of the endocrine, immune, nervous and cardiovascular systems is observed in the progeny. However, it remains to be understood whether the haematopoietic system itself also represents a portrait of foetal programming. Here, we provide evidence, reporting and discussing related theories, and results of studies described in the literature. In addition, we have outlined our opinions and suggest how it is possible to intervene to correct foetal mal-programming. Some pro-health interventions and recommendations are proposed, with the hope of guarantee the health of future generations and trying to combat the continuous increase in age-related diseases in human populations.
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Sellers ZP, Bolkun L, Kloczko J, Wojtaszewska ML, Lewandowski K, Moniuszko M, Ratajczak MZ, Schneider G. Increased methylation upstream of the MEG3 promotor is observed in acute myeloid leukemia patients with better overall survival. Clin Epigenetics 2019; 11:50. [PMID: 30876483 PMCID: PMC6419839 DOI: 10.1186/s13148-019-0643-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/28/2019] [Indexed: 12/24/2022] Open
Abstract
Background The delta-like non-canonical Notch ligand 1 (DLK1)-maternally expressed 3(MEG3) locus (DLK1-MEG3 locus) plays a critical role in the maintenance and differentiation of hematopoietic stem cells. Accumulating evidence implicates the imprinted genes from this locus, DLK1 and MEG3, in the development and progression of acute myeloid leukemia (AML). However, the contribution of this locus to the treatment response of patients and their survival is unknown. Methods DNA methylation of select CG dinucleotide-containing amplicons (CpG sites) within the DLK1-MEG3 locus and within differentially methylated regions of other imprinted loci was assessed in the mononuclear cells of 45 AML patients by combined bisulfite restriction analysis. Methylation results were compared with patient response to first-round induction therapy and overall survival. Multivariable analysis was employed to identify independent prognostic factors for patient overall survival in AML. Results Increased methylation at CpG sites within the MEG3 promotor region was observed in AML patients having longer overall survival. In addition, patients with shorter overall survival had increased expression of DLK1 and MEG3, and methylation at the MEG3-DMR CpG site inversely correlated with MEG3 expression. Multivariable analysis revealed that methylation at CG9, a non-imprinted CpG site within the MEG3 promotor region which contains a CCCTC-binding factor (CTCF)-binding DNA sequence, is an independent prognostic factor for the overall survival of AML patients. Conclusions The results of our pilot study underscore the importance of the DLK1-MEG3 locus in AML development and progression. We identify CG9 methylation as an independent prognostic factor for AML patient survival, which suggests that distinct miRNA signatures from the DLK1-MEG3 locus could reflect varying degrees of cell stemness and present novel opportunities for personalized therapies in the future. These data provide a foundation for future studies into the role of higher-order chromatin structure at DLK1-MEG3 in AML. Electronic supplementary material The online version of this article (10.1186/s13148-019-0643-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zachariah Payne Sellers
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Lukasz Bolkun
- Department of Hematology, Medical University of Bialystok, Bialystok, Poland
| | - Janusz Kloczko
- Department of Hematology, Medical University of Bialystok, Bialystok, Poland
| | | | - Krzysztof Lewandowski
- Department of Hematology and Bone Marrow Transplantation, University of Medical Sciences, Poznań, Poland
| | - Marcin Moniuszko
- Department of Allergology, Medical University of Bialystok, Bialystok, Poland.,Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
| | - Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA. .,Department of Regenerative Medicine, Medical University of Warsaw, Warsaw, Poland.
| | - Gabriela Schneider
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA.
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Kikuchi K, Sasaki K, Akizawa H, Tsukahara H, Bai H, Takahashi M, Nambo Y, Hata H, Kawahara M. Identification and expression analysis of cDNA encoding insulin-like growth factor 2 in horses. J Reprod Dev 2018; 64:57-64. [PMID: 29151450 PMCID: PMC5830359 DOI: 10.1262/jrd.2017-124] [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] [Indexed: 11/30/2022] Open
Abstract
Insulin-like growth factor 2 (IGF2) is responsible for a broad range of physiological processes during fetal development and adulthood, but genomic analyses of IGF2 containing the 5ʹ- and
3ʹ-untranslated regions (UTRs) in equines have been limited. In this study, we characterized the IGF2 mRNA containing the UTRs, and determined its expression pattern in the fetal tissues of horses. The
complete equine IGF2 mRNA sequence harboring another exon approximately 2.8 kb upstream from the canonical transcription start site was identified as a new transcript variant. As this upstream exon did
not contain the start codon, the amino acid sequence was identical to the canonical variant. Analysis of the deduced amino acid sequence revealed that the protein possessed two major domains, IlGF and IGF2_C, and
analysis of IGF2 sequence polymorphism in fetal tissues of Hokkaido native horse and Thoroughbreds revealed a single nucleotide polymorphism (T to C transition) at position 398 in Thoroughbreds, which
caused an amino acid substitution at position 133 in the IGF2 sequence. Furthermore, the expression pattern of the IGF2 mRNA in the fetal tissues of horses was determined for the first time, and was
found to be consistent with those of other species. Taken together, these results suggested that the transcriptional and translational products of the IGF2 gene have conserved functions in the fetal
development of mammals, including horses.
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Affiliation(s)
- Kohta Kikuchi
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Keisuke Sasaki
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan.,Present: Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Hiroki Akizawa
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Hayato Tsukahara
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Hanako Bai
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Masashi Takahashi
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Yasuo Nambo
- Equine Science Division, Hidaka Training and Research Center, Japan Racing Association, Hokkaido 057-0171, Japan.,Present: Department of Clinical Veterinary Sciences, Obihiro University of Agriculture and Veterinary Medicine, Hokkaido 080-8555, Japan
| | - Hiroshi Hata
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido 060-0811, Japan
| | - Manabu Kawahara
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
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Xing LB, Gao YT. Progress in research of surface markers of liver cancer stem cells. Shijie Huaren Xiaohua Zazhi 2016; 24:4231-4237. [DOI: 10.11569/wcjd.v24.i31.4231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In recent years, cancer stem cell theory, in which a tumor is considered to consist of a handful of tumor stem cells and most common tumor cells, has been put forward by many scientists, which helps researchers to understand cancer from a new perspective. Isolating tumor stem cells is based mainly on their markers and in this way, many kinds of cancer stem cell markers have been confirmed, including live cancer stem cells. Isolating and identifying live cancer stem cells will provide a new hope for curing cancer. This paper mainly discusses seven liver cancer stem cell surface markers and their clinical significance.
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Swanzey E, Stadtfeld M. A reporter model to visualize imprinting stability at the Dlk1 locus during mouse development and in pluripotent cells. Development 2016; 143:4161-4166. [PMID: 27729406 PMCID: PMC5117214 DOI: 10.1242/dev.138255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/29/2016] [Indexed: 12/15/2022]
Abstract
Genomic imprinting results in the monoallelic expression of genes that encode important regulators of growth and proliferation. Dysregulation of imprinted genes, such as those within the Dlk1-Dio3 locus, is associated with developmental syndromes and specific diseases. Our ability to interrogate causes of imprinting instability has been hindered by the absence of suitable model systems. Here, we describe a Dlk1 knock-in reporter mouse that enables single-cell visualization of allele-specific expression and prospective isolation of cells, simultaneously. We show that this ‘imprinting reporter mouse’ can be used to detect tissue-specific Dlk1 expression patterns in developing embryos. We also apply this system to pluripotent cell culture and demonstrate that it faithfully indicates DNA methylation changes induced upon cellular reprogramming. Finally, the reporter system reveals the role of elevated oxygen levels in eroding imprinted Dlk1 expression during prolonged culture and in vitro differentiation. The possibility to study allele-specific expression in different contexts makes our reporter system a useful tool to dissect the regulation of genomic imprinting in normal development and disease. Summary: A Dlk1 knock-in reporter mouse reports allele- and tissue-specific Dlk1 expression in developing embryos that can be used to study changes in genomic imprinting during cellular reprogramming.
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Affiliation(s)
- Emily Swanzey
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Matthias Stadtfeld
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
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9
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Schneider G, Sellers ZP, Ratajczak MZ. Parentally imprinted genes regulate hematopoiesis-new evidence from the Dlk1-Gtl2 locus. Stem Cell Investig 2016; 3:29. [PMID: 27580759 DOI: 10.21037/sci.2016.06.09] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/06/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Gabriela Schneider
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Zachariah Payne Sellers
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA;; Department of Regenerative Medicine, Medical University of Warsaw, Warsaw, Poland
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10
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Thomas DD, Sommer AG, Balazs AB, Beerman I, Murphy GJ, Rossi D, Mostoslavsky G. Insulin-like growth factor 2 modulates murine hematopoietic stem cell maintenance through upregulation of p57. Exp Hematol 2016; 44:422-433.e1. [PMID: 26872540 DOI: 10.1016/j.exphem.2016.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/29/2016] [Accepted: 01/31/2016] [Indexed: 01/12/2023]
Abstract
Hematopoietic stem cells (HSC) rely on a highly regulated molecular network to balance self-renewal and lineage specification to sustain life-long hematopoiesis. Despite a plethora of studies aimed at identifying molecules governing HSC fate, our current knowledge of the genes responsible is limited. We have found insulin-like growth factor 2 (IGF2) to be expressed predominantly within long-term HSCs. This study examines IGF2 expression patterns and the effects of the gene in HSCs. Through the overexpression and knockdown of IGF2 within purified HSCs, we report that IGF2 expression increases HSC-derived multilineage colonies in vitro and enhances hematopoietic contribution in vivo on competitive bone marrow transplantation. The effects of IGF2 are mediated by direct upregulation of the CDKi p57, exclusively within long-term HSCs, via activation of the PI3K-Akt pathway. Increased expression of p57 resulted in a concomitant increase in HSCs in the G0/G1 stage of the cell cycle. Analysis of genomic DNA methylation revealed that HSCs exhibited a hypomethylated state within the promoter region of the CDKN1C (p57) gene, providing a potential mechanism for the exclusive effects of IGF2 within HSCs. Our studies indicate a novel role for IGF2 in regulating HSC cell cycle and illustrate potential novel therapeutic targets for hematologic diseases.
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Affiliation(s)
- Dolly D Thomas
- Section of Gastroenterology, Department of Medicine, Boston University School of Medicine, Boston, MA; Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, Boston, MA
| | - Andreia Gianotti Sommer
- Section of Gastroenterology, Department of Medicine, Boston University School of Medicine, Boston, MA; Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, Boston, MA
| | | | - Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard Medical School, Boston, MA
| | - George J Murphy
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, Boston, MA
| | - Derrick Rossi
- Department of Stem Cell and Regenerative Biology, Harvard Medical School, Boston, MA
| | - Gustavo Mostoslavsky
- Section of Gastroenterology, Department of Medicine, Boston University School of Medicine, Boston, MA; Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, Boston, MA.
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Ogawa H, Takyu R, Morimoto H, Toei S, Sakon H, Goto S, Moriya S, Kono T. Cell proliferation potency is independent of FGF4 signaling in trophoblast stem cells derived from androgenetic embryos. J Reprod Dev 2015; 62:51-8. [PMID: 26498204 PMCID: PMC4768778 DOI: 10.1262/jrd.2015-097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously established trophoblast stem cells from mouse androgenetic embryos (AGTS cells). In this study, to further characterize AGTS cells, we compared cell proliferation activity between trophoblast stem (TS) cells and AGTS cells under fibroblast growth factor 4 (FGF4) signaling. TS cells continued to proliferate and maintained mitotic cell division in the presence of FGF4. After FGF4 deprivation, the cell proliferation stopped, the rate of M-phase cells decreased, and trophoblast giant cells formed. In contrast, some of AGTS cells continued to proliferate, and the rate of M-phase cells did not decrease after FGF4 deprivation, although the other cells differentiated into giant cells. RO3306, an ATP competitor that selectively inhibits CDK1, inhibited the cell proliferation of both TS and AGTS cells. Under RO3306 treatment, cell death was induced in AGTS cells but not in TS cells. These results indicate that RO3306 caused TS cells to shift mitotic cell division to endoreduplication but that some of AGTS cells did not shift to endoreduplication and induced cell death. In conclusion, the paternal genome facilitated the proliferation of trophoblast cells without FGF4 signaling.
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Affiliation(s)
- Hidehiko Ogawa
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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12
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Imprinted genes in myeloid lineage commitment in normal and malignant hematopoiesis. Leukemia 2015; 29:1233-42. [PMID: 25703588 DOI: 10.1038/leu.2015.47] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 01/27/2015] [Accepted: 02/16/2015] [Indexed: 12/12/2022]
Abstract
Genomic imprinting is characterized by the parent-of-origin monoallelic expression of several diploid genes because of epigenetic regulation. Imprinted genes (IGs) are key factors in development, supporting the ability of a genotype to produce phenotypes in response to environmental stimuli. IGs are highly expressed during prenatal stages but are downregulated after birth. They also affect aspects of life other than growth such as cognition, behavior, adaption to novel environments, social dominance and memory consolidation. Deregulated genomic imprinting leads to developmental disorders and is associated with solid and blood cancer as well. Several data have been published highlighting the involvement of IGs in as early as the very small embryonic-like stem cells stage and further during myeloid lineage commitment in normal and malignant hematopoiesis. Therefore, we have assembled the current knowledge on the topic, based mainly on recent findings, trying not to focus on a particular cluster but rather to have a global view of several different IGs in hematopoiesis.
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Delta-Like Homologue 1 and Its Role in the Bone Marrow Niche and Hematologic Malignancies. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2014; 14:451-5. [DOI: 10.1016/j.clml.2014.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/08/2014] [Accepted: 06/17/2014] [Indexed: 01/08/2023]
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14
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Wei Y, Su J, Liu H, Lv J, Wang F, Yan H, Wen Y, Liu H, Wu Q, Zhang Y. MetaImprint: an information repository of mammalian imprinted genes. Development 2014; 141:2516-23. [DOI: 10.1242/dev.105320] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genomic imprinting is a complex genetic and epigenetic phenomenon that plays important roles in mammalian development and diseases. Mammalian imprinted genes have been identified widely by experimental strategies or predicted using computational methods. Systematic information for these genes would be necessary for the identification of novel imprinted genes and the analysis of their regulatory mechanisms and functions. Here, a well-designed information repository, MetaImprint (http://bioinfo.hrbmu.edu.cn/MetaImprint), is presented, which focuses on the collection of information concerning mammalian imprinted genes. The current version of MetaImprint incorporates 539 imprinted genes, including 255 experimentally confirmed genes, and their detailed research courses from eight mammalian species. MetaImprint also hosts genome-wide genetic and epigenetic information of imprinted genes, including imprinting control regions, single nucleotide polymorphisms, non-coding RNAs, DNA methylation and histone modifications. Information related to human diseases and functional annotation was also integrated into MetaImprint. To facilitate data extraction, MetaImprint supports multiple search options, such as by gene ID and disease name. Moreover, a configurable Imprinted Gene Browser was developed to visualize the information on imprinted genes in a genomic context. In addition, an Epigenetic Changes Analysis Tool is provided for online analysis of DNA methylation and histone modification differences of imprinted genes among multiple tissues and cell types. MetaImprint provides a comprehensive information repository of imprinted genes, allowing researchers to investigate systematically the genetic and epigenetic regulatory mechanisms of imprinted genes and their functions in development and diseases.
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Affiliation(s)
- Yanjun Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jianzhong Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hongbo Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Jie Lv
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Fang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Haidan Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yanhua Wen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hui Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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Khan QES, Sehic A, Skalleberg N, Landin MA, Khuu C, Risnes S, Osmundsen H. Expression of delta-like 1 homologue and insulin-like growth factor 2 through epigenetic regulation of the genes during development of mouse molar. Eur J Oral Sci 2013; 120:292-302. [PMID: 22813219 DOI: 10.1111/j.1600-0722.2012.00976.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Delta-like 1 homolog (Dlk1) and insulin-like growth factor 2 (Igf2) are two of six well-studied mouse imprinted gene clusters that are paternally expressed. Their expression is also linked to their maternally expressed non-coding RNAs, encoded by Gene trap locus 2 (Gtl2) and Imprinted maternally expressed transcript (H19), co-located as imprinted gene clusters. Using deoxyoligonucleotide microarrays and real-time RT-PCR analysis we showed Dlk1 and Gtl2 to exhibit a time-course of expression during tooth development that was similar to that of Igf2 and H19. Western blot analysis of proteins encoded by Dlk1 and Igf2 suggested that the levels of these proteins reflected those of the corresponding mRNAs. Immunohistochemical studies of DLK1 in murine molars detected the protein in both epithelial and mesenchymal regions, in developing cusp mesenchyme, and in newly synthesized enamel and dentin tubules. IGF2 protein was detected primarily at prenatal stages, suggesting that it may be active before birth. Analysis of methylation of cytosine-phosphate-guanine (CpG) islands in both Dlk1 and Igf2 suggested the presence of an increasing fraction of hypermethylated bases with increasing time of development. The increased levels of hypermethylation coincided both with the diminished levels of expression of Dlk1 and Igf2 and with decreased levels of DLK1 and IGF2 proteins in the tooth germ, suggesting that their expression is regulated via methylation of CpG islands present in these genes.
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Berg JS, Lin KK, Sonnet C, Boles NC, Weksberg DC, Nguyen H, Holt LJ, Rickwood D, Daly RJ, Goodell MA. Imprinted genes that regulate early mammalian growth are coexpressed in somatic stem cells. PLoS One 2011; 6:e26410. [PMID: 22039481 PMCID: PMC3198398 DOI: 10.1371/journal.pone.0026410] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 09/26/2011] [Indexed: 01/21/2023] Open
Abstract
Lifelong, many somatic tissues are replenished by specialized adult stem cells. These stem cells are generally rare, infrequently dividing, occupy a unique niche, and can rapidly respond to injury to maintain a steady tissue size. Despite these commonalities, few shared regulatory mechanisms have been identified. Here, we scrutinized data comparing genes expressed in murine long-term hematopoietic stem cells with their differentiated counterparts and observed that a disproportionate number were members of the developmentally-important, monoallelically expressed imprinted genes. Studying a subset, which are members of a purported imprinted gene network (IGN), we found their expression in HSCs rapidly altered upon hematopoietic perturbations. These imprinted genes were also predominantly expressed in stem/progenitor cells of the adult epidermis and skeletal muscle in mice, relative to their differentiated counterparts. The parallel down-regulation of these genes postnatally in response to proliferation and differentiation suggests that the IGN could play a mechanistic role in both cell growth and tissue homeostasis.
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Affiliation(s)
- Jonathan S. Berg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kuanyin K. Lin
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Corinne Sonnet
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nathan C. Boles
- Interdepartmental Program of Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - David C. Weksberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hoang Nguyen
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lowenna J. Holt
- Diabetes and Obesity Research Program, Garvan Institute of Medical Research, Sydney, Australia
| | - Danny Rickwood
- Cancer Research Program, Garvan Institute of Medical Research, Sydney, Australia
| | - Roger J. Daly
- Cancer Research Program, Garvan Institute of Medical Research, Sydney, Australia
| | - Margaret A. Goodell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, United States of America
- Interdepartmental Program of Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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Christodoulou C, Longmire TA, Shen SS, Bourdon A, Sommer CA, Gadue P, Spira A, Gouon-Evans V, Murphy GJ, Mostoslavsky G, Kotton DN. Mouse ES and iPS cells can form similar definitive endoderm despite differences in imprinted genes. J Clin Invest 2011; 121:2313-25. [PMID: 21537085 DOI: 10.1172/jci43853] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 03/08/2011] [Indexed: 11/17/2022] Open
Abstract
The directed differentiation of iPS and ES cells into definitive endoderm (DE) would allow the derivation of otherwise inaccessible progenitors for endodermal tissues. However, a global comparison of the relative equivalency of DE derived from iPS and ES populations has not been performed. Recent reports of molecular differences between iPS and ES cells have raised uncertainty as to whether iPS cells could generate autologous endodermal lineages in vitro. Here, we show that both mouse iPS and parental ES cells exhibited highly similar in vitro capacity to undergo directed differentiation into DE progenitors. With few exceptions, both cell types displayed similar surges in gene expression of specific master transcriptional regulators and global transcriptomes that define the developmental milestones of DE differentiation. Microarray analysis showed considerable overlap between the genetic programs of DE derived from ES/iPS cells in vitro and authentic DE from mouse embryos in vivo. Intriguingly, iPS cells exhibited aberrant silencing of imprinted genes known to participate in endoderm differentiation, yet retained a robust ability to differentiate into DE. Our results show that, despite some molecular differences, iPS cells can be efficiently differentiated into DE precursors, reinforcing their potential for development of cell-based therapies for diseased endoderm-derived tissues.
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Affiliation(s)
- Constantina Christodoulou
- Boston University Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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