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Harmoush B, Viebahn C, Tsikolia N. Development of node architecture and emergence of molecular organizer characteristics in the pig embryo. Dev Dyn 2024. [PMID: 38733144 DOI: 10.1002/dvdy.715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/17/2024] [Accepted: 03/30/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND The avian node is the equivalent of the amphibian Spemann's organizer, as indicated by its ability to induce a secondary axis, cellular contribution, and gene expression, whereas the node of the mouse, which displays limited inductive capacities, was suggested to be a part of spatially distributed signaling. Furthermore, the structural identity of the mouse node is subject of controversy, while little is known about equivalent structures in other mammals. RESULTS We analyzed the node and emerging organizer in the pig using morphology and the expression of selected organizer genes prior to and during gastrulation. The node was defined according to the "four-quarter model" based on comparative consideration. The node of the pig displays a multilayered, dense structure that includes columnar epithelium, bottle-like cells in the dorsal part, and mesenchymal cells ventrally. Expression of goosecoid (gsc), chordin, and brachyury, together with morphology, reveal the consecutive emergence of three distinct domains: the gastrulation precursor domain, the presumptive node, and the mature node. Additionally, gsc displays a ventral expression domain prior to epiblast epithelialization. CONCLUSION Our study defines the morphological and molecular context of the emerging organizer equivalent in the pig and suggests a sequential development of its function.
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Affiliation(s)
- Braah Harmoush
- Institute of Anatomy and Cell Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Christoph Viebahn
- Institute of Anatomy and Cell Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Nikoloz Tsikolia
- Institute of Anatomy and Cell Biology, University Medical Centre Göttingen, Göttingen, Germany
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2
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Rüegg AB, van der Weijden VA, de Sousa JA, von Meyenn F, Pausch H, Ulbrich SE. Developmental progression continues during embryonic diapause in the roe deer. Commun Biol 2024; 7:270. [PMID: 38443549 PMCID: PMC10914810 DOI: 10.1038/s42003-024-05944-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
Embryonic diapause in mammals is a temporary developmental delay occurring at the blastocyst stage. In contrast to other diapausing species displaying a full arrest, the blastocyst of the European roe deer (Capreolus capreolus) proliferates continuously and displays considerable morphological changes in the inner cell mass. We hypothesised that developmental progression also continues during this period. Here we evaluate the mRNA abundance of developmental marker genes in embryos during diapause and elongation. Our results show that morphological rearrangements of the epiblast during diapause correlate with gene expression patterns and changes in cell polarity. Immunohistochemical staining further supports these findings. Primitive endoderm formation occurs during diapause in embryos composed of around 3,000 cells. Gastrulation coincides with elongation and thus takes place after embryo reactivation. The slow developmental progression makes the roe deer an interesting model for unravelling the link between proliferation and differentiation and requirements for embryo survival.
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Affiliation(s)
- Anna B Rüegg
- ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland
| | - Vera A van der Weijden
- ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - João Agostinho de Sousa
- ETH Zurich, Laboratory of Nutrition and Metabolic Epigenetics, Institute of Food, Nutrition and Health, Zurich, Switzerland
| | - Ferdinand von Meyenn
- ETH Zurich, Laboratory of Nutrition and Metabolic Epigenetics, Institute of Food, Nutrition and Health, Zurich, Switzerland
| | - Hubert Pausch
- ETH Zurich, Animal Genomics, Institute of Agricultural Sciences, Zurich, Switzerland
| | - Susanne E Ulbrich
- ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland.
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3
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Nakanoh S, Sham K, Ghimire S, Mohorianu I, Rayon T, Vallier L. Human surface ectoderm and amniotic ectoderm are sequentially specified according to cellular density. SCIENCE ADVANCES 2024; 10:eadh7748. [PMID: 38427729 PMCID: PMC10906920 DOI: 10.1126/sciadv.adh7748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024]
Abstract
Mechanisms specifying amniotic ectoderm and surface ectoderm are unresolved in humans due to their close similarities in expression patterns and signal requirements. This lack of knowledge hinders the development of protocols to accurately model human embryogenesis. Here, we developed a human pluripotent stem cell model to investigate the divergence between amniotic and surface ectoderms. In the established culture system, cells differentiated into functional amnioblast-like cells. Single-cell RNA sequencing analyses of amnioblast differentiation revealed an intermediate cell state with enhanced surface ectoderm gene expression. Furthermore, when the differentiation started at the confluent condition, cells retained the expression profile of surface ectoderm. Collectively, we propose that human amniotic ectoderm and surface ectoderm are specified along a common nonneural ectoderm trajectory based on cell density. Our culture system also generated extraembryonic mesoderm-like cells from the primed pluripotent state. Together, this study provides an integrative understanding of the human nonneural ectoderm development and a model for embryonic and extraembryonic human development around gastrulation.
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Affiliation(s)
- Shota Nakanoh
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge CB22 3AT, UK
| | - Kendig Sham
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Sabitri Ghimire
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Teresa Rayon
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge CB22 3AT, UK
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
- Berlin Institute of Health Centre for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany
- Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
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4
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Lozovska A, Nóvoa A, Kuo YY, Jurberg AD, Martins GG, Hadjantonakis AK, Mallo M. Tgfbr1 regulates lateral plate mesoderm and endoderm reorganization during the trunk to tail transition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554351. [PMID: 37662386 PMCID: PMC10473653 DOI: 10.1101/2023.08.22.554351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
During the trunk to tail transition the mammalian embryo builds the outlets for the intestinal and urogenital tracts, lays down the primordia for the hindlimb and external genitalia, and switches from the epiblast/primitive streak to the tailbud as the driver of axial extension. Genetic and molecular data indicate that Tgfbr1 is a key regulator of the trunk to tail transition. Tgfbr1 has been shown to control the switch of the neuro mesodermal-competent cells from the epiblast to the chordo-neural hinge to generate the tail bud. We now show that Tgfbr1 signaling also controls the remodeling of the lateral plate mesoderm (LPM) and of the embryonic endoderm associated with the trunk to tail transition. In the absence of Tgfbr1 the two LPM layers do not converge at the end of the trunk, extending instead as separate layers enclosing the celomic cavity until the caudal embryonic extremity, and failing to activate markers of primordia for the hindlimb and external genitalia. However, this extended LPM, does not exhibit the molecular signatures characteristic of this tissue in the trunk. The vascular remodeling involving the dorsal aorta and the umbilical artery leading to the connection between embryonic and extraembryonic circulation was also affected in the Tgfbr1 mutant embryos. Similar alterations in the LPM and vascular system were also observed in Isl1 null mutants, indicating that this factor acts in the regulatory cascade downstream of Tgfbr1 in LPM-derived tissues. In addition, in the absence of Tgfbr1 the embryonic endoderm fails to expand to form the endodermal cloaca and to extend posteriorly to generate the tail gut. We present evidence suggesting that the remodeling activity of Tgfbr1 in the LPM and endoderm results from the control of the posterior primitive streak fate after its regression during the trunk to tail transition. Our data, together with previously reported observations, place Tgfbr1 at the top of the regulatory processes controlling the trunk to tail transition.
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5
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Nikaido M, Shirai A, Mizumaki Y, Shigenobu S, Ueno N, Hatta K. Intestinal expression patterns of transcription factors and markers for interstitial cells in the larval zebrafish. Dev Growth Differ 2023; 65:418-428. [PMID: 37452633 DOI: 10.1111/dgd.12878] [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: 04/11/2023] [Revised: 06/26/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
For the digestion of food, it is important for the gut to be differentiated regionally and to have proper motor control. However, the number of transcription factors that regulate its development is still limited. Meanwhile, the interstitial cells of the gastrointestinal (GI) tract are necessary for intestinal motility in addition to the enteric nervous system. There are anoctamine1 (Ano1)-positive and platelet-derived growth factor receptor α (Pdgfra)-positive interstitial cells in mammal, but Pdgfra-positive cells have not been reported in the zebrafish. To identify new transcription factors involved in GI tract development, we used RNA sequencing comparing between larval and adult gut. We isolated 40 transcription factors that were more highly expressed in the larval gut. We demonstrated expression patterns of the 13 genes, 7 of which were newly found to be expressed in the zebrafish larval gut. Six of the 13 genes encode nuclear receptors. The osr2 is expressed in the anterior part, while foxP4 in its distal part. Also, we reported the expression pattern of pdgfra for the first time in the larval zebrafish gut. Our data provide fundamental knowledge for studying vertebrate gut regionalization and motility by live imaging using zebrafish.
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Affiliation(s)
| | - Ayaka Shirai
- School of Science, University of Hyogo, Ako-gun, Japan
| | | | - Shuji Shigenobu
- Trans-Scale Biology Center, National Institute for Basic Biology, Okazaki, Japan
| | - Naoto Ueno
- Trans-Scale Biology Center, National Institute for Basic Biology, Okazaki, Japan
- Unit of Quantitative and Imaging Biology, International Research Collaboration Center, National Institute of Natural Sciences, Okazaki, Japan
| | - Kohei Hatta
- Graduate School of Science, University of Hyogo, Ako-gun, Japan
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6
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Abstract
The midbrain dopamine (mDA) system is composed of molecularly and functionally distinct neuron subtypes that mediate specific behaviours and are linked to various brain diseases. Considerable progress has been made in identifying mDA neuron subtypes, and recent work has begun to unveil how these neuronal subtypes develop and organize into functional brain structures. This progress is important for further understanding the disparate physiological functions of mDA neurons and their selective vulnerability in disease, and will ultimately accelerate therapy development. This Review discusses recent advances in our understanding of molecularly defined mDA neuron subtypes and their circuits, ranging from early developmental events, such as neuron migration and axon guidance, to their wiring and function, and future implications for therapeutic strategies.
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7
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Dupont C, Schäffers OJ, Tan BF, Merzouk S, Bindels EM, Zwijsen A, Huylebroeck D, Gribnau J. Efficient generation of ETX embryoids that recapitulate the entire window of murine egg cylinder development. SCIENCE ADVANCES 2023; 9:eadd2913. [PMID: 36652512 PMCID: PMC9848479 DOI: 10.1126/sciadv.add2913] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
The murine embryonic-trophoblast-extra-embryonic endoderm (ETX) model is an integrated stem cell-based model to study early postimplantation development. It is based on the self-assembly potential of embryonic, trophoblast, and hypoblast/primitive/visceral endoderm-type stem cell lines (ESC, TSC, and XEN, respectively) to arrange into postimplantation egg cylinder-like embryoids. Here, we provide an optimized method for reliable and efficient generation of ETX embryoids that develop into late gastrulation in static culture conditions. It is based on transgenic Gata6-overproducing ESCs and modified assembly and culture conditions. Using this method, up to 43% of assembled ETX embryoids exhibited a correct spatial distribution of the three stem cell derivatives at day 4 of culture. Of those, 40% progressed into ETX embryoids that both transcriptionally and morphologically faithfully mimicked in vivo postimplantation mouse development between E5.5 and E7.5. The ETX model system offers the opportunity to study the murine postimplantation egg cylinder stages and could serve as a source of various cell lineage precursors.
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Affiliation(s)
- Cathérine Dupont
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Olivier J. M. Schäffers
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Obstetrics and Fetal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Beatrice F. Tan
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Sarra Merzouk
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Eric M. Bindels
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - An Zwijsen
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
- Oncode Institute, Erasmus University Medical Center, Rotterdam, Netherlands
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8
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Wesley CC, Levy DL. Differentiation-dependent changes in lamin B1 dynamics and lamin B receptor localization. Mol Biol Cell 2023; 34:ar10. [PMID: 36598800 PMCID: PMC9930530 DOI: 10.1091/mbc.e22-04-0137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The nuclear lamina serves important roles in chromatin organization and structural support, and lamina mutations can result in laminopathies. Less is known about how nuclear lamina structure changes during cellular differentiation-changes that may influence gene regulation. We examined the structure and dynamics of the nuclear lamina in human-induced pluripotent stem cells (iPSCs) and differentiated germ layer cells, focusing on lamin B1. We report that lamin B1 dynamics generally increase as iPSCs differentiate, especially in mesoderm and ectoderm, and that lamin B receptor (LBR) partially redistributes from the nucleus to cytoplasm in mesoderm. Knocking down LBR in iPSCs led to an increase in lamin B1 dynamics, a change that was not observed for ELYS, emerin, or lamin B2 knockdown. LBR knockdown also affected expression of differentiation markers. These data suggest that differentiation-dependent tethering of lamin B1 either directly by LBR or indirectly via LBR-chromatin associations impacts gene expression.
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Affiliation(s)
- Chase C. Wesley
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
| | - Daniel L. Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071,*Address correspondence to: Daniel L. Levy ()
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9
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Developmental cell fate choice in neural tube progenitors employs two distinct cis-regulatory strategies. Dev Cell 2023; 58:3-17.e8. [PMID: 36516856 PMCID: PMC7614300 DOI: 10.1016/j.devcel.2022.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/10/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Abstract
In many developing tissues, the patterns of gene expression that assign cell fate are organized by graded secreted signals. Cis-regulatory elements (CREs) interpret these signals to control gene expression, but how this is accomplished remains poorly understood. In the neural tube, a gradient of the morphogen sonic hedgehog (Shh) patterns neural progenitors. We identify two distinct ways in which CREs translate graded Shh into differential gene expression in mouse neural progenitors. In most progenitors, a common set of CREs control gene activity by integrating cell-type-specific inputs. By contrast, the most ventral progenitors use a unique set of CREs, established by the pioneer factor FOXA2. This parallels the role of FOXA2 in endoderm, where FOXA2 binds some of the same sites. Together, the data identify distinct cis-regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for FOXA2 across tissues.
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10
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Crompton LA, McComish SF, Steward TGJ, Whitcomb DJ, Lane JD, Caldwell MA. Human stem cell-derived ventral midbrain astrocytes exhibit a region-specific secretory profile. Brain Commun 2023; 5:fcad114. [PMID: 37124945 PMCID: PMC10146926 DOI: 10.1093/braincomms/fcad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 11/30/2022] [Accepted: 04/12/2023] [Indexed: 05/02/2023] Open
Abstract
This scientific commentary refers to 'Human stem cell-derived astrocytes exhibit region-specific heterogeneity in their secretory profiles', by Clarke et al. (https://doi.org/10.1093/brain/awaa258) in Brain.
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Affiliation(s)
- Lucy A Crompton
- Correspondence to: Lucy A. Crompton, Department of Applied Sciences, Centre for Research in Biosciences, University of the West of England, Frenchay Campus, Coldharbour Lane, Bristol, UK, BS16 1QY, UK. E-mail:
| | - Sarah F McComish
- Department of Physiology and Trinity College Institute for Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Tom G J Steward
- Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol BS1 3NY, UK
| | - Daniel J Whitcomb
- Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol BS1 3NY, UK
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11
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Transcription networks in liver development and acute liver failure. LIVER RESEARCH 2022. [DOI: 10.1016/j.livres.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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12
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Lin Y, Wang D, Zeng Y. A Maverick Review of Common Stem/Progenitor Markers in Lung Development. Stem Cell Rev Rep 2022; 18:2629-2645. [DOI: 10.1007/s12015-022-10422-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2022] [Indexed: 10/16/2022]
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13
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Pancreatic Transdifferentiation Using β-Cell Transcription Factors for Type 1 Diabetes Treatment. Cells 2022; 11:cells11142145. [PMID: 35883588 PMCID: PMC9315695 DOI: 10.3390/cells11142145] [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: 05/16/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 01/25/2023] Open
Abstract
Type 1 diabetes is a chronic illness in which the native beta (β)-cell population responsible for insulin release has been the subject of autoimmune destruction. This condition requires patients to frequently measure their blood glucose concentration and administer multiple daily exogenous insulin injections accordingly. Current treatments fail to effectively treat the disease without significant side effects, and this has led to the exploration of different approaches for its treatment. Gene therapy and the use of viral vectors has been explored extensively and has been successful in treating a range of diseases. The use of viral vectors to deliver β-cell transcription factors has been researched in the context of type 1 diabetes to induce the pancreatic transdifferentiation of cells to replace the β-cell population destroyed in patients. Studies have used various combinations of pancreatic and β-cell transcription factors in order to induce pancreatic transdifferentiation and have achieved varying levels of success. This review will outline why pancreatic transcription factors have been utilised and how their application can allow the development of insulin-producing cells from non β-cells and potentially act as a cure for type 1 diabetes.
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14
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de Lemos L, Dias A, Nóvoa A, Mallo M. Epha1 is a cell-surface marker for the neuromesodermal competent population. Development 2022; 149:274735. [DOI: 10.1242/dev.198812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/02/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The vertebrate body is built during embryonic development by the sequential addition of new tissue as the embryo grows at its caudal end. During this process, progenitor cells within the neuromesodermal competent (NMC) region generate the postcranial neural tube and paraxial mesoderm. Here, we have applied a genetic strategy to recover the NMC cell population from mouse embryonic tissues and have searched their transcriptome for cell-surface markers that would give access to these cells without previous genetic modifications. We found that Epha1 expression is restricted to the axial progenitor-containing areas of the mouse embryo. Epha1-positive cells isolated from the mouse tailbud generate neural and mesodermal derivatives when cultured in vitro. This observation, together with their enrichment in the Sox2+/Tbxt+ molecular phenotype, indicates a direct association between Epha1 and the NMC population. Additional analyses suggest that tailbud cells expressing low Epha1 levels might also contain notochord progenitors, and that high Epha1 expression might be associated with progenitors entering paraxial mesoderm differentiation. Epha1 could thus be a valuable cell-surface marker for labeling and recovering physiologically active axial progenitors from embryonic tissues.
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Affiliation(s)
- Luisa de Lemos
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - André Dias
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Ana Nóvoa
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Moisés Mallo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
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15
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Ni A, Ernst C. Evidence That Substantia Nigra Pars Compacta Dopaminergic Neurons Are Selectively Vulnerable to Oxidative Stress Because They Are Highly Metabolically Active. Front Cell Neurosci 2022; 16:826193. [PMID: 35308118 PMCID: PMC8931026 DOI: 10.3389/fncel.2022.826193] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/28/2022] [Indexed: 12/21/2022] Open
Abstract
There are 400–500 thousand dopaminergic cells within each side of the human substantia nigra pars compacta (SNpc) making them a minuscule portion of total brain mass. These tiny clusters of cells have an outsized impact on motor output and behavior as seen in disorders such as Parkinson’s disease (PD). SNpc dopaminergic neurons are more vulnerable to oxidative stress compared to other brain cell types, but the reasons for this are not precisely known. Here we provide evidence to support the hypothesis that this selective vulnerability is because SNpc neurons sustain high metabolic rates compared to other neurons. A higher baseline requirement for ATP production may lead to a selective vulnerability to impairments in oxidative phosphorylation (OXPHOS) or genetic insults that impair Complex I of the electron transport chain. We suggest that the energy demands of the unique morphological and electrophysiological properties of SNpc neurons may be one reason these cells produce more ATP than other cells. We further provide evidence to support the hypothesis that transcription factors (TFs) required to drive induction, differentiation, and maintenance of midbrain dopaminergic neural progenitor cells which give rise to terminally differentiated SNpc neurons are uniquely involved in both developmental patterning and metabolism, a dual function unlike other TFs that program neurons in other brain regions. The use of these TFs during induction and differentiation may program ventral midbrain progenitor cells metabolically to higher ATP levels, allowing for the development of those specialized cell processes seen in terminally differentiated cells. This paper provides a cellular and developmental framework for understanding the selective vulnerability of SNpc dopaminergic cells to oxidative stress.
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16
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Sharma K, Asp NT, Harrison SP, Siller R, Baumgarten SF, Gupta S, Chollet ME, Andersen E, Sullivan GJ, Simonsen A. Autophagy modulates cell fate decisions during lineage commitment. Autophagy 2021; 18:1915-1931. [PMID: 34923909 PMCID: PMC9450964 DOI: 10.1080/15548627.2021.2008691] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Early events during development leading to exit from a pluripotent state and commitment toward a specific germ layer still need in depth understanding. Autophagy has been shown to play a crucial role in both development and differentiation. This study employs human embryonic and induced pluripotent stem cells to understand the early events of lineage commitment with respect to the role of autophagy in this process. Our data indicate that a dip in autophagy facilitates exit from pluripotency. Upon exit, we demonstrate that the modulation of autophagy affects SOX2 levels and lineage commitment, with induction of autophagy promoting SOX2 degradation and mesendoderm formation, whereas inhibition of autophagy causes SOX2 accumulation and neuroectoderm formation. Thus, our results indicate that autophagy-mediated SOX2 turnover is a determining factor for lineage commitment. These findings will deepen our understanding of development and lead to improved methods to derive different lineages and cell types.Abbreviations: ACTB: Actin, beta; ATG: Autophagy-related; BafA1: Bafilomycin A1; CAS9: CRISPR associated protein 9; CQ: Chloroquine; DE: Definitive endoderm; hESCs: Human Embryonic Stem Cells; hiPSCs: Human Induced Pluripotent Stem Cells; LAMP1: Lysosomal Associated Membrane Protein 1; MAP1LC3: Microtubule-Associated Protein 1 Light Chain 3; MTOR: Mechanistic Target Of Rapamycin Kinase; NANOG: Nanog Homeobox; PAX6: Paired Box 6; PE: Phosphatidylethanolamine; POU5F1: POU class 5 Homeobox 1; PRKAA2: Protein Kinase AMP-Activated Catalytic Subunit Alpha 2; SOX2: SRY-box Transcription Factor 2; SQSTM1: Sequestosome 1; ULK1: unc-51 like Autophagy Activating Kinase 1; WDFY3: WD Repeat and FYVE Domain Containing 3.
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Affiliation(s)
- Kulbhushan Sharma
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division of Stem Cell and Gene Therapy Research, Institute of Nuclear Medicine and Allied Sciences (INMAS), Delhi, India.,Department of Neurology, Akershus University Hospital, Lørenskog, Norway
| | - Nagham T Asp
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sean P Harrison
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | - Richard Siller
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Saphira F Baumgarten
- Hybrid Technology Hub, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Swapnil Gupta
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Neurology, Akershus University Hospital, Lørenskog, Norway
| | - Maria E Chollet
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Elisabeth Andersen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Gareth J Sullivan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Pediatric Research, Oslo University Hospital, Oslo, Norway.,Hybrid Technology Hub, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Norwegian Center for Stem Cell Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,Institute of Immunology, Oslo University Hospital, Oslo, Norway
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital Montebello, Oslo, Norway
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17
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Abu-Bonsrah KD, Newgreen DF, Dottori M. Development of Functional Thyroid C Cell-like Cells from Human Pluripotent Cells in 2D and in 3D Scaffolds. Cells 2021; 10:cells10112897. [PMID: 34831120 PMCID: PMC8616516 DOI: 10.3390/cells10112897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
Medullary thyroid carcinoma contributes to about 3–4% of thyroid cancers and affects C cells rather than follicular cells. Thyroid C cell differentiation from human pluripotent stem cells has not been reported. We report the stepwise differentiation of human embryonic stem cells into thyroid C cell-like cells through definitive endoderm and anterior foregut endoderm and ultimobranchial body-like intermediates in monolayer and 3D Matrigel culture conditions. The protocol involved sequential treatment with interferon/transferrin/selenium/pyruvate, foetal bovine serum, and activin A, then IGF-1 (Insulin-like growth factor 1), on the basis of embryonic thyroid developmental sequence. As well as expressing C cell lineage relative to follicular-lineage markers by qPCR (quantitative polymerase chain reaction) and immunolabelling, these cells by ELISA (enzyme-linked immunoassay) exhibited functional properties in vitro of calcitonin storage and release of calcitonin on calcium challenge. This method will contribute to developmental studies of the human thyroid gland and facilitate in vitro modelling of medullary thyroid carcinoma and provide a valuable platform for drug screening.
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Affiliation(s)
- Kwaku Dad Abu-Bonsrah
- The Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia
- Correspondence: (K.D.A.-B.); (D.F.N.); (M.D.)
| | - Donald F. Newgreen
- The Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia
- Correspondence: (K.D.A.-B.); (D.F.N.); (M.D.)
| | - Mirella Dottori
- Department of Biomedical Engineering, Department of Anatomy and Neurosciences, University of Melbourne, Parkville, VIC 3010, Australia
- Illawarra Health and Medical Research Institute, School of Medicine, Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
- Correspondence: (K.D.A.-B.); (D.F.N.); (M.D.)
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18
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Abstract
Transcription factors (TFs) are essential mediators of epigenetic regulation and modifiers of penetrance. Studies from the past decades have revealed a sub-class of TF that is capable of remodeling closed chromatin states through targeting nucleosomal motifs. This pioneer factor (PF) class of chromatin remodeler is ATP independent in its roles in epigenetic initiation, with nucleosome-motif recognition and association with repressive chromatin regions. Increasing evidence suggests that the fundamental properties of PFs can be coopted in human cancers. We explore the role of PFs in the larger context of tissue-specific epigenetic regulation. Moreover, we highlight an emerging class of chimeric PF derived from translocation partners in human disease and PFs associated with rare tumors. In the age of site-directed genome editing and targeted protein degradation, increasing our understanding of PFs will provide access to next-generation therapy for human disease driven from altered transcriptional circuitry.
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19
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Świerczek-Lasek B, Dudka D, Bauer D, Czajkowski T, Ilach K, Streminska W, Kominek A, Piwocka K, Ciemerych MA, Archacka K. Comparison of Differentiation Pattern and WNT/SHH Signaling in Pluripotent Stem Cells Cultured under Different Conditions. Cells 2021; 10:cells10102743. [PMID: 34685722 PMCID: PMC8534321 DOI: 10.3390/cells10102743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022] Open
Abstract
Pluripotent stem cells (PSCs) are characterized by the ability to self-renew as well as undergo multidirectional differentiation. Culture conditions have a pivotal influence on differentiation pattern. In the current study, we compared the fate of mouse PSCs using two culture media: (1) chemically defined, free of animal reagents, and (2) standard one relying on the serum supplementation. Moreover, we assessed the influence of selected regulators (WNTs, SHH) on PSC differentiation. We showed that the differentiation pattern of PSCs cultured in both systems differed significantly: cells cultured in chemically defined medium preferentially underwent ectodermal conversion while their endo- and mesodermal differentiation was limited, contrary to cells cultured in serum-supplemented medium. More efficient ectodermal differentiation of PSCs cultured in chemically defined medium correlated with higher activity of SHH pathway while endodermal and mesodermal conversion of cells cultured in serum-supplemented medium with higher activity of WNT/JNK pathway. However, inhibition of either canonical or noncanonical WNT pathway resulted in the limitation of endo- and mesodermal conversion of PSCs. In addition, blocking WNT secretion led to the inhibition of PSC mesodermal differentiation, confirming the pivotal role of WNT signaling in this process. In contrast, SHH turned out to be an inducer of PSC ectodermal, not mesodermal differentiation.
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Affiliation(s)
- Barbara Świerczek-Lasek
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (B.Ś.-L.); (D.D.); (D.B.); (T.C.); (K.I.); (W.S.); (M.A.C.)
| | - Damian Dudka
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (B.Ś.-L.); (D.D.); (D.B.); (T.C.); (K.I.); (W.S.); (M.A.C.)
| | - Damian Bauer
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (B.Ś.-L.); (D.D.); (D.B.); (T.C.); (K.I.); (W.S.); (M.A.C.)
| | - Tomasz Czajkowski
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (B.Ś.-L.); (D.D.); (D.B.); (T.C.); (K.I.); (W.S.); (M.A.C.)
| | - Katarzyna Ilach
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (B.Ś.-L.); (D.D.); (D.B.); (T.C.); (K.I.); (W.S.); (M.A.C.)
| | - Władysława Streminska
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (B.Ś.-L.); (D.D.); (D.B.); (T.C.); (K.I.); (W.S.); (M.A.C.)
| | - Agata Kominek
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland; (A.K.); (K.P.)
| | - Katarzyna Piwocka
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland; (A.K.); (K.P.)
| | - Maria A. Ciemerych
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (B.Ś.-L.); (D.D.); (D.B.); (T.C.); (K.I.); (W.S.); (M.A.C.)
| | - Karolina Archacka
- Department of Cytology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (B.Ś.-L.); (D.D.); (D.B.); (T.C.); (K.I.); (W.S.); (M.A.C.)
- Correspondence: ; Tel.: +48-22-55-42-203
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20
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Tachmatzidi EC, Galanopoulou O, Talianidis I. Transcription Control of Liver Development. Cells 2021; 10:cells10082026. [PMID: 34440795 PMCID: PMC8391549 DOI: 10.3390/cells10082026] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023] Open
Abstract
During liver organogenesis, cellular transcriptional profiles are constantly reshaped by the action of hepatic transcriptional regulators, including FoxA1-3, GATA4/6, HNF1α/β, HNF4α, HNF6, OC-2, C/EBPα/β, Hex, and Prox1. These factors are crucial for the activation of hepatic genes that, in the context of compact chromatin, cannot access their targets. The initial opening of highly condensed chromatin is executed by a special class of transcription factors known as pioneer factors. They bind and destabilize highly condensed chromatin and facilitate access to other "non-pioneer" factors. The association of target genes with pioneer and non-pioneer transcription factors takes place long before gene activation. In this way, the underlying gene regulatory regions are marked for future activation. The process is called "bookmarking", which confers transcriptional competence on target genes. Developmental bookmarking is accompanied by a dynamic maturation process, which prepares the genomic loci for stable and efficient transcription. Stable hepatic expression profiles are maintained during development and adulthood by the constant availability of the main regulators. This is achieved by a self-sustaining regulatory network that is established by complex cross-regulatory interactions between the major regulators. This network gradually grows during liver development and provides an epigenetic memory mechanism for safeguarding the optimal expression of the regulators.
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Affiliation(s)
- Evangelia C. Tachmatzidi
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Department of Biology, University of Crete, 70013 Herakleion, Crete, Greece
| | - Ourania Galanopoulou
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Department of Biology, University of Crete, 70013 Herakleion, Crete, Greece
| | - Iannis Talianidis
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Correspondence:
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21
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Milan M, Diaferia GR, Natoli G. Tumor cell heterogeneity and its transcriptional bases in pancreatic cancer: a tale of two cell types and their many variants. EMBO J 2021; 40:e107206. [PMID: 33844319 PMCID: PMC8246061 DOI: 10.15252/embj.2020107206] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), one of the most highly lethal tumors, is characterized by complex histology, with a massive fibrotic stroma in which both pseudo-glandular structures and compact nests of abnormally differentiated tumor cells are embedded, in different proportions and with different mutual relationships in space. This complexity and the heterogeneity of the tumor component have hindered the development of a broadly accepted, clinically actionable classification of PDACs, either on a morphological or a molecular basis. Here, we discuss evidence suggesting that such heterogeneity can to a large extent, albeit not exclusively, be traced back to two main classes of PDAC cells that commonly coexist in the same tumor: cells that maintained their ability to differentiate toward endodermal, mucin-producing epithelia and epithelial cells unable to form glandular structures and instead characterized by various levels of squamous differentiation and the expression of mesenchymal lineage genes. The underlying gene regulatory networks and how they are controlled by distinct transcription factors, as well as the practical implications of these two different populations of tumor cells, are discussed.
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Affiliation(s)
- Marta Milan
- Department of Experimental OncologyEuropean Institute of Oncology (IEO) IRCCSMilanItaly
- Present address:
The Francis Crick InstituteLondonUK
| | - Giuseppe R Diaferia
- Department of Experimental OncologyEuropean Institute of Oncology (IEO) IRCCSMilanItaly
| | - Gioacchino Natoli
- Department of Experimental OncologyEuropean Institute of Oncology (IEO) IRCCSMilanItaly
- Humanitas UniversityMilanItaly
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22
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Lin M, Mackie PM, Shaerzadeh F, Gamble-George J, Miller DR, Martyniuk CJ, Khoshbouei H. In Parkinson's patient-derived dopamine neurons, the triplication of α-synuclein locus induces distinctive firing pattern by impeding D2 receptor autoinhibition. Acta Neuropathol Commun 2021; 9:107. [PMID: 34099060 PMCID: PMC8185945 DOI: 10.1186/s40478-021-01203-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/17/2021] [Indexed: 12/12/2022] Open
Abstract
Pathophysiological changes in dopamine neurons precede their demise and contribute to the early phases of Parkinson's disease (PD). Intracellular pathological inclusions of the protein α-synuclein within dopaminergic neurons are a cardinal feature of PD, but the mechanisms by which α-synuclein contributes to dopaminergic neuron vulnerability remain unknown. The inaccessibility to diseased tissue has been a limitation in studying progression of pathophysiology prior to degeneration of dopamine neurons. To address these issues, we differentiated induced pluripotent stem cells (iPSCs) from a PD patient carrying the α-synuclein triplication mutation (AST) and an unaffected first-degree relative (NAS) into dopaminergic neurons. In human-like dopamine neurons α-synuclein overexpression reduced the functional availability of D2 receptors, resulting in a stark dysregulation in firing activity, dopamine release, and neuronal morphology. We back-translated these findings into primary mouse neurons overexpressing α-synuclein and found a similar phenotype, supporting the causal role for α-synuclein. Importantly, application of D2 receptor agonist, quinpirole, restored the altered firing activity of AST-derived dopaminergic neurons to normal levels. These results provide novel insights into the pre-degenerative pathophysiological neuro-phenotype induced by α-synuclein overexpression and introduce a potential mechanism for the long-established clinical efficacy of D2 receptor agonists in the treatment of PD.
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Affiliation(s)
- Min Lin
- Department of Neuroscience, University of Florida, Gainesville, FL, 32611, USA
| | - Phillip M Mackie
- Department of Neuroscience, University of Florida, Gainesville, FL, 32611, USA
| | - Fatima Shaerzadeh
- Department of Neuroscience, University of Florida, Gainesville, FL, 32611, USA
| | | | - Douglas R Miller
- Department of Neuroscience, University of Florida, Gainesville, FL, 32611, USA
| | - Chris J Martyniuk
- Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Habibeh Khoshbouei
- Department of Neuroscience, University of Florida, Gainesville, FL, 32611, USA.
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23
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Little DR, Lynch AM, Yan Y, Akiyama H, Kimura S, Chen J. Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo. Nat Commun 2021; 12:2509. [PMID: 33947861 PMCID: PMC8096971 DOI: 10.1038/s41467-021-22817-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/24/2021] [Indexed: 02/06/2023] Open
Abstract
Differential transcription of identical DNA sequences leads to distinct tissue lineages and then multiple cell types within a lineage, an epigenetic process central to progenitor and stem cell biology. The associated genome-wide changes, especially in native tissues, remain insufficiently understood, and are hereby addressed in the mouse lung, where the same lineage transcription factor NKX2-1 promotes the diametrically opposed alveolar type 1 (AT1) and AT2 cell fates. Here, we report that the cell-type-specific function of NKX2-1 is attributed to its differential chromatin binding that is acquired or retained during development in coordination with partner transcriptional factors. Loss of YAP/TAZ redirects NKX2-1 from its AT1-specific to AT2-specific binding sites, leading to transcriptionally exaggerated AT2 cells when deleted in progenitors or AT1-to-AT2 conversion when deleted after fate commitment. Nkx2-1 mutant AT1 and AT2 cells gain distinct chromatin accessible sites, including those specific to the opposite fate while adopting a gastrointestinal fate, suggesting an epigenetic plasticity unexpected from transcriptional changes. Our genomic analysis of single or purified cells, coupled with precision genetics, provides an epigenetic basis for alveolar cell fate and potential, and introduces an experimental benchmark for deciphering the in vivo function of lineage transcription factors.
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Affiliation(s)
- Danielle R Little
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Anne M Lynch
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yun Yan
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | | | - Shioko Kimura
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jichao Chen
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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24
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Theis A, Singer RA, Garofalo D, Paul A, Narayana A, Sussel L. Groucho co-repressor proteins regulate β cell development and proliferation by repressing Foxa1 in the developing mouse pancreas. Development 2021; 148:dev.192401. [PMID: 33658226 DOI: 10.1242/dev.192401] [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: 05/07/2020] [Accepted: 02/24/2021] [Indexed: 11/20/2022]
Abstract
Groucho-related genes (GRGs) are transcriptional co-repressors that are crucial for many developmental processes. Several essential pancreatic transcription factors are capable of interacting with GRGs; however, the in vivo role of GRG-mediated transcriptional repression in pancreas development is still not well understood. In this study, we used complex mouse genetics and transcriptomic analyses to determine that GRG3 is essential for β cell development, and in the absence of Grg3 there is compensatory upregulation of Grg4 Grg3/4 double mutant mice have severe dysregulation of the pancreas gene program with ectopic expression of canonical liver genes and Foxa1, a master regulator of the liver program. Neurod1, an essential β cell transcription factor and predicted target of Foxa1, becomes downregulated in Grg3/4 mutants, resulting in reduced β cell proliferation, hyperglycemia, and early lethality. These findings uncover novel functions of GRG-mediated repression during pancreas development.
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Affiliation(s)
- Alexandra Theis
- Department of Pediatrics and Cell & Developmental Biology, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ruth A Singer
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA.,Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, NY 10032, USA
| | - Diana Garofalo
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Alexander Paul
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA.,Graduate program in Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Anila Narayana
- Department of Pediatrics and Cell & Developmental Biology, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lori Sussel
- Department of Pediatrics and Cell & Developmental Biology, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA .,Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
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25
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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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26
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Probst S, Sagar, Tosic J, Schwan C, Grün D, Arnold SJ. Spatiotemporal sequence of mesoderm and endoderm lineage segregation during mouse gastrulation. Development 2021; 148:dev.193789. [PMID: 33199445 DOI: 10.1242/dev.193789] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/06/2020] [Indexed: 12/20/2022]
Abstract
Anterior mesoderm (AM) and definitive endoderm (DE) progenitors represent the earliest embryonic cell types that are specified during germ layer formation at the primitive streak (PS) of the mouse embryo. Genetic experiments indicate that both lineages segregate from Eomes-expressing progenitors in response to different Nodal signaling levels. However, the precise spatiotemporal pattern of the emergence of these cell types and molecular details of lineage segregation remain unexplored. We combined genetic fate labeling and imaging approaches with single-cell RNA sequencing (scRNA-seq) to follow the transcriptional identities and define lineage trajectories of Eomes-dependent cell types. Accordingly, all cells moving through the PS during the first day of gastrulation express Eomes AM and DE specification occurs before cells leave the PS from Eomes-positive progenitors in a distinct spatiotemporal pattern. ScRNA-seq analysis further suggested the immediate and complete separation of AM and DE lineages from Eomes-expressing cells as last common bipotential progenitor.
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Affiliation(s)
- Simone Probst
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, D-79104 Freiburg, Germany .,Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, D-79104 Freiburg, Germany
| | - Sagar
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Jelena Tosic
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, D-79104 Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, D-79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Carsten Schwan
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, D-79104 Freiburg, Germany
| | - Dominic Grün
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, D-79104 Freiburg, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Sebastian J Arnold
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, D-79104 Freiburg, Germany .,Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, D-79104 Freiburg, Germany
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27
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Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones. Nat Genet 2020; 52:418-427. [PMID: 32203463 PMCID: PMC7901023 DOI: 10.1038/s41588-020-0591-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/14/2020] [Indexed: 12/17/2022]
Abstract
Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. But a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short alpha-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.
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28
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Kadoya M, Sasai N. Negative Regulation of mTOR Signaling Restricts Cell Proliferation in the Floor Plate. Front Neurosci 2019; 13:1022. [PMID: 31607856 PMCID: PMC6773814 DOI: 10.3389/fnins.2019.01022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/09/2019] [Indexed: 01/07/2023] Open
Abstract
The neural tube is composed of a number of neural progenitors and postmitotic neurons distributed in a quantitatively and spatially precise manner. The floor plate, located in the ventral-most region of the neural tube, has a lot of unique characteristics, including a low cell proliferation rate. The mechanisms by which this region-specific proliferation rate is regulated remain elusive. Here we show that the activity of the mTOR signaling pathway, which regulates the proliferation of the neural progenitor cells, is significantly lower in the floor plate than in other domains of the embryonic neural tube. We identified the forkhead-type transcription factor FoxA2 as a negative regulator of mTOR signaling in the floor plate, and showed that FoxA2 transcriptionally induces the expression of the E3 ubiquitin ligase RNF152, which together with its substrate RagA, regulates cell proliferation via the mTOR pathway. Silencing of RNF152 led to the aberrant upregulation of the mTOR signal and aberrant cell division in the floor plate. Taken together, the present findings suggest that floor plate cell number is controlled by the negative regulation of mTOR signaling through the activity of FoxA2 and its downstream effector RNF152.
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Affiliation(s)
- Minori Kadoya
- Developmental Biomedical Science, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Noriaki Sasai
- Developmental Biomedical Science, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
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29
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Abstract
The function of the mammalian heart depends on the interplay between different cardiac cell types. The deployment of these cells, with precise spatiotemporal regulation, is also important during development to establish the heart structure. In this Review, we discuss the diverse origins of cardiac cell types and the lineage relationships between cells of a given type that contribute to different parts of the heart. The emerging lineage tree shows the progression of cell fate diversification, with patterning cues preceding cell type segregation, as well as points of convergence, with overlapping lineages contributing to a given tissue. Several cell lineage markers have been identified. However, caution is required with genetic-tracing experiments in comparison with clonal analyses. Genetic studies on cell populations provided insights into the mechanisms for lineage decisions. In the past 3 years, results of single-cell transcriptomics are beginning to reveal cell heterogeneity and early developmental trajectories. Equating this information with the in vivo location of cells and their lineage history is a current challenge. Characterization of the progenitor cells that form the heart and of the gene regulatory networks that control their deployment is of major importance for understanding the origin of congenital heart malformations and for producing cardiac tissue for use in regenerative medicine.
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30
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Chen B, Yu J, Lu L, Dong F, Zhou F, Tao X, Sun E. Upregulated forkhead-box A3 elevates the expression of forkhead-box A1 and forkhead-box A2 to promote metastasis in esophageal cancer. Oncol Lett 2019; 17:4351-4360. [PMID: 30944629 DOI: 10.3892/ol.2019.10078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/04/2019] [Indexed: 11/06/2022] Open
Abstract
Esophageal cancer (EC) is one of the most lethal cancers currently known. Members of the forkhead-box A (FOXA) family, including FOXA1 and FOXA2, have been reported to regulate EC progression. However, the role of FOXA3, which is another FOXA member, has not yet been investigated. In the present study, public dataset analyses and immunohistochemistry of 96 samples from patients with EC were performed to determine the potential roles of FOXA3 in EC. The results revealed that FOXA3 was significantly upregulated in EC tumor tissues and Barrett's esophagus tissues. In addition, FOXA3 upregulation was positively associated with tumor invasion, distant metastasis, tumor-node-metastasis stage and shorter overall survival in patients with EC, and multivariate analysis identified FOXA3 as an independent prognostic marker. In vitro experiments demonstrated that the migratory and invasive abilities of EC109 and EC9706 cell lines were inhibited following FOXA3 knockdown. Notably, FOXA3 expression levels were positively correlated with FOXA1 and FOXA2 expression levels according to The Cancer Genome Atlas dataset analysis. Furthermore, FOXA3 knockdown decreased the expression levels of FOXA1 and FOXA2 in EC109 and EC9706 cell lines. Conversely, FOXA1 or FOXA2 overexpression compensated for the effects of FOXA3 knockdown on the migratory and invasive capacities of EC cells. In conclusion, the present study demonstrated that FOXA3 upregulation in EC cells promoted metastasis through regulation of other FOXA members.
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Affiliation(s)
- Bing Chen
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Jiegen Yu
- Department of Management Science, School of Humanities and Management, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Linming Lu
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Fangyuan Dong
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Fangfang Zhou
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Xiangxiang Tao
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Entao Sun
- Department of Health Inspection and Quarantine, School of Laboratory Medicine, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
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31
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Hung S, Saiakhova A, Faber ZJ, Bartels CF, Neu D, Bayles I, Ojo E, Hong ES, Pontius WD, Morton AR, Liu R, Kalady MF, Wald DN, Markowitz S, Scacheri PC. Mismatch repair-signature mutations activate gene enhancers across human colorectal cancer epigenomes. eLife 2019; 8:40760. [PMID: 30759065 PMCID: PMC6374075 DOI: 10.7554/elife.40760] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/22/2019] [Indexed: 02/07/2023] Open
Abstract
Commonly-mutated genes have been found for many cancers, but less is known about mutations in cis-regulatory elements. We leverage gains in tumor-specific enhancer activity, coupled with allele-biased mutation detection from H3K27ac ChIP-seq data, to pinpoint potential enhancer-activating mutations in colorectal cancer (CRC). Analysis of a genetically-diverse cohort of CRC specimens revealed that microsatellite instable (MSI) samples have a high indel rate within active enhancers. Enhancers with indels show evidence of positive selection, increased target gene expression, and a subset is highly recurrent. The indels affect short homopolymer tracts of A/T and increase affinity for FOX transcription factors. We further demonstrate that signature mismatch-repair (MMR) mutations activate enhancers using a xenograft tumor metastasis model, where mutations are induced naturally via CRISPR/Cas9 inactivation of MLH1 prior to tumor cell injection. Our results suggest that MMR signature mutations activate enhancers in CRC tumor epigenomes to provide a selective advantage.
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Affiliation(s)
- Stevephen Hung
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Zachary J Faber
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Devin Neu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Ian Bayles
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Evelyn Ojo
- Department of Pathology, Case Western Reserve University, Cleveland, United States
| | - Ellen S Hong
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - W Dean Pontius
- Department of Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Andrew R Morton
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Ruifu Liu
- Department of Pathology, Case Western Reserve University, Cleveland, United States
| | - Matthew F Kalady
- Department of Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Colorectal Surgery, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, United States
| | - David N Wald
- Department of Pathology, Case Western Reserve University, Cleveland, United States.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, United States
| | - Sanford Markowitz
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, United States.,Department of Medicine, Case Western Reserve University, Cleveland, United States
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, United States
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32
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Brodski C, Blaess S, Partanen J, Prakash N. Crosstalk of Intercellular Signaling Pathways in the Generation of Midbrain Dopaminergic Neurons In Vivo and from Stem Cells. J Dev Biol 2019; 7:jdb7010003. [PMID: 30650592 PMCID: PMC6473842 DOI: 10.3390/jdb7010003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 12/25/2022] Open
Abstract
Dopamine-synthesizing neurons located in the mammalian ventral midbrain are at the center stage of biomedical research due to their involvement in severe human neuropsychiatric and neurodegenerative disorders, most prominently Parkinson’s Disease (PD). The induction of midbrain dopaminergic (mDA) neurons depends on two important signaling centers of the mammalian embryo: the ventral midline or floor plate (FP) of the neural tube, and the isthmic organizer (IsO) at the mid-/hindbrain boundary (MHB). Cells located within and close to the FP secrete sonic hedgehog (SHH), and members of the wingless-type MMTV integration site family (WNT1/5A), as well as bone morphogenetic protein (BMP) family. The IsO cells secrete WNT1 and the fibroblast growth factor 8 (FGF8). Accordingly, the FGF8, SHH, WNT, and BMP signaling pathways play crucial roles during the development of the mDA neurons in the mammalian embryo. Moreover, these morphogens are essential for the generation of stem cell-derived mDA neurons, which are critical for the modeling, drug screening, and cell replacement therapy of PD. This review summarizes our current knowledge about the functions and crosstalk of these signaling pathways in mammalian mDA neuron development in vivo and their applications in stem cell-based paradigms for the efficient derivation of these neurons in vitro.
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Affiliation(s)
- Claude Brodski
- Department of Physiology and Cell Biology, Zlotowski Center for Neuroscience, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel.
| | - Sandra Blaess
- Institute of Reconstructive Neurobiology, University of Bonn Medical Center, 53127 Bonn, Germany.
| | - Juha Partanen
- Faculty of Biological and Environmental Sciences, FIN00014-University of Helsinki, P.O. Box 56, Viikinkaari 9, FIN-00014 Helsinki, Finland.
| | - Nilima Prakash
- Department Hamm 2, Hamm-Lippstadt University of Applied Sciences, 59063 Hamm, Germany.
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Cañibano-Hernández A, Saenz del Burgo L, Espona-Noguera A, Orive G, Hernández RM, Ciriza J, Pedraz JL. Hyaluronic Acid Promotes Differentiation of Mesenchymal Stem Cells from Different Sources toward Pancreatic Progenitors within Three-Dimensional Alginate Matrixes. Mol Pharm 2019; 16:834-845. [DOI: 10.1021/acs.molpharmaceut.8b01126] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Alberto Cañibano-Hernández
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - Laura Saenz del Burgo
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - Albert Espona-Noguera
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - Gorka Orive
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - Rosa M. Hernández
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - Jesús Ciriza
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - José Luis Pedraz
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
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34
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A Simple System for Differentiation of Functional Intestinal Stem Cell-like Cells from Bone Marrow Mesenchymal Stem Cells. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 13:110-120. [PMID: 30268688 PMCID: PMC6171535 DOI: 10.1016/j.omtn.2018.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/25/2018] [Accepted: 08/19/2018] [Indexed: 12/12/2022]
Abstract
Disruption of normal barrier function is a fundamental factor in the pathogenesis of inflammatory bowel disease, and intestinal stem cell (ISC) transplantation may be an optional treatment for patients. However, it is complicated and inefficient to isolate ISCs from the intestine, which hampers its wide application in clinic. We developed a two-step protocol in which mesenchymal stem cells (MSCs) were first induced into Sox17- or Foxa2-positive definitive endoderm cells by activin A treatment and then into Lgr5-positive ISC-like cells by miR-17 and FGF2 treatment. Furthermore, these Lgr5-positive cells could differentiate into enterocyte-like cells following induction with EGF. The results from an in vivo experiment showed that the MSC-derived Lgr5-positive cells were able to protect against dextran sulfate sodium-induced colitis. Taken together, our work might provide a new source of autologous ISCs.
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35
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The molecular functions of hepatocyte nuclear factors - In and beyond the liver. J Hepatol 2018; 68:1033-1048. [PMID: 29175243 DOI: 10.1016/j.jhep.2017.11.026] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 12/27/2022]
Abstract
The hepatocyte nuclear factors (HNFs) namely HNF1α/β, FOXA1/2/3, HNF4α/γ and ONECUT1/2 are expressed in a variety of tissues and organs, including the liver, pancreas and kidney. The spatial and temporal manner of HNF expression regulates embryonic development and subsequently the development of multiple tissues during adulthood. Though the HNFs were initially identified individually based on their roles in the liver, numerous studies have now revealed that the HNFs cross-regulate one another and exhibit synergistic relationships in the regulation of tissue development and function. The complex HNF transcriptional regulatory networks have largely been elucidated in rodent models, but less so in human biological systems. Several heterozygous mutations in these HNFs were found to cause diseases in humans but not in rodents, suggesting clear species-specific differences in mutational mechanisms that remain to be uncovered. In this review, we compare and contrast the expression patterns of the HNFs, the HNF cross-regulatory networks and how these liver-enriched transcription factors serve multiple functions in the liver and beyond, extending our focus to the pancreas and kidney. We also summarise the insights gained from both human and rodent studies of mutations in several HNFs that are known to lead to different disease conditions.
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36
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Morgani SM, Metzger JJ, Nichols J, Siggia ED, Hadjantonakis AK. Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning. eLife 2018; 7:e32839. [PMID: 29412136 PMCID: PMC5807051 DOI: 10.7554/elife.32839] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/02/2018] [Indexed: 12/29/2022] Open
Abstract
During gastrulation epiblast cells exit pluripotency as they specify and spatially arrange the three germ layers of the embryo. Similarly, human pluripotent stem cells (PSCs) undergo spatially organized fate specification on micropatterned surfaces. Since in vivo validation is not possible for the human, we developed a mouse PSC micropattern system and, with direct comparisons to mouse embryos, reveal the robust specification of distinct regional identities. BMP, WNT, ACTIVIN and FGF directed mouse epiblast-like cells to undergo an epithelial-to-mesenchymal transition and radially pattern posterior mesoderm fates. Conversely, WNT, ACTIVIN and FGF patterned anterior identities, including definitive endoderm. By contrast, epiblast stem cells, a developmentally advanced state, only specified anterior identities, but without patterning. The mouse micropattern system offers a robust scalable method to generate regionalized cell types present in vivo, resolve how signals promote distinct identities and generate patterns, and compare mechanisms operating in vivo and in vitro and across species.
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Affiliation(s)
- Sophie M Morgani
- Developmental Biology ProgramSloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Wellcome Trust-Medical Research Council Centre for Stem Cell ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | - Jakob J Metzger
- Center for Studies in Physics and BiologyThe Rockefeller UniversityNew YorkUnited States
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Centre for Stem Cell ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | - Eric D Siggia
- Center for Studies in Physics and BiologyThe Rockefeller UniversityNew YorkUnited States
| | - Anna-Katerina Hadjantonakis
- Developmental Biology ProgramSloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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37
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Kuo DH, Hsiao YH. Duplicated FoxA genes in the leech Helobdella: Insights into the evolution of direct development in clitellate annelids. Dev Dyn 2018; 247:763-778. [PMID: 29396890 DOI: 10.1002/dvdy.24621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND As an adaptation to the land, the clitellate annelid had reorganized its embryogenesis to develop "directly" without the ancestral planktonic larval stage. To study the evolution of gut development in the directly developing clitellates, we characterized the expression pattern of the conserved gut gene, FoxA, in the embryonic development of the leech. RESULTS The leech has three FoxA paralogs. Hau-FoxA1 is first expressed in a subset of endoderm cells and then in the foregut and the midgut. Hau-FoxA2 is expressed in the stomodeum, which is secondarily derived from the anterior ectoderm in the clitellates rather than the tissue around the blastopore, the ancestral site of mouth formation in Phylum Annelida. Hau-FoxA3 is expressed during the morphogenesis of segmental ganglia from the ectodermal teloblast lineages, a clitellate-specific trait. Hau-FoxA1 and Hau-FoxA2 are also expressed during the morphogenesis of the leech-specific front sucker. CONCLUSIONS The expression patterns suggested that Hau-FoxA1 carries out most of the conserved function in the endoderm and gut development, while the other two duplicates appear to have evolved unique novel functions in the directly developing clitellate embryos. Therefore, neofunctionalization and co-option of FoxA might have made a significant contribution to the evolution of direct development in Clitellata. Developmental Dynamics 247:763-778, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Dian-Han Kuo
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Hsiang Hsiao
- Department of Life Science, National Taiwan University, Taipei, Taiwan
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38
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Abstract
The ZIC2 transcription factor is one of the most commonly mutated genes in Holoprosencephaly (HPE) probands. HPE is a severe congenital defect of forebrain development which occurs when the cerebral hemispheres fail to separate during the early stages of organogenesis and is typically associated with mispatterning of the embryonic midline. Recent study of genotype-phenotype correlations in HPE cases has defined distinctive features of ZIC2-associated HPE presentation and genetics, revealing that ZIC2 mutation does not produce the craniofacial abnormalities generally thought to characterise HPE but leads to a range of non-forebrain phenotypes. Furthermore, the studies confirm the extent of ZIC2 allelic heterogeneity and that pathogenic variants of ZIC2 are associated with both classic and middle interhemispheric variant (MIHV) HPE which arise from defective ventral and dorsal forebrain patterning, respectively. An allelic series of mouse mutants has helped to delineate the cellular and molecular mechanisms by which one gene leads to defects in these related but distinct embryological processes.
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Affiliation(s)
- Kristen S Barratt
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Ruth M Arkell
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
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39
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Zhang Y, Xiang Y, Yin Q, Du Z, Peng X, Wang Q, Fidalgo M, Xia W, Li Y, Zhao ZA, Zhang W, Ma J, Xu F, Wang J, Li L, Xie W. Dynamic epigenomic landscapes during early lineage specification in mouse embryos. Nat Genet 2018; 50:96-105. [PMID: 29203909 DOI: 10.1038/s41588-017-0003-x] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/01/2017] [Indexed: 12/20/2022]
Abstract
In mammals, all somatic development originates from lineage segregation in early embryos. However, the dynamics of transcriptomes and epigenomes acting in concert with initial cell fate commitment remains poorly characterized. Here we report a comprehensive investigation of transcriptomes and base-resolution methylomes for early lineages in peri- and postimplantation mouse embryos. We found allele-specific and lineage-specific de novo methylation at CG and CH sites that led to differential methylation between embryonic and extraembryonic lineages at promoters of lineage regulators, gene bodies, and DNA-methylation valleys. By using Hi-C experiments to define chromatin architecture across the same developmental period, we demonstrated that both global demethylation and remethylation in early development correlate with chromatin compartments. Dynamic local methylation was evident during gastrulation, which enabled the identification of putative regulatory elements. Finally, we found that de novo methylation patterning does not strictly require implantation. These data reveal dynamic transcriptomes, DNA methylomes, and 3D chromatin landscapes during the earliest stages of mammalian lineage specification.
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Affiliation(s)
- Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yunlong Xiang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China
| | - Qiangzong Yin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xu Peng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China
| | - Miguel Fidalgo
- Department of Cell, Developmental and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Weikun Xia
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yuanyuan Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhen-Ao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wenhao Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jing Ma
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Feng Xu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, Singapore
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.
- THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China.
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40
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Dzama MM, Nigmatullina L, Sayols S, Kreim N, Soshnikova N. Distinct populations of embryonic epithelial progenitors generate Lgr5 + intestinal stem cells. Dev Biol 2017; 432:258-264. [PMID: 29037931 DOI: 10.1016/j.ydbio.2017.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/04/2017] [Accepted: 10/12/2017] [Indexed: 11/19/2022]
Abstract
The adult intestinal stem cells (ISCs) are transcriptionally heterogeneous. As the mechanisms governing their developmental specification are still poorly understood, whether this heterogeneity reflects an early determination of distinct cellular sub-types with potentially distinct physiological functions remains an open question. We investigate the cellular heterogeneity within the mouse embryonic midgut epithelium at the molecular and functional levels. Cell fate mapping analysis revealed that multiple early embryonic epithelial progenitors give rise to Lgr5+ ISCs. The origin of the molecularly distinct early precursors along the anterior-posterior axis defines the transcriptional signature of embryonic Lgr5+ ISC progenitors. We further show that the early epithelial progenitors have different capacity to generate Lgr5+ ISC progenitors and Axin2+ early precursors display the highest potential.
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Affiliation(s)
| | | | - Sergi Sayols
- Institute of Molecular Biology, D-55128 Mainz, Germany
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41
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Bogacheva MS, Khan S, Kanninen LK, Yliperttula M, Leung AW, Lou YR. Differences in definitive endoderm induction approaches using growth factors and small molecules. J Cell Physiol 2017; 233:3578-3589. [DOI: 10.1002/jcp.26214] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/12/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Mariia S. Bogacheva
- Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical Biosciences; University of Helsinki; Helsinki Finland
| | - Sofia Khan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL); National Institute of Advanced Industrial Science and Technology (AIST); Tokyo Japan
| | - Liisa K. Kanninen
- Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical Biosciences; University of Helsinki; Helsinki Finland
| | - Marjo Yliperttula
- Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical Biosciences; University of Helsinki; Helsinki Finland
| | - Alan W. Leung
- Yale Stem Cell Center and Department of Genetics; Yale School of Medicine; Yale University; New Haven Connecticut United States
| | - Yan-Ru Lou
- Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical Biosciences; University of Helsinki; Helsinki Finland
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42
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Abstract
Thyroid hormones are crucial for organismal development and homeostasis. In humans, untreated congenital hypothyroidism due to thyroid agenesis inevitably leads to cretinism, which comprises irreversible brain dysfunction and dwarfism. Elucidating how the thyroid gland - the only source of thyroid hormones in the body - develops is thus key for understanding and treating thyroid dysgenesis, and for generating thyroid cells in vitro that might be used for cell-based therapies. Here, we review the principal mechanisms involved in thyroid organogenesis and functional differentiation, highlighting how the thyroid forerunner evolved from the endostyle in protochordates to the endocrine gland found in vertebrates. New findings on the specification and fate decisions of thyroid progenitors, and the morphogenesis of precursor cells into hormone-producing follicular units, are also discussed.
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Affiliation(s)
- Mikael Nilsson
- Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg, Göteborg SE-40530, Sweden
| | - Henrik Fagman
- Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg, Göteborg SE-40530, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Göteborg SE-41345, Sweden
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43
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Bhargava S, Cox B, Polydorou C, Gresakova V, Korinek V, Strnad H, Sedlacek R, Epp TA, Chawengsaksophak K. The epigenetic modifier Fam208a is required to maintain epiblast cell fitness. Sci Rep 2017; 7:9322. [PMID: 28839193 PMCID: PMC5570896 DOI: 10.1038/s41598-017-09490-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/26/2017] [Indexed: 12/12/2022] Open
Abstract
Gastrulation initiates with the formation of the primitive streak, during which, cells of the epiblast delaminate to form the mesoderm and definitive endoderm. At this stage, the pluripotent cell population of the epiblast undergoes very rapid proliferation and extensive epigenetic programming. Here we show that Fam208a, a new epigenetic modifier, is essential for early post-implantation development. We show that Fam208a mutation leads to impaired primitive streak elongation and delayed epithelial-to-mesenchymal transition. Fam208a mutant epiblasts had increased expression of p53 pathway genes as well as several pluripotency-associated long non-coding RNAs. Fam208a mutants exhibited an increase in p53-driven apoptosis and complete removal of p53 could partially rescue their gastrulation block. This data demonstrates a new in vivo function of Fam208a in maintaining epiblast fitness, establishing it as an important factor at the onset of gastrulation when cells are exiting pluripotency.
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Affiliation(s)
- Shohag Bhargava
- Laboratory of Transgenic Models of Diseases, Division, BIOCEV, Institute of Molecular Genetics of the CAS, v.v.i., Vestec, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Brian Cox
- Department of Physiology, Faculty of Medicine, University of Toronto, Ontario, Canada
| | - Christiana Polydorou
- Laboratory of Transgenic Models of Diseases, Division, BIOCEV, Institute of Molecular Genetics of the CAS, v.v.i., Vestec, Czech Republic
| | - Veronika Gresakova
- Laboratory of Transgenic Models of Diseases, Division, BIOCEV, Institute of Molecular Genetics of the CAS, v.v.i., Vestec, Czech Republic
| | - Vladimir Korinek
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the CAS, v.v.i., Krc, Czech Republic
| | - Hynek Strnad
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the CAS, v.v.i., Krc, Czech Republic
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Division, BIOCEV, Institute of Molecular Genetics of the CAS, v.v.i., Vestec, Czech Republic.,Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics of the CAS, v.v.i., Vestec, Czech Republic
| | - Trevor Allan Epp
- Laboratory of Transgenic Models of Diseases, Division, BIOCEV, Institute of Molecular Genetics of the CAS, v.v.i., Vestec, Czech Republic. .,Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics of the CAS, v.v.i., Vestec, Czech Republic.
| | - Kallayanee Chawengsaksophak
- Laboratory of Transgenic Models of Diseases, Division, BIOCEV, Institute of Molecular Genetics of the CAS, v.v.i., Vestec, Czech Republic. .,Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics of the CAS, v.v.i., Vestec, Czech Republic.
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44
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Forkhead box protein A2, a pioneer factor for hepatogenesis, is involved in the expression of hepatic phenotype of alpha-fetoprotein-producing adenocarcinoma. Pathol Res Pract 2017; 213:1082-1088. [PMID: 28778497 DOI: 10.1016/j.prp.2017.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/19/2017] [Accepted: 07/19/2017] [Indexed: 12/13/2022]
Abstract
Alpha-fetoprotein (AFP)-producing adenocarcinoma is a high-malignant variant of adenocarcinoma with a hepatic or fetal-intestinal phenotype. The number of cases of AFP-producing adenocarcinomas is increasing, but the molecular mechanism underlying the aberrant production of AFP is unclear. Here we sought to assess the role of Forkhead box A (FoxA)2, which is a pioneer transcription factor in the differentiation of hepatoblasts. FoxA2 expression was investigated in five cases of AFP-producing gastric adenocarcinomas by immunohistochemistry, and all cases showed FoxA2 expression. Chromatin immunoprecipitation revealed the DNA binding of FoxA2 on the regulatory element of AFP gene in AFP-producing adenocarcinoma cells. The inhibition of FoxA2 expression with siRNA reduced the mRNA expression of liver-specific proteins, including AFP, albumin, and transferrin. The inhibition of FoxA2 also reduced the expressions of liver-enriched nuclear factors, i.e., hepatocyte nuclear factor (HNF) 4α and HNF6, although the expressions of HNF1α and HNF1β were not affected. The same effect as FoxA2 knockdown in AFP producing adenocarcinoma cells was also observed in hepatocellular carcinoma cells. Our results suggest that FoxA2 plays a key role in the expression of hepatic phenotype of AFP-producing adenocarcinomas.
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45
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Chen X, Yu B, Carriero N, Silva C, Bonneau R. Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility. Nucleic Acids Res 2017; 45:4315-4329. [PMID: 28334916 PMCID: PMC5416775 DOI: 10.1093/nar/gkx174] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 02/28/2017] [Accepted: 03/06/2017] [Indexed: 12/21/2022] Open
Abstract
Differential binding of transcription factors (TFs) at cis-regulatory loci drives the differentiation and function of diverse cellular lineages. Understanding the regulatory interactions that underlie cell fate decisions requires characterizing TF binding sites (TFBS) across multiple cell types and conditions. Techniques, e.g. ChIP-Seq can reveal genome-wide patterns of TF binding, but typically requires laborious and costly experiments for each TF-cell-type (TFCT) condition of interest. Chromosomal accessibility assays can connect accessible chromatin in one cell type to many TFs through sequence motif mapping. Such methods, however, rarely take into account that the genomic context preferred by each factor differs from TF to TF, and from cell type to cell type. To address the differences in TF behaviors, we developed Mocap, a method that integrates chromatin accessibility, motif scores, TF footprints, CpG/GC content, evolutionary conservation and other factors in an ensemble of TFCT-specific classifiers. We show that integration of genomic features, such as CpG islands improves TFBS prediction in some TFCT. Further, we describe a method for mapping new TFCT, for which no ChIP-seq data exists, onto our ensemble of classifiers and show that our cross-sample TFBS prediction method outperforms several previously described methods.
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Affiliation(s)
- Xi Chen
- Department of Biology, New York University, New York, NY 10003, USA
| | - Bowen Yu
- Department of Computer Science, New York University, New York, NY 10003, USA
| | - Nicholas Carriero
- Center for Computational Biology, Flatiron Foundation, Simons Foundation, New York, NY 10010, USA
| | - Claudio Silva
- Department of Computer Science, New York University, New York, NY 10003, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, NY 10003, USA
- Department of Computer Science, New York University, New York, NY 10003, USA
- Center for Computational Biology, Flatiron Foundation, Simons Foundation, New York, NY 10010, USA
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46
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Wolfe AD, Rodriguez AM, Downs KM. STELLA collaborates in distinct mesendodermal cell subpopulations at the fetal-placental interface in the mouse gastrula. Dev Biol 2017; 425:44-57. [PMID: 28322735 PMCID: PMC5510028 DOI: 10.1016/j.ydbio.2017.03.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 03/10/2017] [Accepted: 03/15/2017] [Indexed: 01/22/2023]
Abstract
The allantois-derived umbilical component of the chorio-allantoic placenta shuttles fetal blood to and from the chorion, thereby ensuring fetal-maternal exchange. The progenitor populations that establish and supply the fetal-umbilical interface lie, in part, within the base of the allantois, where the germ line is claimed to segregate from the soma. Results of recent studies in the mouse have reported that STELLA (DPPA-3, PGC7) co-localizes with PRDM1 (BLIMP1), the bimolecular signature of putative primordial germ cells (PGCs) throughout the fetal-placental interface. Thus, if PGCs form extragonadally within the posterior region of the mammal, they cannot be distinguished from the soma on the basis of these proteins. We used immunohistochemistry, immunofluorescence, and confocal microscopy of the mouse gastrula to co-localize STELLA with a variety of gene products, including pluripotency factor OCT-3/4, mesendoderm-associated T and MIXl1, mesendoderm- and endoderm-associated FOXa2 and hematopoietic factor Runx1. While a subpopulation of cells localizing OCT-3/4 was always found independently of STELLA, STELLA always co-localized with OCT-3/4. Despite previous reports that T is involved in specification of the germ line, co-localization of STELLA and T was detected only in a small subset of cells in the base of the allantois. Slightly later in the hindgut lip, STELLA+/(OCT-3/4+) co-localized with FOXa2, as well as with RUNX1, indicative of definitive endoderm and hemangioblasts, respectively. STELLA was never found with MIXl1. On the basis of these and previous results, we conclude that STELLA identifies at least five distinct cell subpopulations within the allantois and hindgut, where they may be involved in mesendodermal differentiation and hematopoiesis at the posterior embryonic-extraembryonic interface. These data provide a new point of departure for understanding STELLA's potential roles in building the fetal-placental connection.
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Affiliation(s)
- Adam D Wolfe
- Department of Pediatrics, Division of Pediatric Hematology, Oncology & Bone Marrow Transplant, University of Wisconsin-Madison School of Medicine and Public Health, 1111 Highland Avenue, 4105 WIMR, Madison, WI 53705, United States
| | - Adriana M Rodriguez
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Ave, Madison, WI 53706, United States
| | - Karen M Downs
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Ave, Madison, WI 53706, United States
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47
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In vitro generation of mature midbrain-type dopamine neurons by adjusting exogenous Nurr1 and Foxa2 expressions to their physiologic patterns. Exp Mol Med 2017; 49:e300. [PMID: 28280264 PMCID: PMC5382556 DOI: 10.1038/emm.2016.163] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 09/24/2016] [Accepted: 11/09/2016] [Indexed: 12/23/2022] Open
Abstract
Developmental information aids stem cell biologists in producing tissue-specific cells. Recapitulation of the developmental profile of a specific cell type in an in vitro stem cell system provides a strategy for manipulating cell-fate choice during the differentiation process. Nurr1 and Foxa2 are potential candidates for genetic engineering to generate midbrain-type dopamine (DA) neurons for experimental and therapeutic applications in Parkinson's disease (PD), as forced expression of these genes in neural stem/precursor cells (NPCs) yields cells with a complete battery of midbrain DA neuron-specific genes. However, simple overexpression without considering their expression pattern in the developing midbrain tends to generate DA cells without adequate neuronal maturation and long-term maintenance of their phenotype in vitro and in vivo after transplantation. We here show that the physiological levels and timing of Nurr1 and Foxa2 expression can be replicated in NPCs by choosing the right vectors and promoters. Controlled expression combined with a strategy for transgene expression maintenance induced generation of fully mature midbrain-type DA neurons. These findings demonstrate the feasibility of cellular engineering for artificial cell-fate specification.
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48
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Villasenor A, Stainier DYR. On the development of the hepatopancreatic ductal system. Semin Cell Dev Biol 2017; 66:69-80. [PMID: 28214561 DOI: 10.1016/j.semcdb.2017.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/03/2017] [Accepted: 02/13/2017] [Indexed: 12/13/2022]
Abstract
The hepatopancreatic ductal system is the collection of ducts that connect the liver and pancreas to the digestive tract. The formation of this system is necessary for the transport of exocrine secretions, for the correct assembly of the pancreatobiliary ductal system, and for the overall function of the digestive system. Studies on endoderm organ formation have significantly advanced our understanding of the molecular mechanisms that govern organ induction, organ specification and morphogenesis of the major foregut-derived organs. However, little is known about the mechanisms that control the development of the hepatopancreatic ductal system. Here, we provide a description of the different components of the system, summarize its development from the endoderm to a complex system of tubes, list the pathologies produced by anomalies in its development, as well as the molecules and signaling pathways that are known to be involved in its formation. Finally, we discuss its proposed potential as a multipotent cell reservoir and the unresolved questions in the field.
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Affiliation(s)
- Alethia Villasenor
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
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49
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Abstract
Forkhead box (Fox) transcription factors are evolutionarily conserved in organisms ranging from yeast to humans. They regulate diverse biological processes both during development and throughout adult life. Mutations in many Fox genes are associated with human disease and, as such, various animal models have been generated to study the function of these transcription factors in mechanistic detail. In many cases, the absence of even a single Fox transcription factor is lethal. In this Primer, we provide an overview of the Fox family, highlighting several key Fox transcription factor families that are important for mammalian development.
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Affiliation(s)
- Maria L Golson
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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50
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Rastegar-Pouyani S, Khazaei N, Wee P, Mohammadnia A, Yaqubi M. Role of Hepatic-Specific Transcription Factors and Polycomb Repressive Complex 2 during Induction of Fibroblasts to Hepatic Fate. PLoS One 2016; 11:e0167081. [PMID: 27902735 PMCID: PMC5130264 DOI: 10.1371/journal.pone.0167081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/08/2016] [Indexed: 01/08/2023] Open
Abstract
Direct reprogramming using defined sets of transcription factors (TFs) is a recent strategy for generating induced hepatocytes (iHeps) from fibroblasts for use in regenerative medicine and drug development. Comprehensive studies detailing the regulatory role of TFs during this reprogramming process could help increase its efficiency. This study aimed to find the TFs with the greatest influences on the generation of iHeps from fibroblasts, and to further understand their roles in the regulation of the gene expression program. Here, we used systems biology approaches to analyze high quality expression data sets in combination with TF-binding sites data and protein-protein interactions data during the direct reprogramming of fibroblasts to iHeps. Our results revealed two main patterns for differentially expressed genes (DEGs): up-regulated genes were categorized as hepatic-specific pattern, and down-regulated genes were categorized as mesoderm- and fibroblast-specific pattern. Interestingly, hepatic-specific genes co-expressed and were regulated by hepatic-specific TFs, specifically Hnf4a and Foxa2. Conversely, the mesoderm- and fibroblast-specific pattern was mainly silenced by polycomb repressive complex 2 (PRC2) members, including Suz12, Mtf2, Ezh2, and Jarid2. Independent analysis of both the gene and core regulatory network of DE-TFs showed significant roles for Hnf4a, Foxa2, and PRC2 members in the regulation of the gene expression program and in biological processes during the direct conversion process. Altogether, using systems biology approaches, we clarified the role of Hnf4a and Foxa2 as hepatic-specific TFs, and for the first time, introduced the PRC2 complex as the main regulator that favors the direct reprogramming process in cooperation with hepatic-specific factors.
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Affiliation(s)
- Shima Rastegar-Pouyani
- Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Niusha Khazaei
- Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ping Wee
- Department of Medical Genetics and Signal Transduction Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Abdulshakour Mohammadnia
- Department of Human Genetics, Division of Hematology and Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Moein Yaqubi
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec, Canada
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
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