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Soszyńska A, Krawczyk K, Szpila M, Winek E, Szpakowska A, Suwińska A. Exposure of chimaeric embryos to exogenous FGF4 leads to the production of pure ESC-derived mice. Theriogenology 2024; 222:10-21. [PMID: 38603966 DOI: 10.1016/j.theriogenology.2024.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/28/2024] [Accepted: 03/31/2024] [Indexed: 04/13/2024]
Abstract
Producing chimaeras constitutes the most reliable method of verifying the pluripotency of newly established cells. Moreover, forming chimaeras by injecting genetically modified embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) into the embryo is part of the procedure for generating transgenic mice, which are used for understanding gene function. Conventional methods for generating transgenic mice, including the breeding of chimaeras and tetraploid complementation, are time-consuming and cost-inefficient, with significant limitations that hinder their effectiveness and widespread applications. In the present study, we modified the traditional method of chimaera generation to significantly speed up this process by generating mice exclusively derived from ESCs. This study aimed to assess whether fully ESC-derived mice could be obtained by modulating fibroblast growth factor 4 (FGF4) levels in the culture medium and changing the direction of cell differentiation in the chimaeric embryo. We found that exogenous FGF4 directs all host blastomeres to the primitive endoderm fate, but does not affect the localisation of ESCs in the epiblast of the chimaeric embryos. Consequently, all FGF4-treated chimaeric embryos contained an epiblast composed exclusively of ESCs, and following transfer into recipient mice, these embryos developed into fully ESC-derived newborns. Collectively, this simple approach could accelerate the generation of ESC-derived animals and thus optimise ESC-mediated transgenesis and the verification of cell pluripotency. Compared to traditional methods, it could speed up functional studies by several weeks and significantly reduce costs related to maintaining and breeding chimaeras. Moreover, since the effect of stimulating the FGF signalling pathway is universal across different animal species, our approach can be applied not only to rodents but also to other animals, offering its utility beyond laboratory settings.
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Affiliation(s)
- Anna Soszyńska
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Katarzyna Krawczyk
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Marcin Szpila
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Eliza Winek
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Anna Szpakowska
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Aneta Suwińska
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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2
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Kubo N, Chen PB, Hu R, Ye Z, Sasaki H, Ren B. H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation. Mol Cell 2024; 84:1742-1752.e5. [PMID: 38513661 PMCID: PMC11069443 DOI: 10.1016/j.molcel.2024.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/17/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Histone H3 lysine 4 mono-methylation (H3K4me1) marks poised or active enhancers. KMT2C (MLL3) and KMT2D (MLL4) catalyze H3K4me1, but their histone methyltransferase activities are largely dispensable for transcription during early embryogenesis in mammals. To better understand the role of H3K4me1 in enhancer function, we analyze dynamic enhancer-promoter (E-P) interactions and gene expression during neural differentiation of the mouse embryonic stem cells. We found that KMT2C/D catalytic activities were only required for H3K4me1 and E-P contacts at a subset of candidate enhancers, induced upon neural differentiation. By contrast, a majority of enhancers retained H3K4me1 in KMT2C/D catalytic mutant cells. Surprisingly, H3K4me1 signals at these KMT2C/D-independent sites were reduced after acute depletion of KMT2B, resulting in aggravated transcriptional defects. Our observations therefore implicate KMT2B in the catalysis of H3K4me1 at enhancers and provide additional support for an active role of H3K4me1 in enhancer-promoter interactions and transcription in mammalian cells.
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Affiliation(s)
- Naoki Kubo
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA; Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Poshen B Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA; Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore; Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 7 Engineering Drive 1, Singapore 117574, Singapore
| | - Rong Hu
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Zhen Ye
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA; Center for Epigenomics, Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genome Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
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3
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Lee M, Guo Q, Kim M, Choi J, Segura A, Genceroglu A, LeBlanc L, Ramirez N, Jang YJ, Jang Y, Lee BK, Marcotte EM, Kim J. Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches. Genome Res 2024; 34:484-497. [PMID: 38580401 PMCID: PMC11067882 DOI: 10.1101/gr.277926.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/21/2024] [Indexed: 04/07/2024]
Abstract
Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.
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Affiliation(s)
- Muyoung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Qingqing Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Mijeong Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Joonhyuk Choi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alia Segura
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alper Genceroglu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Nereida Ramirez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yu Jin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yeejin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York 12144, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA;
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Giri A, Kar S. Interlinked bi-stable switches govern the cell fate commitment of embryonic stem cells. FEBS Lett 2024; 598:915-934. [PMID: 38408774 DOI: 10.1002/1873-3468.14832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/23/2023] [Accepted: 02/03/2024] [Indexed: 02/28/2024]
Abstract
The development of embryonic stem (ES) cells to extraembryonic trophectoderm and primitive endoderm lineages manifests distinct steady-state expression patterns of two key transcription factors-Oct4 and Nanog. How dynamically such kind of steady-state expressions are maintained remains elusive. Herein, we demonstrate that steady-state dynamics involving two bistable switches which are interlinked via a stepwise (Oct4) and a mushroom-like (Nanog) manner orchestrate the fate specification of ES cells. Our hypothesis qualitatively reconciles various experimental observations and elucidates how different feedback and feedforward motifs orchestrate the extraembryonic development and stemness maintenance of ES cells. Importantly, the model predicts strategies to optimize the dynamics of self-renewal and differentiation of embryonic stem cells that may have therapeutic relevance in the future.
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Affiliation(s)
- Amitava Giri
- Department of Chemistry, IIT Bombay, Powai, India
| | - Sandip Kar
- Department of Chemistry, IIT Bombay, Powai, India
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Polat S, Yazir Y, Duruksu G, Kiliç KC, Mert S, Gacar G, Öncel Duman B, Halbutoğullari ZS. Investigation of the differentiation potential of pericyte cells as an alternative source of mesenchymal stem cells. Acta Histochem 2024; 126:152145. [PMID: 38432161 DOI: 10.1016/j.acthis.2024.152145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND The mesenchymal stem cells (MSCs) with characterized by their multipotency and capacity to differentiate into various tissue cell types, have led to their incorporation in regenerative medicine research. However, the limited numbers of MSCs in the human body and their diverse differentiation capabilities in tissues highlight the need for exploring alternative regenerative cell sources. In this study, therefore, we conducted molecular level examinations to determine whether pericytes, specialized cell communities situated near blood vessels, could serve as a substitute for human bone marrow-derived mesenchymal stem cells (hBM-MSCs). In this context, the potential application of pericytes surrounds the vessels when MSCs are insufficient for functional purposes. METHODS The pericytes utilized in this investigation were derived from the placenta and characterized at the third passage. Similarly, the hBM-MSCs were also characterized at the third passage. The pluripotent properties of the two cell types were assessed at the gene expression level. Thereafter, both pericytes and hBM-MSCs were directed towards adipogenic, osteogenic and chondrogenic differentiation. The cells in both groups were examined on days 7, 14, and, 21 and their differentiation status was compared both immunohistochemically and through gene expression analysis. RESULTS Upon comparing the pluripotency characteristics of placental pericytes and hBM-MSCs, it was discovered that there was a substantial upregulation of the pluripotency genes FoxD3, Sox2, ZPF42, UTF1, and, Lin28 in both cell types. However, no significant expression of the genes Msx1, Nr6a1, Pdx1, and, GATA6 was observed in either cell type. It was also noted that pericytes differentiate into adipogenic, osteogenic and, chondrogenic lineages similar to hBM-MSCs. DISCUSSION As a result, it has been determined that pericytes exhibit high differentiation and proliferation properties similar to those of MSCs, and therefore can be considered a suitable alternative cell source for regenerative medicine and tissue engineering research, in cases where MSCs are not available or insufficient. It is notable that pericytes have been suggested as a potential substitute in studies where MSCs are lacking.
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Affiliation(s)
- Selen Polat
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey
| | - Yusufhan Yazir
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey; Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Histology and Embryology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey.
| | - Gökhan Duruksu
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey; Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey
| | - Kamil Can Kiliç
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey
| | - Serap Mert
- Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Chemistry and Chemical Processing Technologies, Kocaeli University, Kocaeli, Turkey; Department of Polymer Science and Technology, Kocaeli University, Kocaeli, Turkey
| | - Gülçin Gacar
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey; Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey
| | - Büşra Öncel Duman
- Medical Laboratory Techniques Program, European Vocational School, Kocaeli Health and Technology University, Kocaeli, Turkey
| | - Zehra Seda Halbutoğullari
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey; Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
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6
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Lodewijk GA, Kozuki S, Han C, Topacio BR, Zargari A, Lee S, Knight G, Ashton R, Qi LS, Shariati SA. Self-organization of embryonic stem cells into a reproducible embryo model through epigenome editing. bioRxiv 2024:2024.03.05.583597. [PMID: 38496557 PMCID: PMC10942404 DOI: 10.1101/2024.03.05.583597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Embryonic stem cells (ESCs) can self-organize in vitro into developmental patterns with spatial organization and molecular similarity to that of early embryonic stages. This self-organization of ESCs requires transmission of signaling cues, via addition of small molecule chemicals or recombinant proteins, to induce distinct embryonic cellular fates and subsequent assembly into structures that can mimic aspects of early embryonic development. During natural embryonic development, different embryonic cell types co-develop together, where each cell type expresses specific fate-inducing transcription factors through activation of non-coding regulatory elements and interactions with neighboring cells. However, previous studies have not fully explored the possibility of engineering endogenous regulatory elements to shape self-organization of ESCs into spatially-ordered embryo models. Here, we hypothesized that cell-intrinsic activation of a minimum number of such endogenous regulatory elements is sufficient to self-organize ESCs into early embryonic models. Our results show that CRISPR-based activation (CRISPRa) of only two endogenous regulatory elements in the genome of pluripotent stem cells is sufficient to generate embryonic patterns that show spatial and molecular resemblance to that of pre-gastrulation mouse embryonic development. Quantitative single-cell live fluorescent imaging showed that the emergence of spatially-ordered embryonic patterns happens through the intrinsic induction of cell fate that leads to an orchestrated collective cellular motion. Based on these results, we propose a straightforward approach to efficiently form 3D embryo models through intrinsic CRISPRa-based epigenome editing and independent of external signaling cues. CRISPRa-Programmed Embryo Models (CPEMs) show highly consistent composition of major embryonic cell types that are spatially-organized, with nearly 80% of the structures forming an embryonic cavity. Single cell transcriptomics confirmed the presence of main embryonic cell types in CPEMs with transcriptional similarity to pre-gastrulation mouse embryos and revealed novel signaling communication links between different embryonic cell types. Our findings offer a programmable embryo model and demonstrate that minimum intrinsic epigenome editing is sufficient to self-organize ESCs into highly consistent pre-gastrulation embryo models.
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Affiliation(s)
- Gerrald A Lodewijk
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
- Equal contribution to this work
| | - Sayaka Kozuki
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
- Equal contribution to this work
| | - Clara Han
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
| | - Benjamin R Topacio
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
| | - Abolfazl Zargari
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, CA
| | - Seungho Lee
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
| | - Gavin Knight
- Neurosetta LLC, Madison, WI
- Wisconsin Institute for Discovery, Madison, WI
| | - Randolph Ashton
- Neurosetta LLC, Madison, WI
- Wisconsin Institute for Discovery, Madison, WI
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA
- Sarafan ChEM-H, Stanford University, Stanford, CA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA
| | - S Ali Shariati
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
- Genomics Institute, University of California, Santa Cruz, CA
- Institute for The Biology of Stem Cells, University of California, Santa Cruz, CA
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7
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Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages. Nat Struct Mol Biol 2024; 31:125-140. [PMID: 38053013 PMCID: PMC10897904 DOI: 10.1038/s41594-023-01130-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 09/18/2023] [Indexed: 12/07/2023]
Abstract
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages: the trophectoderm, the epiblast and the primitive endoderm. Although key signaling pathways and transcription factors that control these early embryonic decisions have been identified, the non-coding regulatory elements through which transcriptional regulators enact these fates remain understudied. Here, we characterize, at a genome-wide scale, enhancer activity and 3D connectivity in embryo-derived stem cell lines that represent each of the early developmental fates. We observe extensive enhancer remodeling and fine-scale 3D chromatin rewiring among the three lineages, which strongly associate with transcriptional changes, although distinct groups of genes are irresponsive to topological changes. In each lineage, a high degree of connectivity, or 'hubness', positively correlates with levels of gene expression and enriches for cell-type specific and essential genes. Genes within 3D hubs also show a significantly stronger probability of coregulation across lineages compared to genes in linear proximity or within the same contact domains. By incorporating 3D chromatin features, we build a predictive model for transcriptional regulation (3D-HiChAT) that outperforms models using only 1D promoter or proximal variables to predict levels and cell-type specificity of gene expression. Using 3D-HiChAT, we identify, in silico, candidate functional enhancers and hubs in each cell lineage, and with CRISPRi experiments, we validate several enhancers that control gene expression in their respective lineages. Our study identifies 3D regulatory hubs associated with the earliest mammalian lineages and describes their relationship to gene expression and cell identity, providing a framework to comprehensively understand lineage-specific transcriptional behaviors.
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Affiliation(s)
- Dylan Murphy
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Eralda Salataj
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- 3D Chromatin Conformation and RNA Genomics Laboratory, Center for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Langone Health, New York, NY, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Langone Health, New York, NY, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Erin Char
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Christopher M Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ly-Sha Ee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - UkJin Lee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Matthias Stadtfeld
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Health, New York, NY, USA.
- Department of Medicine, New York University Langone Health, New York, NY, USA.
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA.
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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Ori C, Ansari M, Angelidis I, Olmer R, Martin U, Theis FJ, Schiller HB, Drukker M. Human pluripotent stem cell fate trajectories toward lung and hepatocyte progenitors. iScience 2023; 26:108205. [PMID: 38026193 PMCID: PMC10663741 DOI: 10.1016/j.isci.2023.108205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 07/13/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
In this study, we interrogate molecular mechanisms underlying the specification of lung progenitors from human pluripotent stem cells (hPSCs). We employ single-cell RNA-sequencing with high temporal precision, alongside an optimized differentiation protocol, to elucidate the transcriptional hierarchy of lung specification to chart the associated single-cell trajectories. Our findings indicate that Sonic hedgehog, TGF-β, and Notch activation are essential within an ISL1/NKX2-1 trajectory, leading to the emergence of lung progenitors during the foregut endoderm phase. Additionally, the induction of HHEX delineates an alternate trajectory at the early definitive endoderm stage, preceding the lung pathway and giving rise to a significant hepatoblast population. Intriguingly, neither KDR+ nor mesendoderm progenitors manifest as intermediate stages in the lung and hepatic lineage development. Our multistep model offers insights into lung organogenesis and provides a foundation for in-depth study of early human lung development and modeling using hPSCs.
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Affiliation(s)
- Chaido Ori
- Institute of Stem Cell Research, Helmholtz Munich, Neuherberg, Munich, Germany
| | - Meshal Ansari
- Comprehensive Pneumology Center Munich (CPC-M), Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Munich, Germany
| | - Ilias Angelidis
- Comprehensive Pneumology Center Munich (CPC-M), Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Ruth Olmer
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, 30625 Hannover, Germany
- REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, 30625 Hannover, Germany
- REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Fabian J. Theis
- Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Herbert B. Schiller
- Comprehensive Pneumology Center Munich (CPC-M), Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Munich, Neuherberg, Munich, Germany
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
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9
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Ravid Lustig L, Sampath Kumar A, Schwämmle T, Dunkel I, Noviello G, Limberg E, Weigert R, Pacini G, Buschow R, Ghauri A, Stötzel M, Wittler L, Meissner A, Schulz EG. GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers. Nat Cell Biol 2023; 25:1704-1715. [PMID: 37932452 PMCID: PMC10635832 DOI: 10.1038/s41556-023-01266-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/22/2023] [Indexed: 11/08/2023]
Abstract
X-chromosome inactivation (XCI) balances gene expression between the sexes in female mammals. Shortly after fertilization, upregulation of Xist RNA from one X chromosome initiates XCI, leading to chromosome-wide gene silencing. XCI is maintained in all cell types, except the germ line and the pluripotent state where XCI is reversed. The mechanisms triggering Xist upregulation have remained elusive. Here we identify GATA transcription factors as potent activators of Xist. Through a pooled CRISPR activation screen in murine embryonic stem cells, we demonstrate that GATA1, as well as other GATA transcription factors can drive ectopic Xist expression. Moreover, we describe GATA-responsive regulatory elements in the Xist locus bound by different GATA factors. Finally, we show that GATA factors are essential for XCI induction in mouse preimplantation embryos. Deletion of GATA1/4/6 or GATA-responsive Xist enhancers in mouse zygotes effectively prevents Xist upregulation. We propose that the activity or complete absence of various GATA family members controls initial Xist upregulation, XCI maintenance in extra-embryonic lineages and XCI reversal in the epiblast.
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Affiliation(s)
- Liat Ravid Lustig
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Abhishek Sampath Kumar
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Till Schwämmle
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ilona Dunkel
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gemma Noviello
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Elodie Limberg
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Raha Weigert
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Guido Pacini
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - René Buschow
- Microscopy and Cryo-Electron Microscopy, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Afrah Ghauri
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maximilian Stötzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Edda G Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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10
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Pham PD, Lu H, Han H, Zhou JJ, Madan A, Wang W, Murre C, Cho KWY. Transcriptional network governing extraembryonic endoderm cell fate choice. Dev Biol 2023; 502:20-37. [PMID: 37423592 PMCID: PMC10550205 DOI: 10.1016/j.ydbio.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023]
Abstract
The mechanism by which transcription factor (TF) network instructs cell-type-specific transcriptional programs to drive primitive endoderm (PrE) progenitors to commit to parietal endoderm (PE) versus visceral endoderm (VE) cell fates remains poorly understood. To address the question, we analyzed the single-cell transcriptional signatures defining PrE, PE, and VE cell states during the onset of the PE-VE lineage bifurcation. By coupling with the epigenomic comparison of active enhancers unique to PE and VE cells, we identified GATA6, SOX17, and FOXA2 as central regulators for the lineage divergence. Transcriptomic analysis of cXEN cells, an in vitro model for PE cells, after the acute depletion of GATA6 or SOX17 demonstrated that these factors induce Mycn, imparting the self-renewal properties of PE cells. Concurrently, they suppress the VE gene program, including key genes like Hnf4a and Ttr, among others. We proceeded with RNA-seq analysis on cXEN cells with FOXA2 knockout, in conjunction with GATA6 or SOX17 depletion. We found FOXA2 acts as a potent suppressor of Mycn while simultaneously activating the VE gene program. The antagonistic gene regulatory activities of GATA6/SOX17 and FOXA2 in promoting alternative cell fates, and their physical co-bindings at the enhancers provide molecular insights to the plasticity of the PrE lineage. Finally, we show that the external cue, BMP signaling, promotes the VE cell fate by activation of VE TFs and repression of PE TFs including GATA6 and SOX17. These data reveal a putative core gene regulatory module that underpins PE and VE cell fate choice.
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Affiliation(s)
- Paula Duyen Pham
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Hanbin Lu
- School of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, 92039, USA
| | - Han Han
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Jeff Jiajing Zhou
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Aarushi Madan
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Cornelis Murre
- School of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, 92039, USA
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA.
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11
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Weatherbee BAT, Gantner CW, Iwamoto-Stohl LK, Daza RM, Hamazaki N, Shendure J, Zernicka-Goetz M. Pluripotent stem cell-derived model of the post-implantation human embryo. Nature 2023; 622:584-593. [PMID: 37369347 PMCID: PMC10584688 DOI: 10.1038/s41586-023-06368-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
The human embryo undergoes morphogenetic transformations following implantation into the uterus, but our knowledge of this crucial stage is limited by the inability to observe the embryo in vivo. Models of the embryo derived from stem cells are important tools for interrogating developmental events and tissue-tissue crosstalk during these stages1. Here we establish a model of the human post-implantation embryo, a human embryoid, comprising embryonic and extraembryonic tissues. We combine two types of extraembryonic-like cell generated by overexpression of transcription factors with wild-type embryonic stem cells and promote their self-organization into structures that mimic several aspects of the post-implantation human embryo. These self-organized aggregates contain a pluripotent epiblast-like domain surrounded by extraembryonic-like tissues. Our functional studies demonstrate that the epiblast-like domain robustly differentiates into amnion, extraembryonic mesenchyme and primordial germ cell-like cells in response to bone morphogenetic protein cues. In addition, we identify an inhibitory role for SOX17 in the specification of anterior hypoblast-like cells2. Modulation of the subpopulations in the hypoblast-like compartment demonstrates that extraembryonic-like cells influence epiblast-like domain differentiation, highlighting functional tissue-tissue crosstalk. In conclusion, we present a modular, tractable, integrated3 model of the human embryo that will enable us to probe key questions of human post-implantation development, a critical window during which substantial numbers of pregnancies fail.
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Affiliation(s)
- Bailey A T Weatherbee
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Carlos W Gantner
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Lisa K Iwamoto-Stohl
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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12
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Knudsen TE, Hamilton WB, Proks M, Lykkegaard M, Linneberg-Agerholm M, Nielsen AV, Perera M, Malzard LL, Trusina A, Brickman JM. A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation. Cell Syst 2023; 14:788-805.e8. [PMID: 37633265 DOI: 10.1016/j.cels.2023.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 03/22/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
Cooperative DNA binding of transcription factors (TFs) integrates the cellular context to support cell specification during development. Naive mouse embryonic stem cells are derived from early development and can sustain their pluripotent identity indefinitely. Here, we ask whether TFs associated with pluripotency evolved to directly support this state or if the state emerges from their combinatorial action. NANOG and ESRRB are key pluripotency factors that co-bind DNA. We find that when both factors are expressed, ESRRB supports pluripotency. However, when NANOG is absent, ESRRB supports a bistable culture of cells with an embryo-like primitive endoderm identity ancillary to pluripotency. The stoichiometry between NANOG and ESRRB allows quantitative titration of this differentiation, and in silico modeling of bipartite ESRRB activity suggests it safeguards plasticity in differentiation. Thus, the concerted activity of cooperative TFs can transform their effect to sustain intermediate cell identities and allow ex vivo expansion of immortal stem cells. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Teresa E Knudsen
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - William B Hamilton
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
| | - Martin Proks
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Maria Lykkegaard
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Madeleine Linneberg-Agerholm
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | | | - Marta Perera
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | | | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joshua M Brickman
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
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13
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Abel A, Sozen B. Shifting early embryology paradigms: Applications of stem cell-based embryo models in bioengineering. Curr Opin Genet Dev 2023; 81:102069. [PMID: 37392541 PMCID: PMC10530566 DOI: 10.1016/j.gde.2023.102069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/16/2023] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
Technologies to reproduce specific aspects of early mammalian embryogenesis in vitro using stem cells have skyrocketed over the last several years. With these advances, we have gained new perspectives on how embryonic and extraembryonic cells self-organize to form the embryo. These reductionist approaches hold promise for the future implementation of precise environmental and genetic controls to understand variables affecting embryo development. Our review discusses recent progress in cellular models of early mammalian embryo development and bioengineering advancements that can be leveraged to study the embryo-maternal interface. We summarize current gaps in the field, emphasizing the importance of understanding how intercellular interactions at this interface contribute to reproductive and developmental health.
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Affiliation(s)
- Ashley Abel
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06520, USA. https://twitter.com/@caitrionacunn
| | - Berna Sozen
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, Yale University, New Haven, CT 06520, USA.
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14
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Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression. bioRxiv 2023:2023.07.19.549714. [PMID: 37577543 PMCID: PMC10422694 DOI: 10.1101/2023.07.19.549714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages, the trophectoderm (TE), the epiblast (EPI) and the primitive endoderm (PrE). Although key signaling pathways and transcription factors that control these early embryonic decisions have been identified, the non-coding regulatory elements via which transcriptional regulators enact these fates remain understudied. To address this gap, we have characterized, at a genome-wide scale, enhancer activity and 3D connectivity in embryo-derived stem cell lines that represent each of the early developmental fates. We observed extensive enhancer remodeling and fine-scale 3D chromatin rewiring among the three lineages, which strongly associate with transcriptional changes, although there are distinct groups of genes that are irresponsive to topological changes. In each lineage, a high degree of connectivity or "hubness" positively correlates with levels of gene expression and enriches for cell-type specific and essential genes. Genes within 3D hubs also show a significantly stronger probability of coregulation across lineages, compared to genes in linear proximity or within the same contact domains. By incorporating 3D chromatin features, we build a novel predictive model for transcriptional regulation (3D-HiChAT), which outperformed models that use only 1D promoter or proximal variables in predicting levels and cell-type specificity of gene expression. Using 3D-HiChAT, we performed genome-wide in silico perturbations to nominate candidate functional enhancers and hubs in each cell lineage, and with CRISPRi experiments we validated several novel enhancers that control expression of one or more genes in their respective lineages. Our study comprehensively identifies 3D regulatory hubs associated with the earliest mammalian lineages and describes their relationship to gene expression and cell identity, providing a framework to understand lineage-specific transcriptional behaviors.
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Affiliation(s)
- Dylan Murphy
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Eralda Salataj
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
- 3D Chromatin Conformation and RNA genomics laboratory, Instituto Italiano di Tecnologia (IIT), Center for Human Technologies (CHT), Genova, Italy (current affiliation)
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Erin Char
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, 10065, New York, USA
| | - Christopher M. Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Ly-sha Ee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - UkJin Lee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Matthias Stadtfeld
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
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15
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Lubatti G, Stock M, Iturbide A, Ruiz Tejada Segura ML, Riepl M, Tyser RCV, Danese A, Colomé-Tatché M, Theis FJ, Srinivas S, Torres-Padilla ME, Scialdone A. CIARA: a cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data. Development 2023; 150:dev201264. [PMID: 37294170 DOI: 10.1242/dev.201264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/25/2023] [Indexed: 05/18/2023]
Abstract
A powerful feature of single-cell genomics is the possibility of identifying cell types from their molecular profiles. In particular, identifying novel rare cell types and their marker genes is a key potential of single-cell RNA sequencing. Standard clustering approaches perform well in identifying relatively abundant cell types, but tend to miss rarer cell types. Here, we have developed CIARA (Cluster Independent Algorithm for the identification of markers of RAre cell types), a cluster-independent computational tool designed to select genes that are likely to be markers of rare cell types. Genes selected by CIARA are subsequently integrated with common clustering algorithms to single out groups of rare cell types. CIARA outperforms existing methods for rare cell type detection, and we use it to find previously uncharacterized rare populations of cells in a human gastrula and among mouse embryonic stem cells treated with retinoic acid. Moreover, CIARA can be applied more generally to any type of single-cell omic data, thus allowing the identification of rare cells across multiple data modalities. We provide implementations of CIARA in user-friendly packages available in R and Python.
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Affiliation(s)
- Gabriele Lubatti
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, D-81377 Munich, Germany
- Institute of Functional Epigenetics, Helmholtz Munich, D-85764 Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Munich, D-85764 Neuherberg, Germany
| | - Marco Stock
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, D-81377 Munich, Germany
- Institute of Functional Epigenetics, Helmholtz Munich, D-85764 Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Munich, D-85764 Neuherberg, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, D-85354 Freising, Germany
| | - Ane Iturbide
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, D-81377 Munich, Germany
| | - Mayra L Ruiz Tejada Segura
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, D-81377 Munich, Germany
- Institute of Functional Epigenetics, Helmholtz Munich, D-85764 Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Munich, D-85764 Neuherberg, Germany
| | - Melina Riepl
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, D-81377 Munich, Germany
- Institute of Functional Epigenetics, Helmholtz Munich, D-85764 Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Munich, D-85764 Neuherberg, Germany
| | - Richard C V Tyser
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Anna Danese
- Biomedical Center Munich (BMC), Physiological Genomics, Faculty of Medicine, Ludwig Maximilians University, D-82152 Munich, Germany
| | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Munich, D-85764 Neuherberg, Germany
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, Ludwig Maximilians University, D-82152 Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Munich, D-85764 Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, D-85748 Munich, Germany
| | - Shankar Srinivas
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, D-81377 Munich, Germany
- Faculty of Biology, Ludwig-Maximilians University, D-82152 Munich, Germany
| | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, D-81377 Munich, Germany
- Institute of Functional Epigenetics, Helmholtz Munich, D-85764 Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Munich, D-85764 Neuherberg, Germany
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16
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Xie G, Lee JE, Senft AD, Park YK, Jang Y, Chakraborty S, Thompson JJ, McKernan K, Liu C, Macfarlan TS, Rocha PP, Peng W, Ge K. MLL3/MLL4 methyltransferase activities control early embryonic development and embryonic stem cell differentiation in a lineage-selective manner. Nat Genet 2023; 55:693-705. [PMID: 37012455 DOI: 10.1038/s41588-023-01356-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/27/2023] [Indexed: 04/05/2023]
Abstract
H3K4me1 methyltransferases MLL3 (KMT2C) and MLL4 (KMT2D) are critical for enhancer activation, cell differentiation and development. However, roles of MLL3/4 enzymatic activities and MLL3/4-mediated enhancer H3K4me1 in these processes remain unclear. Here we report that constitutive elimination of both MLL3 and MLL4 enzymatic activities prevents initiation of gastrulation and leads to early embryonic lethality in mice. However, selective elimination of MLL3/4 enzymatic activities in embryonic, but not extraembryonic, lineages leaves gastrulation largely intact. Consistent with this, embryonic stem cells (ESCs) lacking MLL3/4 enzymatic activities can differentiate toward the three embryonic germ layers but show aberrant differentiation to extraembryonic endoderm (ExEn) and trophectoderm. The failure in ExEn differentiation can be attributed to markedly reduced enhancer-binding of the lineage-determining transcription factor GATA6. Furthermore, we show that MLL3/4-catalyzed H3K4me1 is largely dispensable for enhancer activation during ESC differentiation. Together, our findings suggest a lineage-selective, but enhancer activation-independent, role of MLL3/4 methyltransferase activities in early embryonic development and ESC differentiation.
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Affiliation(s)
- Guojia Xie
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ji-Eun Lee
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anna D Senft
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Young-Kwon Park
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Younghoon Jang
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shreeta Chakraborty
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Joyce J Thompson
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kaitlin McKernan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Weiqun Peng
- Departments of Physics and Anatomy and Cell Biology, The George Washington University, Washington, DC, USA
| | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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17
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Garg V, Yang Y, Nowotschin S, Setty M, Kuo YY, Sharma R, Polyzos A, Salataj E, Murphy D, Jang A, Pe’er D, Apostolou E, Hadjantonakis AK. Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities. bioRxiv 2023:2023.03.28.534648. [PMID: 37034770 PMCID: PMC10081288 DOI: 10.1101/2023.03.28.534648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Two distinct fates, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common progenitor cells, the inner cell mass (ICM), in mammalian embryos. To study how these sister identities are forged, we leveraged embryonic (ES) and eXtraembryonic ENdoderm (XEN) stem cells - in vitro counterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses uncovered distinct rates, efficiencies and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions. While GATA4-mediated ES-to-iXEN conversion was rapid and nearly deterministic, OCT4, KLF4 and SOX2-induced XEN-to-iPS reprogramming progressed with diminished efficiency and kinetics. The dominant PrE transcriptional program, safeguarded by Gata4, and globally elevated chromatin accessibility of EPI underscored the differential plasticities of the two states. Mapping in vitro trajectories to embryos revealed reprogramming in either direction tracked along, and toggled between, EPI and PrE in vivo states without transitioning through the ICM.
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Affiliation(s)
- Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Yang Yang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Manu Setty
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ying-Yi Kuo
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Roshan Sharma
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Polyzos
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Eralda Salataj
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Dylan Murphy
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Amy Jang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Pe’er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Effie Apostolou
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
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18
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Wei Y, Han S, Wen J, Liao J, Liang J, Yu J, Chen X, Xiang S, Huang Z, Zhang B. E26 transformation-specific transcription variant 5 in development and cancer: modification, regulation and function. J Biomed Sci 2023; 30:17. [PMID: 36872348 PMCID: PMC9987099 DOI: 10.1186/s12929-023-00909-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
E26 transformation-specific (ETS) transcription variant 5 (ETV5), also known as ETS-related molecule (ERM), exerts versatile functions in normal physiological processes, including branching morphogenesis, neural system development, fertility, embryonic development, immune regulation, and cell metabolism. In addition, ETV5 is repeatedly found to be overexpressed in multiple malignant tumors, where it is involved in cancer progression as an oncogenic transcription factor. Its roles in cancer metastasis, proliferation, oxidative stress response and drug resistance indicate that it is a potential prognostic biomarker, as well as a therapeutic target for cancer treatment. Post-translational modifications, gene fusion events, sophisticated cellular signaling crosstalk and non-coding RNAs contribute to the dysregulation and abnormal activities of ETV5. However, few studies to date systematically summarized the role and molecular mechanisms of ETV5 in benign diseases and in oncogenic progression. In this review, we specify the molecular structure and post-translational modifications of ETV5. In addition, its critical roles in benign and malignant diseases are summarized to draw a panorama for specialists and clinicians. The updated molecular mechanisms of ETV5 in cancer biology and tumor progression are delineated. Finally, we prospect the further direction of ETV5 research in oncology and its potential translational applications in the clinic.
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Affiliation(s)
- Yi Wei
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China
- Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shenqi Han
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China
- Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingyuan Wen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China
- Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingyu Liao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China
- Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junnan Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China
- Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingjing Yu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China
- Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China
- Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- Key Laboratory of Organ Transplantation, National Health Commission, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Shuai Xiang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China.
- Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Zhao Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China.
- Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China.
- Hubei Key Laboratory of Hepato-Pancreatic-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China.
- Key Laboratory of Organ Transplantation, National Health Commission, Wuhan, China.
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China.
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19
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Athanasouli P, Balli M, De Jaime-Soguero A, Boel A, Papanikolaou S, van der Veer BK, Janiszewski A, Vanhessche T, Francis A, El Laithy Y, Nigro AL, Aulicino F, Koh KP, Pasque V, Cosma MP, Verfaillie C, Zwijsen A, Heindryckx B, Nikolaou C, Lluis F. The Wnt/TCF7L1 transcriptional repressor axis drives primitive endoderm formation by antagonizing naive and formative pluripotency. Nat Commun 2023; 14:1210. [PMID: 36869101 PMCID: PMC9984534 DOI: 10.1038/s41467-023-36914-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
Early during preimplantation development and in heterogeneous mouse embryonic stem cells (mESC) culture, pluripotent cells are specified towards either the primed epiblast or the primitive endoderm (PE) lineage. Canonical Wnt signaling is crucial for safeguarding naive pluripotency and embryo implantation, yet the role and relevance of canonical Wnt inhibition during early mammalian development remains unknown. Here, we demonstrate that transcriptional repression exerted by Wnt/TCF7L1 promotes PE differentiation of mESCs and in preimplantation inner cell mass. Time-series RNA sequencing and promoter occupancy data reveal that TCF7L1 binds and represses genes encoding essential naive pluripotency factors and indispensable regulators of the formative pluripotency program, including Otx2 and Lef1. Consequently, TCF7L1 promotes pluripotency exit and suppresses epiblast lineage formation, thereby driving cells into PE specification. Conversely, TCF7L1 is required for PE specification as deletion of Tcf7l1 abrogates PE differentiation without restraining epiblast priming. Taken together, our study underscores the importance of transcriptional Wnt inhibition in regulating lineage specification in ESCs and preimplantation embryo development as well as identifies TCF7L1 as key regulator of this process.
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Affiliation(s)
- Paraskevi Athanasouli
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Martina Balli
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Anchel De Jaime-Soguero
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium.
| | - Annekatrien Boel
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Department for Human Structure and Repair, Ghent University Hospital, 9000, Ghent, Belgium
| | - Sofia Papanikolaou
- Department of Rheumatology, Clinical Immunology, Medical School, University of Crete, 70013, Heraklion, Greece.,Computational Genomics Group, Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Athens, Greece
| | - Bernard K van der Veer
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Adrian Janiszewski
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Tijs Vanhessche
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Annick Francis
- Department of Cardiovascular Sciences, KU Leuven, 3000, Leuven, Belgium
| | - Youssef El Laithy
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Antonio Lo Nigro
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Francesco Aulicino
- Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003, Barcelona, Spain
| | - Kian Peng Koh
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Vincent Pasque
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium.,KU Leuven Institute for Single-Cell Omics (LISCO), 3000, Leuven, Belgium
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003, Barcelona, Spain.,ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Catherine Verfaillie
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - An Zwijsen
- Department of Cardiovascular Sciences, KU Leuven, 3000, Leuven, Belgium
| | - Björn Heindryckx
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Department for Human Structure and Repair, Ghent University Hospital, 9000, Ghent, Belgium
| | - Christoforos Nikolaou
- Computational Genomics Group, Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Athens, Greece
| | - Frederic Lluis
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium.
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20
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Yelagandula R, Stecher K, Novatchkova M, Michetti L, Michlits G, Wang J, Hofbauer P, Vainorius G, Pribitzer C, Isbel L, Mendjan S, Schübeler D, Elling U, Brennecke J, Bell O. ZFP462 safeguards neural lineage specification by targeting G9A/GLP-mediated heterochromatin to silence enhancers. Nat Cell Biol 2023; 25:42-55. [PMID: 36604593 PMCID: PMC10038669 DOI: 10.1038/s41556-022-01051-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/10/2022] [Indexed: 01/07/2023]
Abstract
ZNF462 haploinsufficiency is linked to Weiss-Kruszka syndrome, a genetic disorder characterized by neurodevelopmental defects, including autism. Though conserved in vertebrates and essential for embryonic development, the molecular functions of ZNF462 remain unclear. We identified its murine homologue ZFP462 in a screen for mediators of epigenetic gene silencing. Here we show that ZFP462 safeguards neural lineage specification of mouse embryonic stem cells (ESCs) by targeting the H3K9-specific histone methyltransferase complex G9A/GLP to silence meso-endodermal genes. ZFP462 binds to transposable elements that are potential enhancers harbouring pluripotency and meso-endoderm transcription factor binding sites. Recruiting G9A/GLP, ZFP462 seeds heterochromatin, restricting transcription factor binding. Loss of ZFP462 in ESCs results in increased chromatin accessibility at target sites and ectopic expression of meso-endodermal genes. Taken together, ZFP462 confers lineage and locus specificity to the broadly expressed epigenetic regulator G9A/GLP. Our results suggest that aberrant activation of lineage non-specific genes in the neuronal lineage underlies ZNF462-associated neurodevelopmental pathology.
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Affiliation(s)
- Ramesh Yelagandula
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Karin Stecher
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Vienna, Austria
| | - Maria Novatchkova
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Luca Michetti
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Pablo Hofbauer
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Gintautas Vainorius
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Carina Pribitzer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
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21
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Chowdhary S, Hadjantonakis AK. Journey of the mouse primitive endoderm: from specification to maturation. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210252. [PMID: 36252215 PMCID: PMC9574636 DOI: 10.1098/rstb.2021.0252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/25/2022] [Indexed: 12/22/2022] Open
Abstract
The blastocyst is a conserved stage and distinct milestone in the development of the mammalian embryo. Blastocyst stage embryos comprise three cell lineages which arise through two sequential binary cell fate specification steps. In the first, extra-embryonic trophectoderm (TE) cells segregate from inner cell mass (ICM) cells. Subsequently, ICM cells acquire a pluripotent epiblast (Epi) or extra-embryonic primitive endoderm (PrE, also referred to as hypoblast) identity. In the mouse, nascent Epi and PrE cells emerge in a salt-and-pepper distribution in the early blastocyst and are subsequently sorted into adjacent tissue layers by the late blastocyst stage. Epi cells cluster at the interior of the ICM, while PrE cells are positioned on its surface interfacing the blastocyst cavity, where they display apicobasal polarity. As the embryo implants into the maternal uterus, cells at the periphery of the PrE epithelium, at the intersection with the TE, break away and migrate along the TE as they mature into parietal endoderm (ParE). PrE cells remaining in association with the Epi mature into visceral endoderm. In this review, we discuss our current understanding of the PrE from its specification to its maturation. This article is part of the theme issue 'Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom'.
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Affiliation(s)
- Sayali Chowdhary
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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22
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Thompson JJ, Lee DJ, Mitra A, Frail S, Dale RK, Rocha PP. Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages. Nat Commun 2022; 13. [PMID: 35871075 PMCID: PMC9308780 DOI: 10.1038/s41467-022-31938-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 07/11/2022] [Indexed: 11/26/2022] Open
Abstract
Fate-determining transcription factors (TFs) can promote lineage-restricted transcriptional programs from common progenitor states. The inner cell mass (ICM) of mouse blastocysts co-expresses the TFs NANOG and GATA6, which drive the bifurcation of the ICM into either the epiblast (Epi) or the primitive endoderm (PrE), respectively. Here, we induce GATA6 in embryonic stem cells–that also express NANOG–to characterize how a state of co-expression of opposing TFs resolves into divergent lineages. Surprisingly, we find that GATA6 and NANOG co-bind at the vast majority of Epi and PrE enhancers, a phenomenon we also observe in blastocysts. The co-bound state is followed by eviction and repression of Epi TFs, and quick remodeling of chromatin and enhancer-promoter contacts thus establishing the PrE lineage while repressing the Epi fate. We propose that co-binding of GATA6 and NANOG at shared enhancers maintains ICM plasticity and promotes the rapid establishment of Epi- and PrE-specific transcriptional programs. The authors show that the transcription factors NANOG and GATA6 co-bind the same enhancers in common progenitors before divergent epiblast and primitive endoderm lineages emerge. This may help maintain plasticity at early stages and facilitate bifurcation into distinct lineages
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23
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Moauro A, Kruger RE, O'Hagan D, Ralston A. Fluorescent Reporters Distinguish Stem Cell Colony Subtypes During Somatic Cell Reprogramming. Cell Reprogram 2022; 24:353-362. [PMID: 36342671 PMCID: PMC9805857 DOI: 10.1089/cell.2022.0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Somatic cell reprogramming was first developed to create induced pluripotent stem (iPS) cells. Since that time, the highly dynamic and heterogeneous nature of the reprogramming process has come to be appreciated. Remarkably, a distinct type of stem cell, called induced extraembryonic endoderm (iXEN) stem cell, is also formed during reprogramming of mouse somatic cells by ectopic expression of the transcription factors, OCT4, SOX2, KLF4, and MYC (OSKM). The mechanisms leading somatic cells to adopt differing stem cell fates are challenging to resolve given that formation of either stem cell type is slow, stochastic, and rare. For these reasons, fluorescent gene expression reporters have provided an invaluable tool for revealing the path from the somatic state to pluripotency. However, no such reporters have been established for comparable studies of iXEN cell formation. In this study, we examined the expression of multiple fluorescent reporters, including Nanog, Oct4, and the endodermal genes, Gata4 and Gata6-alone and in combination, during reprogramming. We show that only simultaneous evaluation of Nanog and Gata4 reliably distinguishes iPS and iXEN cell colonies during reprogramming.
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Affiliation(s)
- Alexandra Moauro
- Molecular, Cellular and Integrative Physiology Ph.D. Program, Michigan State University, East Lansing, Michigan, USA
- D.O.-Ph.D. Program, Michigan State University, East Lansing, Michigan, USA
| | - Robin E. Kruger
- Cell and Molecular Biology Ph.D. Program, Michigan State University, East Lansing, Michigan, USA
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
| | - Daniel O'Hagan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Amy Ralston
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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24
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Wang Z, Fan R, Russo A, Cernilogar FM, Nuber A, Schirge S, Shcherbakova I, Dzhilyanova I, Ugur E, Anton T, Richter L, Leonhardt H, Lickert H, Schotta G. Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm. Nat Commun 2022; 13:5447. [PMID: 36123357 DOI: 10.1038/s41467-022-32978-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Silencing of endogenous retroviruses (ERVs) is largely mediated by repressive chromatin modifications H3K9me3 and DNA methylation. On ERVs, these modifications are mainly deposited by the histone methyltransferase Setdb1 and by the maintenance DNA methyltransferase Dnmt1. Knock-out of either Setdb1 or Dnmt1 leads to ERV de-repression in various cell types. However, it is currently not known if H3K9me3 and DNA methylation depend on each other for ERV silencing. Here we show that conditional knock-out of Setdb1 in mouse embryonic endoderm results in ERV de-repression in visceral endoderm (VE) descendants and does not occur in definitive endoderm (DE). Deletion of Setdb1 in VE progenitors results in loss of H3K9me3 and reduced DNA methylation of Intracisternal A-particle (IAP) elements, consistent with up-regulation of this ERV family. In DE, loss of Setdb1 does not affect H3K9me3 nor DNA methylation, suggesting Setdb1-independent pathways for maintaining these modifications. Importantly, Dnmt1 knock-out results in IAP de-repression in both visceral and definitive endoderm cells, while H3K9me3 is unaltered. Thus, our data suggest a dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm cells. Our findings suggest that Setdb1-meditated H3K9me3 is not sufficient for IAP silencing, but rather critical for maintaining high DNA methylation. Silencing of endogenous retroviruses is crucial for maintaining transcriptional and genomic integrity of cells and is maintained by histone H3K9 methylation and/or DNA methylation in various cell types. Here the authors show that loss of DNA methyltransferase DNMT1 in endoderm results in ERV derepression while H3K9me3 is unaltered.
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25
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Khateb M, Perovanovic J, Ko KD, Jiang K, Feng X, Acevedo-Luna N, Chal J, Ciuffoli V, Genzor P, Simone J, Haase AD, Pourquié O, Dell'Orso S, Sartorelli V. Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution. Cell Rep 2022; 40:111219. [PMID: 35977485 DOI: 10.1016/j.celrep.2022.111219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/11/2022] [Accepted: 07/25/2022] [Indexed: 11/03/2022] Open
Abstract
Embryonic stem cells (ESCs) can adopt lineage-specific gene-expression programs by stepwise exposure to defined factors, resulting in the generation of functional cell types. Bulk and single-cell-based assays were employed to catalog gene expression, histone modifications, chromatin conformation, and accessibility transitions in ESC populations and individual cells acquiring a presomitic mesoderm fate and undergoing further specification toward myogenic and neurogenic lineages. These assays identified cis-regulatory regions and transcription factors presiding over gene-expression programs occurring at defined ESC transitions and revealed the presence of heterogeneous cell populations within discrete ESC developmental stages. The datasets were employed to identify previously unappreciated genomic elements directing the initial activation of Pax7 and myogenic and neurogenic gene-expression programs. This study provides a resource for the discovery of genomic and transcriptional features of pluripotent, mesoderm-induced ESCs and ESC-derived cell lineages.
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Affiliation(s)
- Mamduh Khateb
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Jelena Perovanovic
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Kyung Dae Ko
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Kan Jiang
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD, USA
| | - Xuesong Feng
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Natalia Acevedo-Luna
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Jérome Chal
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Boston, MA, USA
| | - Veronica Ciuffoli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Pavol Genzor
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - James Simone
- FlowCytometry Section, NIAMS, NIH, Bethesda, MD, USA
| | - Astrid D Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Boston, MA, USA
| | | | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA.
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Langkabel J, Horne A, Bonaguro L, Holsten L, Hesse T, Knaus A, Riedel Y, Becker M, Händler K, Elmzzahi T, Bassler K, Reusch N, Yeghiazarian LH, Pecht T, Saglam A, Ulas T, Aschenbrenner AC, Kaiser F, Kubaczka C, Schultze JL, Schorle H. Induction of Rosette-to-Lumen stage embryoids using reprogramming paradigms in ESCs. Nat Commun 2021; 12:7322. [PMID: 34916498 DOI: 10.1038/s41467-021-27586-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 11/19/2021] [Indexed: 01/01/2023] Open
Abstract
Blastocyst-derived stem cell lines were shown to self-organize into embryo-like structures in 3D cell culture environments. Here, we provide evidence that embryo-like structures can be generated solely based on transcription factor-mediated reprogramming of embryonic stem cells in a simple 3D co-culture system. Embryonic stem cells in these cultures self-organize into elongated, compartmentalized embryo-like structures reflecting aspects of the inner regions of the early post-implantation embryo. Single-cell RNA-sequencing reveals transcriptional profiles resembling epiblast, primitive-/visceral endoderm, and extraembryonic ectoderm of early murine embryos around E4.5-E5.5. In this stem cell-based embryo model, progression from rosette formation to lumenogenesis accompanied by progression from naïve- to primed pluripotency was observed within Epi-like cells. Additionally, lineage specification of primordial germ cells and distal/anterior visceral endoderm-like cells was observed in epiblast- or visceral endoderm-like compartments, respectively. The system presented in this study allows for fast and reproducible generation of embryo-like structures, providing an additional tool to study aspects of early embryogenesis.
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Zhang ML, Jin Y, Zhao LH, Zhang J, Zhou M, Li MS, Yin ZB, Wang ZX, Zhao LX, Li XH, Li RF. Derivation of Porcine Extra-Embryonic Endoderm Cell Lines Reveals Distinct Signaling Pathway and Multipotency States. Int J Mol Sci 2021; 22:ijms222312918. [PMID: 34884722 PMCID: PMC8657774 DOI: 10.3390/ijms222312918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 11/16/2022] Open
Abstract
The inner cell mass of the pre-implantation blastocyst consists of the epiblast and hypoblast from which embryonic stem cells (ESCs) and extra-embryonic endoderm (XEN) stem cells, respectively, can be derived. Importantly, each stem cell type retains the defining properties and lineage restriction of its in vivo tissue origin. We have developed a novel approach for deriving porcine XEN (pXEN) cells via culturing the blastocysts with a chemical cocktail culture system. The pXEN cells were positive for XEN markers, including Gata4, Gata6, Sox17, and Sall4, but not for pluripotent markers Oct4, Sox2, and Nanog. The pXEN cells also retained the ability to undergo visceral endoderm (VE) and parietal endoderm (PE) differentiation in vitro. The maintenance of pXEN required FGF/MEK+TGFβ signaling pathways. The pXEN cells showed a stable phenotype through more than 50 passages in culture and could be established repeatedly from blastocysts or converted from the naïve-like ESCs established in our lab. These cells provide a new tool for exploring the pathways of porcine embryo development and differentiation and providing further reference to the establishment of porcine ESCs with potency of germline chimerism and gamete development.
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Affiliation(s)
- Man-Ling Zhang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010020, China; (M.-L.Z.); (J.Z.); (L.-X.Z.)
| | - Yong Jin
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (Y.J.); (L.-H.Z.); (M.Z.); (M.-S.L.); (Z.-B.Y.)
| | - Li-Hua Zhao
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (Y.J.); (L.-H.Z.); (M.Z.); (M.-S.L.); (Z.-B.Y.)
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Jia Zhang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010020, China; (M.-L.Z.); (J.Z.); (L.-X.Z.)
| | - Meng Zhou
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (Y.J.); (L.-H.Z.); (M.Z.); (M.-S.L.); (Z.-B.Y.)
| | - Mei-Shuang Li
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (Y.J.); (L.-H.Z.); (M.Z.); (M.-S.L.); (Z.-B.Y.)
| | - Zhi-Bao Yin
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (Y.J.); (L.-H.Z.); (M.Z.); (M.-S.L.); (Z.-B.Y.)
| | - Zi-Xin Wang
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot 011517, China;
| | - Li-Xia Zhao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010020, China; (M.-L.Z.); (J.Z.); (L.-X.Z.)
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot 011517, China;
| | - Xi-He Li
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010020, China; (M.-L.Z.); (J.Z.); (L.-X.Z.)
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot 011517, China;
- Correspondence: (X.-H.L.); (R.-F.L.)
| | - Rong-Feng Li
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China; (Y.J.); (L.-H.Z.); (M.Z.); (M.-S.L.); (Z.-B.Y.)
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
- Correspondence: (X.-H.L.); (R.-F.L.)
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29
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Lea RA, McCarthy A, Boeing S, Fallesen T, Elder K, Snell P, Christie L, Adkins S, Shaikly V, Taranissi M, Niakan KK. KLF17 promotes human naïve pluripotency but is not required for its establishment. Development 2021; 148:272511. [PMID: 34661235 PMCID: PMC8645209 DOI: 10.1242/dev.199378] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/11/2021] [Indexed: 12/11/2022]
Abstract
Current knowledge of the transcriptional regulation of human pluripotency is incomplete, with lack of interspecies conservation observed. Single-cell transcriptomics analysis of human embryos previously enabled us to identify transcription factors, including the zinc-finger protein KLF17, that are enriched in the human epiblast and naïve human embryonic stem cells (hESCs). Here, we show that KLF17 is expressed coincident with the known pluripotency-associated factors NANOG and SOX2 across human blastocyst development. We investigate the function of KLF17 using primed and naïve hESCs for gain- and loss-of-function analyses. We find that ectopic expression of KLF17 in primed hESCs is sufficient to induce a naïve-like transcriptome and that KLF17 can drive transgene-mediated resetting to naïve pluripotency. This implies a role for KLF17 in establishing naïve pluripotency. However, CRISPR-Cas9-mediated knockout studies reveal that KLF17 is not required for naïve pluripotency acquisition in vitro. Transcriptome analysis of naïve hESCs identifies subtle effects on metabolism and signalling pathways following KLF17 loss of function, and possible redundancy with other KLF paralogues. Overall, we show that KLF17 is sufficient, but not necessary, for naïve pluripotency under the given in vitro conditions. Summary: Given that KLF17 was shown to be sufficient, but not necessary, to establish naïve pluripotent hESCs, KLF17 might function as a peripheral regulator of human pluripotent stem cells.
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Affiliation(s)
- Rebecca A Lea
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Afshan McCarthy
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Service, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Todd Fallesen
- Crick Advanced Light Microscopy, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Kay Elder
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | - Phil Snell
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | | | - Sarah Adkins
- Assisted Reproduction and Gynaecology Centre, London W1G 6LP, UK
| | - Valerie Shaikly
- Assisted Reproduction and Gynaecology Centre, London W1G 6LP, UK
| | | | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
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30
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Raina D, Bahadori A, Stanoev A, Protzek M, Koseska A, Schröter C. Cell-cell communication through FGF4 generates and maintains robust proportions of differentiated cell types in embryonic stem cells. Development 2021; 148:dev199926. [PMID: 34651174 PMCID: PMC8602943 DOI: 10.1242/dev.199926] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/04/2021] [Indexed: 01/20/2023]
Abstract
During embryonic development and tissue homeostasis, reproducible proportions of differentiated cell types are specified from populations of multipotent precursor cells. Molecular mechanisms that enable both robust cell-type proportioning despite variable initial conditions in the precursor cells, and the re-establishment of these proportions upon perturbations in a developing tissue remain to be characterized. Here, we report that the differentiation of robust proportions of epiblast-like and primitive endoderm-like cells in mouse embryonic stem cell cultures emerges at the population level through cell-cell communication via a short-range fibroblast growth factor 4 (FGF4) signal. We characterize the molecular and dynamical properties of the communication mechanism and show how it controls both robust cell-type proportioning from a wide range of experimentally controlled initial conditions, as well as the autonomous re-establishment of these proportions following the isolation of one cell type. The generation and maintenance of reproducible proportions of discrete cell types is a new function for FGF signaling that might operate in a range of developing tissues.
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Affiliation(s)
| | | | | | | | | | - Christian Schröter
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
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31
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Olivieri D, Castelli E, Kawamura YK, Papasaikas P, Lukonin I, Rittirsch M, Hess D, Smallwood SA, Stadler MB, Peters AHFM, Betschinger J. Cooperation between HDAC3 and DAX1 mediates lineage restriction of embryonic stem cells. EMBO J 2021; 40:e106818. [PMID: 33909924 PMCID: PMC8204867 DOI: 10.15252/embj.2020106818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/13/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
Mouse embryonic stem cells (mESCs) are biased toward producing embryonic rather than extraembryonic endoderm fates. Here, we identify the mechanism of this barrier and report that the histone deacetylase Hdac3 and the transcriptional corepressor Dax1 cooperatively limit the lineage repertoire of mESCs by silencing an enhancer of the extraembryonic endoderm-specifying transcription factor Gata6. This restriction is opposed by the pluripotency transcription factors Nr5a2 and Esrrb, which promote cell type conversion. Perturbation of the barrier extends mESC potency and allows formation of 3D spheroids that mimic the spatial segregation of embryonic epiblast and extraembryonic endoderm in early embryos. Overall, this study shows that transcriptional repressors stabilize pluripotency by biasing the equilibrium between embryonic and extraembryonic lineages that is hardwired into the mESC transcriptional network.
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Affiliation(s)
- Daniel Olivieri
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Eleonora Castelli
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of SciencesUniversity of BaselBaselSwitzerland
| | - Yumiko K Kawamura
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Swiss Institute of BioinformaticsBaselSwitzerland
| | - Ilya Lukonin
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Melanie Rittirsch
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | | | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Swiss Institute of BioinformaticsBaselSwitzerland
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of SciencesUniversity of BaselBaselSwitzerland
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
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32
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Janiszewski A, Georgolopoulos G, Balli M, Athanasouli P, Lluis F, Pasque V. Keep the fate: how chromatin regulators safeguard embryonic stem cell identity. EMBO J 2021; 40:e108437. [PMID: 33998023 DOI: 10.15252/embj.2021108437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
Segregation of cells that form the embryo from those that produce the surrounding extra-embryonic tissues is critical for early mammalian development, but the regulatory layers governing these first cell fate decisions remain poorly understood. Recent work in The EMBO Journal identifies two chromatin regulators, Hdac3 and Dax1, that synergistically restrict the developmental potential of mouse embryonic stem cells and act as a lineage barrier to primitive endoderm formation.
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Affiliation(s)
- Adrian Janiszewski
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,KU Leuven Institute for Single Cell Omics (LISCO), Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
| | - Grigorios Georgolopoulos
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,KU Leuven Institute for Single Cell Omics (LISCO), Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
| | - Martina Balli
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
| | - Paraskevi Athanasouli
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
| | - Frederic Lluis
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration, KU Leuven-University of Leuven, Leuven, Belgium.,KU Leuven Institute for Single Cell Omics (LISCO), Leuven, Belgium.,Leuven Stem Cell Institute, Leuven, Belgium
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33
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Vincentz JW, Firulli BA, Toolan KP, Osterwalder M, Pennacchio LA, Firulli AB. HAND transcription factors cooperatively specify the aorta and pulmonary trunk. Dev Biol 2021; 476:1-10. [PMID: 33757801 DOI: 10.1016/j.ydbio.2021.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 01/11/2023]
Abstract
Congenital heart defects (CHDs) affecting the cardiac outflow tract (OFT) constitute a significant cause of morbidity and mortality. The OFT develops from migratory cell populations which include the cardiac neural crest cells (cNCCs) and secondary heart field (SHF) derived myocardium and endocardium. The related transcription factors HAND1 and HAND2 have been implicated in human CHDs involving the OFT. Although Hand1 is expressed within the OFT, Hand1 NCC-specific conditional knockout mice (H1CKOs) are viable. Here we show that these H1CKOs present a low penetrance of OFT phenotypes, whereas SHF-specific Hand1 ablation does not reveal any cardiac phenotypes. Further, HAND1 and HAND2 appear functionally redundant within the cNCCs, as a reduction/ablation of Hand2 on an NCC-specific H1CKO background causes pronounced OFT defects. Double conditional Hand1 and Hand2 NCC knockouts exhibit persistent truncus arteriosus (PTA) with 100% penetrance. NCC lineage-tracing and Sema3c in situ mRNA expression reveal that Sema3c-expressing cells are mis-localized, resulting in a malformed septal bridge within the OFTs of H1CKO;H2CKO embryos. Interestingly, Hand1 and Hand2 also genetically interact within the SHF, as SHF H1CKOs on a heterozygous Hand2 background exhibit Ventricular Septal Defects (VSDs) with incomplete penetrance. Previously, we identified a BMP, HAND2, and GATA-dependent Hand1 OFT enhancer sufficient to drive reporter gene expression within the nascent OFT and aorta. Using these transcription inputs as a probe, we identify a novel Hand2 OFT enhancer, suggesting that a conserved BMP-GATA dependent mechanism transcriptionally regulates both HAND factors. These findings support the hypothesis that HAND factors interpret BMP signaling within the cNCCs to cooperatively coordinate OFT morphogenesis.
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Affiliation(s)
- Joshua W Vincentz
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA.
| | - Beth A Firulli
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA
| | - Kevin P Toolan
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 35, 3008, Bern, Switzerland
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA; Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Anthony B Firulli
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA.
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34
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Toyooka Y. Pluripotent stem cells in the research for extraembryonic cell differentiation. Dev Growth Differ 2021; 63:127-139. [PMID: 33583019 DOI: 10.1111/dgd.12716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/24/2022]
Abstract
Mouse embryonic stem cells (mESCs) are pluripotent stem cell populations derived from the preimplantation embryo and are used to study the differentiation of many types of somatic and germ cells in developing embryos. They are also used to study cell lineages of extraembryonic tissues, such as the trophectoderm (TE) and the primitive endoderm (PrE). mESC cultures are suitable systems for reproducing cellular and molecular events occurring during the differentiation of these cell types, such as changes in gene expression patterns, signaling events, and genome rearrangements although the consistency between the results obtained using mESCs and those of in vivo studies on embryos should be carefully taken into account. Since TE and PrE cells can be induced from mESCs in vitro, mESC cultures are useful systems to study differentiation of these cell lineages during development, if used appropriately. In addition, human pluripotent stem cells (hPSCs), such as human embryonic stem cells (hESCs) and human-induced pluripotent stem cells (hiPSCs), are capable of generating extraembryonic lineages in vitro and are promising tools to study the differentiation of these lineages in the human embryo.
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Affiliation(s)
- Yayoi Toyooka
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
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35
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Ruis P, Van Ly D, Borel V, Kafer GR, McCarthy A, Howell S, Blassberg R, Snijders AP, Briscoe J, Niakan KK, Marzec P, Cesare AJ, Boulton SJ. TRF2-independent chromosome end protection during pluripotency. Nature 2021; 589:103-109. [PMID: 33239783 PMCID: PMC7614352 DOI: 10.1038/s41586-020-2960-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022]
Abstract
Mammalian telomeres protect chromosome ends from aberrant DNA repair1. TRF2, a component of the telomere-specific shelterin protein complex, facilitates end protection through sequestration of the terminal telomere repeat sequence within a lariat T-loop structure2,3. Deleting TRF2 (also known as TERF2) in somatic cells abolishes T-loop formation, which coincides with telomere deprotection, chromosome end-to-end fusions and inviability3-9. Here we establish that, by contrast, TRF2 is largely dispensable for telomere protection in mouse pluripotent embryonic stem (ES) and epiblast stem cells. ES cell telomeres devoid of TRF2 instead activate an attenuated telomeric DNA damage response that lacks accompanying telomere fusions, and propagate for multiple generations. The induction of telomere dysfunction in ES cells, consistent with somatic deletion of Trf2 (also known as Terf2), occurs only following the removal of the entire shelterin complex. Consistent with TRF2 being largely dispensable for telomere protection specifically during early embryonic development, cells exiting pluripotency rapidly switch to TRF2-dependent end protection. In addition, Trf2-null embryos arrest before implantation, with evidence of strong DNA damage response signalling and apoptosis specifically in the non-pluripotent compartment. Finally, we show that ES cells form T-loops independently of TRF2, which reveals why TRF2 is dispensable for end protection during pluripotency. Collectively, these data establish that telomere protection is solved by distinct mechanisms in pluripotent and somatic tissues.
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Affiliation(s)
- Phil Ruis
- The Francis Crick Institute, London, UK
| | - David Van Ly
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
- School of Medicine, The University of Notre Dame Australia, Sydney, New South Wales, Australia
| | | | - Georgia R Kafer
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | | | | | | | | | | | | | | | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.
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Qin J, Wang C, Zhu Y, Su T, Dong L, Huang Y, Hao K. Mga safeguards embryonic stem cells from acquiring extraembryonic endoderm fates. Sci Adv 2021; 7:7/4/eabe5689. [PMID: 33523934 PMCID: PMC7821913 DOI: 10.1126/sciadv.abe5689] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/24/2020] [Indexed: 05/17/2023]
Abstract
Polycomb group (PcG) proteins form multiprotein complexes that affect stem cell identity and fate decisions by still largely unexplored mechanisms. Here, by performing a CRISPR-based loss-of-function screen in embryonic stem cells (ESCs), we identify PcG gene Mga involved in the repression of endodermal transcription factor Gata6 We report that deletion of Mga results in peri-implantation embryonic lethality in mice. We further demonstrate that Mga-null ESCs exhibit impaired self-renewal and spontaneous differentiation to primitive endoderm (PE). Our data support a model in which Mga might serve as a scaffold for PRC1.6 assembly and guide this multimeric complex to specific genomic targets including genes that encode endodermal factors Gata4, Gata6, and Sox17. Our findings uncover an unexpected function of Mga in ESCs, where it functions as a gatekeeper to prevent ESCs from entering into the PE lineage by directly repressing expression of a set of endoderm differentiation master genes.
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Affiliation(s)
- Jinzhong Qin
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China.
| | - Congcong Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Yaru Zhu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Ting Su
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Lixia Dong
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Yikai Huang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Kunying Hao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
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37
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Weatherbee BAT, Cui T, Zernicka-Goetz M. Modeling human embryo development with embryonic and extra-embryonic stem cells. Dev Biol 2021; 474:91-9. [PMID: 33333069 DOI: 10.1016/j.ydbio.2020.12.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022]
Abstract
Early human post-implantation development involves extensive growth combined with a series of complex morphogenetic events. The lack of precise spatial and temporal control over these processes leads to pregnancy loss. Given the ethical and technical limitations in studying the natural human embryo, alternative approaches are needed to investigate mechanisms underlying this critical stage of human development. Here, we present an overview of the different stem cells and stem cell-derived models which serve as useful, albeit imperfect, tools in understanding human embryogenesis. Current models include stem cells that represent each of the three earliest lineages: human embryonic stem cells corresponding to the epiblast, hypoblast-like stem cells and trophoblast stem cells. We also review the use of human embryonic stem cells to model complex aspects of epiblast morphogenesis and differentiation. Additionally, we propose that the combination of both embryonic and extra-embryonic stem cells to form three-dimensional embryo models will provide valuable insights into cell-cell chemical and mechanical interactions that are essential for natural embryogenesis.
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38
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Park CH, Jeoung YH, Uh KJ, Park KE, Bridge J, Powell A, Li J, Pence L, Zhang L, Liu T, Sun HX, Gu Y, Shen Y, Wu J, Izpisua Belmonte JC, Telugu BP. Extraembryonic Endoderm (XEN) Cells Capable of Contributing to Embryonic Chimeras Established from Pig Embryos. Stem Cell Reports 2020; 16:212-223. [PMID: 33338433 PMCID: PMC7897585 DOI: 10.1016/j.stemcr.2020.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/24/2022] Open
Abstract
Most of our current knowledge regarding early lineage specification and embryo-derived stem cells comes from studies in rodent models. However, key gaps remain in our understanding of these developmental processes from nonrodent species. Here, we report the detailed characterization of pig extraembryonic endoderm (pXEN) cells, which can be reliably and reproducibly generated from primitive endoderm (PrE) of blastocyst. Highly expandable pXEN cells express canonical PrE markers and transcriptionally resemble rodent XENs. The pXEN cells contribute both to extraembryonic tissues including visceral yolk sac as well as embryonic gut when injected into host blastocysts, and generate live offspring when used as a nuclear donor in somatic cell nuclear transfer (SCNT). The pXEN cell lines provide a novel model for studying lineage segregation, as well as a source for genome editing in livestock. Primitive endoderm (PrE) is the predominant lineage emerging from pig blastocyst outgrowths pXEN cells exhibit key features of PrE-progenitors and resemble rodent XEN cells pXEN cells contribute to extraembryonic and embryonic (gut) endoderm in vivo pXEN cells can support full-term development via somatic cell nuclear transfer
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Affiliation(s)
- Chi-Hun Park
- Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; Animal Bioscience and Biotechnology Laboratory, USDA, ARS, Beltsville, MD 20705, USA.
| | - Young-Hee Jeoung
- Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; Animal Bioscience and Biotechnology Laboratory, USDA, ARS, Beltsville, MD 20705, USA
| | - Kyung-Jun Uh
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Ki-Eun Park
- Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; Animal Bioscience and Biotechnology Laboratory, USDA, ARS, Beltsville, MD 20705, USA; RenOVAte Biosciences Inc, Reisterstown, MD 21136, USA
| | - Jessica Bridge
- Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; Animal Bioscience and Biotechnology Laboratory, USDA, ARS, Beltsville, MD 20705, USA
| | - Anne Powell
- Animal Bioscience and Biotechnology Laboratory, USDA, ARS, Beltsville, MD 20705, USA; RenOVAte Biosciences Inc, Reisterstown, MD 21136, USA
| | - Jie Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen, 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China; Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Guangdong, China
| | - Laramie Pence
- Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; Animal Bioscience and Biotechnology Laboratory, USDA, ARS, Beltsville, MD 20705, USA
| | - Luhui Zhang
- Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Tianbin Liu
- BGI-Shenzhen, Shenzhen, 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China; Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Guangdong, China
| | - Hai-Xi Sun
- BGI-Shenzhen, Shenzhen, 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China; Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Guangdong, China
| | - Ying Gu
- BGI-Shenzhen, Shenzhen, 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China; Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Guangdong, China
| | - Yue Shen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen, 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, 518120, China; Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Guangdong, China; Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Shenzhen, 518120, China
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Bhanu P Telugu
- Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; Animal Bioscience and Biotechnology Laboratory, USDA, ARS, Beltsville, MD 20705, USA; RenOVAte Biosciences Inc, Reisterstown, MD 21136, USA.
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Kubota Y, Seki M, Kawai T, Isobe T, Yoshida M, Sekiguchi M, Kimura S, Watanabe K, Sato-Otsubo A, Yoshida K, Suzuki H, Kataoka K, Fujii Y, Shiraishi Y, Chiba K, Tanaka H, Hiwatari M, Oka A, Hayashi Y, Miyano S, Ogawa S, Hata K, Tanaka Y, Takita J. Comprehensive genetic analysis of pediatric germ cell tumors identifies potential drug targets. Commun Biol 2020; 3:544. [PMID: 32999426 PMCID: PMC7528104 DOI: 10.1038/s42003-020-01267-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022] Open
Abstract
To elucidate the molecular pathogenesis of pediatric germ cell tumors (GCTs), we performed DNA methylation array analysis, whole transcriptome sequencing, targeted capture sequencing, and single-nucleotide polymorphism array analysis using 51 GCT samples (25 female, 26 male), including 6 germinomas, 2 embryonal carcinomas, 4 immature teratomas, 3 mature teratomas, 30 yolk sac tumors, and 6 mixed germ cell tumors. Among the 51 samples, 11 were from infants, 23 were from young children, and 17 were from those aged ≥10 years. Sixteen of the 51 samples developed in the extragonadal regions. Germinomas showed upregulation of pluripotent genes and global hypomethylation. Pluripotent genes were also highly expressed in embryonal carcinomas. These genes may play essential roles in embryonal carcinomas given that their binding sites are hypomethylated. Yolk sac tumors exhibited overexpression of endodermal genes, such as GATA6 and FOXA2, the binding sites of which were hypomethylated. Interestingly, infant yolk sac tumors had different DNA methylation patterns from those observed in older children. Teratomas had higher expression of ectodermal genes, suggesting a tridermal nature. Based on our results, we suggest that KIT, TNFRSF8, and ERBB4 may be suitable targets for the treatment of germinoma, embryonal carcinomas, and yolk sac tumors, respectively. Yasuo Kubota et al. report a multi-omic analysis of pediatric germ cell tumors from 51 patients ranging in age from 2 months to 19 years. They identify unique methylation, expression, and mutational patterns for each of the main subtypes and propose potential target genes for treatments against the three main subtypes.
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Affiliation(s)
- Yasuo Kubota
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Misa Yoshida
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Clinical Research Institute and Department of Pathology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Masahiro Sekiguchi
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shunsuke Kimura
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan
| | - Kentaro Watanabe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Aiko Sato-Otsubo
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoichi Fujii
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Section of Genome Analysis Platform, Center for Cancer Genomic and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Kenichi Chiba
- Section of Genome Analysis Platform, Center for Cancer Genomic and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Mitsuteru Hiwatari
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Cell Therapy and Transplantation Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuhide Hayashi
- Institute of Physiology and Medicine, Jobu University, Takasaki, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden.,Institute for the Advanced Study of Human Biology (WPI ASHBi), Kyoto University, Kyoto, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yukichi Tanaka
- Clinical Research Institute and Department of Pathology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. .,Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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40
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Mahadevaiah SK, Sangrithi MN, Hirota T, Turner JMA. A single-cell transcriptome atlas of marsupial embryogenesis and X inactivation. Nature 2020; 586:612-617. [PMID: 32814901 DOI: 10.1038/s41586-020-2629-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/20/2020] [Indexed: 11/09/2022]
Abstract
Single-cell RNA sequencing of embryos can resolve the transcriptional landscape of development at unprecedented resolution. To date, single-cell RNA-sequencing studies of mammalian embryos have focused exclusively on eutherian species. Analysis of mammalian outgroups has the potential to identify deeply conserved lineage specification and pluripotency factors, and can extend our understanding of X dosage compensation. Metatherian (marsupial) mammals diverged from eutherians around 160 million years ago. They exhibit distinctive developmental features, including late implantation1 and imprinted X chromosome inactivation2, which is associated with expression of the XIST-like noncoding RNA RSX3. Here we perform a single-cell RNA-sequencing analysis of embryogenesis and X chromosome inactivation in a marsupial, the grey short-tailed opossum (Monodelphis domestica). We resolve the developmental trajectory and transcriptional signatures of the epiblast, primitive endoderm and trophectoderm, and identify deeply conserved lineage-specific markers that pre-date the eutherian-marsupial divergence. RSX coating and inactivation of the X chromosome occurs early and rapidly. This observation supports the hypothesis that-in organisms with early X chromosome inactivation-imprinted X chromosome inactivation prevents biallelic X silencing. We identify XSR, an RSX antisense transcript expressed from the active X chromosome, as a candidate for the regulator of imprinted X chromosome inactivation. Our datasets provide insights into the evolution of mammalian embryogenesis and X dosage compensation.
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Affiliation(s)
| | - Mahesh N Sangrithi
- Division of Obstetrics and Gynaecology, KK Women's and Children's Hospital, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Takayuki Hirota
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK.
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41
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Huang B, Lu M, Galbraith M, Levine H, Onuchic JN, Jia D. Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation. J R Soc Interface 2020; 17:20200500. [PMID: 32781932 PMCID: PMC7482558 DOI: 10.1098/rsif.2020.0500] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022] Open
Abstract
Stem cells can precisely and robustly undergo cellular differentiation and lineage commitment, referred to as stemness. However, how the gene network underlying stemness regulation reliably specifies cell fates is not well understood. To address this question, we applied a recently developed computational method, random circuit perturbation (RACIPE), to a nine-component gene regulatory network (GRN) governing stemness, from which we identified robust gene states. Among them, four out of the five most probable gene states exhibit gene expression patterns observed in single mouse embryonic cells at 32-cell and 64-cell stages. These gene states can be robustly predicted by the stemness GRN but not by randomized versions of the stemness GRN. Strikingly, we found a hierarchical structure of the GRN with the Oct4/Cdx2 motif functioning as the first decision-making module followed by Gata6/Nanog. We propose that stem cell populations, instead of being viewed as all having a specific cellular state, can be regarded as a heterogeneous mixture including cells in various states. Upon perturbations by external signals, stem cells lose the capacity to access certain cellular states, thereby becoming differentiated. The new gene states and key parameters regulating transitions among gene states proposed by RACIPE can be used to guide experimental strategies to better understand differentiation and design reprogramming. The findings demonstrate that the functions of the stemness GRN is mainly determined by its well-evolved network topology rather than by detailed kinetic parameters.
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Affiliation(s)
- Bin Huang
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Mingyang Lu
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Madeline Galbraith
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
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42
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Sun X, Yu W, Li L, Sun Y. ADNP Controls Gene Expression Through Local Chromatin Architecture by Association With BRG1 and CHD4. Front Cell Dev Biol 2020; 8:553. [PMID: 32714933 PMCID: PMC7341970 DOI: 10.3389/fcell.2020.00553] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/10/2020] [Indexed: 01/31/2023] Open
Abstract
ADNP (Activity Dependent Neuroprotective Protein) is proposed as a neuroprotective protein whose aberrant expression has been frequently linked to rare neural developmental disorders and cancers, including the recently described neurodevelopmental Helsmoortel-Van der Aa syndrome. Recent studies have suggested that ADNP functions as an important chromatin regulator. However, how ADNP-regulated chromatin mechanisms control gene expression and stem cell fate commitment remains unclear. Here we show that ADNP interacts with two chromatin remodelers, BRG1 and CHD4. ADNP is required for proper establishment of chromatin accessibility, nucleosome configuration, and bivalent histone modifications of developmental genes. Loss of ADNP leads to enhancer over-activation and increased ratio of H3K4me3/H3K27me3 at key primitive endoderm (PrE) gene promoters, resulting in prominent up-regulation of these genes and priming ES cell differentiation toward endodermal cell types. Thus, our work revealed a key role of ADNP in the establishment of local chromatin landscape and structure of developmental genes by association with BRG1 and CHD4. These findings provide further insights into the role of ADNP in the pathology of the Helsmoortel-Van der Aa syndrome.
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Affiliation(s)
- XiaoYun Sun
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - WenJun Yu
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Li Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - YuHua Sun
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, China
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43
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Fischer SC, Corujo-Simon E, Lilao-Garzon J, Stelzer EHK, Muñoz-Descalzo S. The transition from local to global patterns governs the differentiation of mouse blastocysts. PLoS One 2020; 15:e0233030. [PMID: 32413083 PMCID: PMC7228118 DOI: 10.1371/journal.pone.0233030] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/27/2020] [Indexed: 01/06/2023] Open
Abstract
During mammalian blastocyst development, inner cell mass (ICM) cells differentiate into epiblast (Epi) or primitive endoderm (PrE). These two fates are characterized by the expression of the transcription factors NANOG and GATA6, respectively. Here, we investigate the spatio-temporal distribution of NANOG and GATA6 expressing cells in the ICM of the mouse blastocysts with quantitative three-dimensional single cell-based neighbourhood analyses. We define the cell neighbourhood by local features, which include the expression levels of both fate markers expressed in each cell and its neighbours, and the number of neighbouring cells. We further include the position of a cell relative to the centre of the ICM as a global positional feature. Our analyses reveal a local three-dimensional pattern that is already present in early blastocysts: 1) Cells expressing the highest NANOG levels are surrounded by approximately nine neighbours, while 2) cells expressing GATA6 cluster according to their GATA6 levels. This local pattern evolves into a global pattern in the ICM that starts to emerge in mid blastocysts. We show that FGF/MAPK signalling is involved in the three-dimensional distribution of the cells and, using a mutant background, we further show that the GATA6 neighbourhood is regulated by NANOG. Our quantitative study suggests that the three-dimensional cell neighbourhood plays a role in Epi and PrE precursor specification. Our results highlight the importance of analysing the three-dimensional cell neighbourhood while investigating cell fate decisions during early mouse embryonic development.
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Affiliation(s)
- Sabine C. Fischer
- Physikalische Biologie, Buchmann Institute for Molecular Life Sciences, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Elena Corujo-Simon
- Department of Biology and Biochemistry, University of Bath, Bath, England, United Kingdom
| | - Joaquin Lilao-Garzon
- Department of Biology and Biochemistry, University of Bath, Bath, England, United Kingdom
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Universidad Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Ernst H. K. Stelzer
- Physikalische Biologie, Buchmann Institute for Molecular Life Sciences, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Silvia Muñoz-Descalzo
- Department of Biology and Biochemistry, University of Bath, Bath, England, United Kingdom
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Universidad Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
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44
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Shao Y, Fu J. Synthetic human embryology: towards a quantitative future. Curr Opin Genet Dev 2020; 63:30-5. [PMID: 32172182 DOI: 10.1016/j.gde.2020.02.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 12/15/2022]
Abstract
Study of early human embryo development is essential for advancing reproductive and regenerative medicine. Traditional human embryological studies rely on embryonic tissue specimens, which are difficult to acquire due to technical challenges and ethical restrictions. The availability of human stem cells with developmental potentials comparable to pre-implantation and peri-implantation human embryonic and extraembryonic cells, together with properly engineered in vitro culture environments, allow for the first time researchers to generate self-organized multicellular structures in vitro that mimic the structural and molecular features of their in vivo counterparts. The development of these stem cell-based, synthetic human embryo models offers a paradigm-shifting experimental system for quantitative measurements and perturbations of multicellular development, critical for advancing human embryology and reproductive and regenerative medicine without using intact human embryos.
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45
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Rodríguez-López M, Gonzalez S, Hillson O, Tunnacliffe E, Codlin S, Tallada VA, Bähler J, Rallis C. The GATA Transcription Factor Gaf1 Represses tRNAs, Inhibits Growth, and Extends Chronological Lifespan Downstream of Fission Yeast TORC1. Cell Rep 2020; 30:3240-3249.e4. [PMID: 32160533 PMCID: PMC7068653 DOI: 10.1016/j.celrep.2020.02.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/17/2019] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Target of Rapamycin Complex 1 (TORC1) signaling promotes growth and aging. Inhibition of TORC1 leads to reduced protein translation, which promotes longevity. TORC1-dependent post-transcriptional regulation of protein translation has been well studied, while analogous transcriptional regulation is less understood. Here we screen fission yeast mutants for resistance to Torin1, which inhibits TORC1 and cell growth. Cells lacking the GATA factor Gaf1 (gaf1Δ) grow normally even in high doses of Torin1. The gaf1Δ mutation shortens the chronological lifespan of non-dividing cells and diminishes Torin1-mediated longevity. Expression profiling and genome-wide binding experiments show that upon TORC1 inhibition, Gaf1 directly upregulates genes for small-molecule metabolic pathways and indirectly represses genes for protein translation. Surprisingly, Gaf1 binds to and downregulates the tRNA genes, so it also functions as a transcription factor for RNA polymerase III. Thus, Gaf1 controls the transcription of both protein-coding and tRNA genes to inhibit translation and growth downstream of TORC1.
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Affiliation(s)
- María Rodríguez-López
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Suam Gonzalez
- School of Health, Sport and Bioscience, University of East London, Stratford Campus, London E14 4LZ, UK
| | - Olivia Hillson
- School of Health, Sport and Bioscience, University of East London, Stratford Campus, London E14 4LZ, UK
| | - Edward Tunnacliffe
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Sandra Codlin
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Victor A Tallada
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC, 41013 Sevilla, Spain
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK.
| | - Charalampos Rallis
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK; School of Health, Sport and Bioscience, University of East London, Stratford Campus, London E14 4LZ, UK; School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
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46
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Linneberg-Agerholm M, Wong YF, Romero Herrera JA, Monteiro RS, Anderson KGV, Brickman JM. Naïve human pluripotent stem cells respond to Wnt, Nodal and LIF signalling to produce expandable naïve extra-embryonic endoderm. Development 2019; 146:dev.180620. [PMID: 31740534 DOI: 10.1242/dev.180620] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/11/2019] [Indexed: 12/17/2022]
Abstract
Embryonic stem cells (ESCs) exist in at least two states that transcriptionally resemble different stages of embryonic development. Naïve ESCs resemble peri-implantation stages and primed ESCs the pre-gastrulation epiblast. In mouse, primed ESCs give rise to definitive endoderm in response to the pathways downstream of Nodal and Wnt signalling. However, when these pathways are activated in naïve ESCs, they differentiate to a cell type resembling early primitive endoderm (PrE), the blastocyst-stage progenitor of the extra-embryonic endoderm. Here, we apply this context dependency to human ESCs, showing that activation of Nodal and Wnt signalling drives the differentiation of naïve pluripotent cells toward extra-embryonic PrE, or hypoblast, and these can be expanded as an in vitro model for naïve extra-embryonic endoderm (nEnd). Consistent with observations made in mouse, human PrE differentiation is dependent on FGF signalling in vitro, and we show that, by inhibiting FGF receptor signalling, we can simplify naïve pluripotent culture conditions, such that the inhibitor requirements closer resemble those used in mouse. The expandable nEnd cultures reported here represent stable extra-embryonic endoderm, or human hypoblast, cell lines.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Madeleine Linneberg-Agerholm
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Yan Fung Wong
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Jose Alejandro Romero Herrera
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Rita S Monteiro
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Kathryn G V Anderson
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
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47
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Pang CY, Bai MZ, Zhang C, Chen J, Lu XR, Deng TX, Ma XY, Duan AQ, Liang SS, Huang YQ, Xiu Z, Liang XW. Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo. PeerJ 2019; 7:e8185. [PMID: 31824777 PMCID: PMC6894430 DOI: 10.7717/peerj.8185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/10/2019] [Indexed: 12/03/2022] Open
Abstract
Background Water buffalo (Bubalus bubalis) are divided into river buffalo and swamp buffalo subspecies and are essential livestock for agriculture and the local economy. Studies on buffalo reproduction have primarily focused on optimal fertility and embryonic mortality. There is currently limited knowledge on buffalo embryonic development, especially during the preimplantation period. Assembly of the river buffalo genome offers a reference for omics studies and facilitates transcriptomic analysis of preimplantation embryo development (PED). Methods We revealed transcriptomic profile of four stages (2-cell, 8-cell, Morula and Blastocyst) of PED via RNA-seq (Illumina HiSeq4000). Each stage comprised three biological replicates. The data were analyzed according to the basic RNA-seq analysis process. Ingenuity analysis of cell lineage control, especially transcription factor (TF) regulatory networks, was also performed. Results A total of 21,519 expressed genes and 67,298 transcripts were predicted from approximately 81.94 Gb of raw data. Analysis of transcriptome-wide expression, gene coexpression networks, and differentially expressed genes (DEGs) allowed for the characterization of gene-specific expression levels and relationships for each stage. The expression patterns of TFs, such as POU5F1, TEAD4, CDX4 and GATAs, were elucidated across diverse time series; most TF expression levels were increased during the blastocyst stage, during which time cell differentiation is initiated. All of these TFs were involved in the composition of the regulatory networks that precisely specify cell fate. These findings offer a deeper understanding of PED at the transcriptional level in the river buffalo.
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Affiliation(s)
- Chun-Ying Pang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - Ming-Zhou Bai
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, PR China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, PR China
| | - Junhui Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, PR China
| | - Xing-Rong Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - Ting-Xian Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - Xiao-Ya Ma
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - An-Qin Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - Sha-Sha Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
| | - Yun-Qi Huang
- Shandong Agricultural University, Taian, PR China
| | - Zhihui Xiu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, PR China
| | - Xian-Wei Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Rural Affairs (Guangxi), Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, P. R. China
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48
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Zhang Z, Zhuang L, Lin CP. Roles of MicroRNAs in Establishing and Modulating Stem Cell Potential. Int J Mol Sci 2019; 20:E3643. [PMID: 31349654 DOI: 10.3390/ijms20153643] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
Early embryonic development in mammals, from fertilization to implantation, can be viewed as a process in which stem cells alternate between self-renewal and differentiation. During this process, the fates of stem cells in embryos are gradually specified, from the totipotent state, through the segregation of embryonic and extraembryonic lineages, to the molecular and cellular defined progenitors. Most of those stem cells with different potencies in vivo can be propagated in vitro and recapitulate their differentiation abilities. Complex and coordinated regulations, such as epigenetic reprogramming, maternal RNA clearance, transcriptional and translational landscape changes, as well as the signal transduction, are required for the proper development of early embryos. Accumulated studies suggest that Dicer-dependent noncoding RNAs, including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs), are involved in those regulations and therefore modulate biological properties of stem cells in vitro and in vivo. Elucidating roles of these noncoding RNAs will give us a more comprehensive picture of mammalian embryonic development and enable us to modulate stem cell potencies. In this review, we will discuss roles of miRNAs in regulating the maintenance and cell fate potential of stem cells in/from mouse and human early embryos.
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49
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Shparberg RA, Glover HJ, Morris MB. Modeling Mammalian Commitment to the Neural Lineage Using Embryos and Embryonic Stem Cells. Front Physiol 2019; 10:705. [PMID: 31354503 PMCID: PMC6637848 DOI: 10.3389/fphys.2019.00705] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/20/2019] [Indexed: 12/21/2022] Open
Abstract
Early mammalian embryogenesis relies on a large range of cellular and molecular mechanisms to guide cell fate. In this highly complex interacting system, molecular circuitry tightly controls emergent properties, including cell differentiation, proliferation, morphology, migration, and communication. These molecular circuits include those responsible for the control of gene and protein expression, as well as metabolism and epigenetics. Due to the complexity of this circuitry and the relative inaccessibility of the mammalian embryo in utero, mammalian neural commitment remains one of the most challenging and poorly understood areas of developmental biology. In order to generate the nervous system, the embryo first produces two pluripotent populations, the inner cell mass and then the primitive ectoderm. The latter is the cellular substrate for gastrulation from which the three multipotent germ layers form. The germ layer definitive ectoderm, in turn, is the substrate for multipotent neurectoderm (neural plate and neural tube) formation, representing the first morphological signs of nervous system development. Subsequent patterning of the neural tube is then responsible for the formation of most of the central and peripheral nervous systems. While a large number of studies have assessed how a competent neurectoderm produces mature neural cells, less is known about the molecular signatures of definitive ectoderm and neurectoderm and the key molecular mechanisms driving their formation. Using pluripotent stem cells as a model, we will discuss the current understanding of how the pluripotent inner cell mass transitions to pluripotent primitive ectoderm and sequentially to the multipotent definitive ectoderm and neurectoderm. We will focus on the integration of cell signaling, gene activation, and epigenetic control that govern these developmental steps, and provide insight into the novel growth factor-like role that specific amino acids, such as L-proline, play in this process.
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Affiliation(s)
| | | | - Michael B. Morris
- Embryonic Stem Cell Laboratory, Discipline of Physiology, School of Medical Sciences, Bosch Institute, University of Sydney, Sydney, NSW, Australia
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50
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Tian TV, Di Stefano B, Stik G, Vila-Casadesús M, Sardina JL, Vidal E, Dasti A, Segura-Morales C, De Andrés-Aguayo L, Gómez A, Goldmann J, Jaenisch R, Graf T. Whsc1 links pluripotency exit with mesendoderm specification. Nat Cell Biol 2019; 21:824-834. [PMID: 31235934 DOI: 10.1038/s41556-019-0342-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 05/09/2019] [Indexed: 12/19/2022]
Abstract
How pluripotent stem cells differentiate into the main germ layers is a key question of developmental biology. Here, we show that the chromatin-related factor Whsc1 (also known as Nsd2 and MMSET) has a dual role in pluripotency exit and germ layer specification of embryonic stem cells. On induction of differentiation, a proportion of Whsc1-depleted embryonic stem cells remain entrapped in a pluripotent state and fail to form mesendoderm, although they are still capable of generating neuroectoderm. These functions of Whsc1 are independent of its methyltransferase activity. Whsc1 binds to enhancers of the mesendodermal regulators Gata4, T (Brachyury), Gata6 and Foxa2, together with Brd4, and activates the expression of these genes. Depleting each of these regulators also delays pluripotency exit, suggesting that they mediate the effects observed with Whsc1. Our data indicate that Whsc1 links silencing of the pluripotency regulatory network with activation of mesendoderm lineages.
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Affiliation(s)
- Tian V Tian
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Bruno Di Stefano
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Grégoire Stik
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maria Vila-Casadesús
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - José Luis Sardina
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Enrique Vidal
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Alessandro Dasti
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carolina Segura-Morales
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luisa De Andrés-Aguayo
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Gómez
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Johanna Goldmann
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,The Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Rudolf Jaenisch
- The Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas Graf
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
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