1
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Santini L, Kowald S, Cerron-Alvan LM, Huth M, Fabing AP, Sestini G, Rivron N, Leeb M. FoxO transcription factors actuate the formative pluripotency specific gene expression programme. Nat Commun 2024; 15:7879. [PMID: 39251582 PMCID: PMC11384738 DOI: 10.1038/s41467-024-51794-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 08/16/2024] [Indexed: 09/11/2024] Open
Abstract
Naïve pluripotency is sustained by a self-reinforcing gene regulatory network (GRN) comprising core and naïve pluripotency-specific transcription factors (TFs). Upon exiting naïve pluripotency, embryonic stem cells (ESCs) transition through a formative post-implantation-like pluripotent state, where they acquire competence for lineage choice. However, the mechanisms underlying disengagement from the naïve GRN and initiation of the formative GRN are unclear. Here, we demonstrate that phosphorylated AKT acts as a gatekeeper that prevents nuclear localisation of FoxO TFs in naïve ESCs. PTEN-mediated reduction of AKT activity upon exit from naïve pluripotency allows nuclear entry of FoxO TFs, enforcing a cell fate transition by binding and activating formative pluripotency-specific enhancers. Indeed, FoxO TFs are necessary and sufficient for the activation of the formative pluripotency-specific GRN. Our work uncovers a pivotal role for FoxO TFs in establishing formative post-implantation pluripotency, a critical early embryonic cell fate transition.
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Affiliation(s)
- Laura Santini
- Max Perutz Laboratories Vienna, University of Vienna, Vienna BioCenter, 1030, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030, Vienna, Austria
| | - Saskia Kowald
- Max Perutz Laboratories Vienna, University of Vienna, Vienna BioCenter, 1030, Vienna, Austria
| | - Luis Miguel Cerron-Alvan
- Max Perutz Laboratories Vienna, University of Vienna, Vienna BioCenter, 1030, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030, Vienna, Austria
| | - Michelle Huth
- Max Perutz Laboratories Vienna, University of Vienna, Vienna BioCenter, 1030, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030, Vienna, Austria
| | - Anna Philina Fabing
- Max Perutz Laboratories Vienna, University of Vienna, Vienna BioCenter, 1030, Vienna, Austria
| | - Giovanni Sestini
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, 1030, Vienna, Austria
| | - Nicolas Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, 1030, Vienna, Austria
| | - Martin Leeb
- Max Perutz Laboratories Vienna, University of Vienna, Vienna BioCenter, 1030, Vienna, Austria.
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2
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Smith A. Propagating pluripotency - The conundrum of self-renewal. Bioessays 2024:e2400108. [PMID: 39180242 DOI: 10.1002/bies.202400108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/26/2024]
Abstract
The discovery of mouse embryonic stem cells in 1981 transformed research in mammalian developmental biology and functional genomics. The subsequent generation of human pluripotent stem cells (PSCs) and the development of molecular reprogramming have opened unheralded avenues for drug discovery and cell replacement therapy. Here, I review the history of PSCs from the perspective that long-term self-renewal is a product of the in vitro signaling environment, rather than an intrinsic feature of embryos. I discuss the relationship between pluripotent states captured in vitro to stages of epiblast in the embryo and suggest key considerations for evaluation of PSCs. A remaining fundamental challenge is to determine whether naïve pluripotency can be propagated from the broad range of mammals by exploiting common principles in gene regulatory architecture.
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Affiliation(s)
- Austin Smith
- Living Systems Institute, University of Exeter, Exeter, UK
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3
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Mulas C, Stammers M, Salomaa SI, Heinzen C, Suter DM, Smith A, Chalut KJ. ERK signalling eliminates Nanog and maintains Oct4 to drive the formative pluripotency transition. Development 2024; 151:dev203106. [PMID: 39069943 DOI: 10.1242/dev.203106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 07/30/2024]
Abstract
Naïve epiblast cells in the embryo and pluripotent stem cells in vitro undergo developmental progression to a formative state competent for lineage specification. During this transition, transcription factors and chromatin are rewired to encode new functional features. Here, we examine the role of mitogen-activated protein kinase (ERK1/2) signalling in pluripotent state transition. We show that a primary consequence of ERK activation in mouse embryonic stem cells is elimination of Nanog, which precipitates breakdown of the naïve state gene regulatory network. Variability in pERK dynamics results in heterogeneous loss of Nanog and metachronous state transition. Knockdown of Nanog allows exit without ERK activation. However, transition to formative pluripotency does not proceed and cells collapse to an indeterminate identity. This outcome is due to failure to maintain expression of the central pluripotency factor Oct4. Thus, during formative transition ERK signalling both dismantles the naïve state and preserves pluripotency. These results illustrate how a single signalling pathway can both initiate and secure transition between cell states.
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Affiliation(s)
- Carla Mulas
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Randall Centre for Cell and Molecular Biology, King's College London, London SE1 1YR, UK
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge CB21 6GP, UK
| | - Melanie Stammers
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Siiri I Salomaa
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge CB21 6GP, UK
| | - Constanze Heinzen
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt 60439, Germany
| | - David M Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Austin Smith
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Kevin J Chalut
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge CB21 6GP, UK
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4
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Katznelson A, Hernandez B, Fahning H, Zhang J, Burton A, Torres-Padilla ME, Plachta N, Zaret KS, McCarthy RL. Heterochromatin protein ERH represses alternative cell fates during early mammalian differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597604. [PMID: 38895478 PMCID: PMC11185749 DOI: 10.1101/2024.06.06.597604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
During development, H3K9me3 heterochromatin is dynamically rearranged, silencing repeat elements and protein coding genes to restrict cell identity. Enhancer of Rudimentary Homolog (ERH) is an evolutionarily conserved protein originally characterized in fission yeast and recently shown to be required for H3K9me3 maintenance in human fibroblasts, but its function during development remains unknown. Here, we show that ERH is required for proper segregation of the inner cell mass and trophectoderm cell lineages during mouse development by repressing totipotent and alternative lineage programs. During human embryonic stem cell (hESC) differentiation into germ layer lineages, ERH is crucial for silencing naïve and pluripotency genes, transposable elements, and alternative lineage genes. Strikingly, ERH depletion in somatic cells reverts the H3K9me3 landscape to an hESC state and enables naïve and pluripotency gene and transposable element activation during iPSC reprogramming. Our findings reveal a role for ERH in initiation and maintenance of developmentally established gene repression.
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5
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Lin YC, Ku CC, Wuputra K, Liu CJ, Wu DC, Satou M, Mitsui Y, Saito S, Yokoyama KK. Possible Strategies to Reduce the Tumorigenic Risk of Reprogrammed Normal and Cancer Cells. Int J Mol Sci 2024; 25:5177. [PMID: 38791215 PMCID: PMC11120835 DOI: 10.3390/ijms25105177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The reprogramming of somatic cells to pluripotent stem cells has immense potential for use in regenerating or redeveloping tissues for transplantation, and the future application of this method is one of the most important research topics in regenerative medicine. These cells are generated from normal cells, adult stem cells, or neoplastic cancer cells. They express embryonic stem cell markers, such as OCT4, SOX2, and NANOG, and can differentiate into all tissue types in adults, both in vitro and in vivo. However, tumorigenicity, immunogenicity, and heterogeneity of cell populations may hamper the use of this method in medical therapeutics. The risk of cancer formation is dependent on mutations of these stemness genes during the transformation of pluripotent stem cells to cancer cells and on the alteration of the microenvironments of stem cell niches at genetic and epigenetic levels. Recent reports have shown that the generation of induced pluripotent stem cells (iPSCs) derived from human fibroblasts could be induced using chemicals, which is a safe, easy, and clinical-grade manufacturing strategy for modifying the cell fate of human cells required for regeneration therapies. This strategy is one of the future routes for the clinical application of reprogramming therapy. Therefore, this review highlights the recent progress in research focused on decreasing the tumorigenic risk of iPSCs or iPSC-derived organoids and increasing the safety of iPSC cell preparation and their application for therapeutic benefits.
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Affiliation(s)
- Ying-Chu Lin
- School of Dentistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Cha-Chien Ku
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.)
- Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-J.L.); (D.-C.W.)
- Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Kenly Wuputra
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.)
- Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-J.L.); (D.-C.W.)
- Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Chung-Jung Liu
- Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-J.L.); (D.-C.W.)
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Deng-Chyang Wu
- Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-J.L.); (D.-C.W.)
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Maki Satou
- Research Institute, Horus Co., Ltd., Iruma 358-0032, Saitama, Japan; (M.S.); (Y.M.)
| | - Yukio Mitsui
- Research Institute, Horus Co., Ltd., Iruma 358-0032, Saitama, Japan; (M.S.); (Y.M.)
| | - Shigeo Saito
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.)
- Research Institute, Horus Co., Ltd., Iruma 358-0032, Saitama, Japan; (M.S.); (Y.M.)
- Saito Laboratory of Cell Technology, Yaita 329-1571, Tochigi, Japan
| | - Kazunari K. Yokoyama
- School of Dentistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.)
- Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-J.L.); (D.-C.W.)
- Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
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6
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Yu Y, Liu L, Cao J, Huang R, Duan Q, Ye SD. Tbl1 promotes Wnt-β-catenin signaling-induced degradation of the Tcf7l1 protein in mouse embryonic stem cells. J Cell Sci 2024; 137:jcs261241. [PMID: 38639717 DOI: 10.1242/jcs.261241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Activation of the Wnt-β-catenin signaling pathway by CHIR99021, a specific inhibitor of GSK3β, induces Tcf7l1 protein degradation, which facilitates the maintenance of an undifferentiated state in mouse embryonic stem cells (mESCs); however, the precise mechanism is still unclear. Here, we showed that the overexpression of transducin-β-like protein 1 (Tbl1, also known as Tbl1x) or its family member Tblr1 (also known as Tbl1xr1) can decrease Tcf7l1 protein levels, whereas knockdown of each gene increases Tcf7l1 levels without affecting Tcf7l1 transcription. Interestingly, only Tbl1, and not Tblr1, interacts with Tcf7l1. Mechanistically, Tbl1 translocates from the cytoplasm into the nucleus in association with β-catenin (CTNNB1) after the addition of CHIR99021 and functions as an adaptor to promote ubiquitylation of the Tcf7l1 protein. Functional assays further revealed that enforced expression of Tbl1 is capable of delaying mESC differentiation. In contrast, knockdown of Tbl1 attenuates the effect of CHIR99021 on Tcf7l1 protein stability and mESC self-renewal. Our results provide insight into the regulatory network of the Wnt-β-catenin signaling pathway involved in promoting the maintenance of naïve pluripotency.
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Affiliation(s)
- Yang Yu
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
| | - Liwei Liu
- College of Medical Technology, Anhui Medical College, Hefei, Anhui, 230601, China
| | - Jianjian Cao
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
| | - Ru Huang
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
| | - Quanchao Duan
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
| | - Shou-Dong Ye
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
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7
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Ji J, Cao J, Chen P, Huang R, Ye SD. Inhibition of protein kinase C increases Prdm14 level to promote self-renewal of embryonic stem cells through reducing Suv39h-induced H3K9 methylation. J Biol Chem 2024; 300:105714. [PMID: 38309502 PMCID: PMC10909794 DOI: 10.1016/j.jbc.2024.105714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/19/2023] [Accepted: 01/28/2024] [Indexed: 02/05/2024] Open
Abstract
Inhibition of protein kinase C (PKC) efficiently promoted the self-renewal of embryonic stem cells (ESCs). However, information about the function of PKC inhibition remains lacking. Here, RNA-sequencing showed that the addition of Go6983 significantly inhibited the expression of de novo methyltransferases (Dnmt3a and Dnmt3b) and their regulator Dnmt3l, resulting in global hypomethylation of DNA in mouse ESCs. Mechanistically, PR domain-containing 14 (Prdm14), a site-specific transcriptional activator, partially contributed to Go6983-mediated repression of Dnmt3 genes. Administration of Go6983 increased Prdm14 expression mainly through the inhibition of PKCδ. High constitutive expression of Prdm14 phenocopied the ability of Go6983 to maintain` mouse ESC stemness in the absence of self-renewal-promoting cytokines. In contrast, the knockdown of Prdm14 eliminated the response to PKC inhibition and substantially impaired the Go6983-induced resistance of mouse ESCs to differentiation. Furthermore, liquid chromatography-mass spectrometry profiling and Western blotting revealed low levels of Suv39h1 and Suv39h2 in Go6983-treated mouse ESCs. Suv39h enzymes are histone methyltransferases that recognize dimethylated and trimethylated histone H3K9 specifically and usually function as transcriptional repressors. Consistently, the inhibition of Suv39h1 by RNA interference or the addition of the selective inhibitor chaetocin increased Prdm14 expression. Moreover, chromatin immunoprecipitation assay showed that Go6983 treatment led to decreased enrichment of dimethylation and trimethylation of H3K9 at the Prdm14 promoter but increased RNA polymerase Ⅱ binding affinity. Together, our results provide novel insights into the pivotal association between PKC inhibition-mediated self-renewal and epigenetic changes, which will help us better understand the regulatory network of stem cell pluripotency.
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Affiliation(s)
- Junxiang Ji
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, PR China
| | - Jianjian Cao
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, PR China
| | - Peng Chen
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, PR China
| | - Ru Huang
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, PR China
| | - Shou-Dong Ye
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, PR China.
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8
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Shojaee A, Huang SSC. Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions. Brief Bioinform 2023; 24:bbad370. [PMID: 37897702 PMCID: PMC10612495 DOI: 10.1093/bib/bbad370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/06/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023] Open
Abstract
Gene regulatory networks (GRNs) drive organism structure and functions, so the discovery and characterization of GRNs is a major goal in biological research. However, accurate identification of causal regulatory connections and inference of GRNs using gene expression datasets, more recently from single-cell RNA-seq (scRNA-seq), has been challenging. Here we employ the innovative method of Causal Inference Using Composition of Transactions (CICT) to uncover GRNs from scRNA-seq data. The basis of CICT is that if all gene expressions were random, a non-random regulatory gene should induce its targets at levels different from the background random process, resulting in distinct patterns in the whole relevance network of gene-gene associations. CICT proposes novel network features derived from a relevance network, which enable any machine learning algorithm to predict causal regulatory edges and infer GRNs. We evaluated CICT using simulated and experimental scRNA-seq data in a well-established benchmarking pipeline and showed that CICT outperformed existing network inference methods representing diverse approaches with many-fold higher accuracy. Furthermore, we demonstrated that GRN inference with CICT was robust to different levels of sparsity in scRNA-seq data, the characteristics of data and ground truth, the choice of association measure and the complexity of the supervised machine learning algorithm. Our results suggest aiming at directly predicting causality to recover regulatory relationships in complex biological networks substantially improves accuracy in GRN inference.
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Affiliation(s)
- Abbas Shojaee
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Shao-shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
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9
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Kohler TN, De Jonghe J, Ellermann AL, Yanagida A, Herger M, Slatery EM, Weberling A, Munger C, Fischer K, Mulas C, Winkel A, Ross C, Bergmann S, Franze K, Chalut K, Nichols J, Boroviak TE, Hollfelder F. Plakoglobin is a mechanoresponsive regulator of naive pluripotency. Nat Commun 2023; 14:4022. [PMID: 37419903 PMCID: PMC10329048 DOI: 10.1038/s41467-023-39515-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/09/2023] [Indexed: 07/09/2023] Open
Abstract
Biomechanical cues are instrumental in guiding embryonic development and cell differentiation. Understanding how these physical stimuli translate into transcriptional programs will provide insight into mechanisms underlying mammalian pre-implantation development. Here, we explore this type of regulation by exerting microenvironmental control over mouse embryonic stem cells. Microfluidic encapsulation of mouse embryonic stem cells in agarose microgels stabilizes the naive pluripotency network and specifically induces expression of Plakoglobin (Jup), a vertebrate homolog of β-catenin. Overexpression of Plakoglobin is sufficient to fully re-establish the naive pluripotency gene regulatory network under metastable pluripotency conditions, as confirmed by single-cell transcriptome profiling. Finally, we find that, in the epiblast, Plakoglobin was exclusively expressed at the blastocyst stage in human and mouse embryos - further strengthening the link between Plakoglobin and naive pluripotency in vivo. Our work reveals Plakoglobin as a mechanosensitive regulator of naive pluripotency and provides a paradigm to interrogate the effects of volumetric confinement on cell-fate transitions.
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Affiliation(s)
- Timo N Kohler
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Joachim De Jonghe
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Anna L Ellermann
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Ayaka Yanagida
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Veterinary Anatomy, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
- Stem Cell Therapy Laboratory, Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Michael Herger
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Erin M Slatery
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Antonia Weberling
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Clara Munger
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Katrin Fischer
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Carla Mulas
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Alex Winkel
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Connor Ross
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Sophie Bergmann
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Kristian Franze
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Institute of Medical Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 91, 91052, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91054, Erlangen, Germany
| | - Kevin Chalut
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Thorsten E Boroviak
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK.
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10
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Noviello G, Gjaltema RAF, Schulz EG. CasTuner is a degron and CRISPR/Cas-based toolkit for analog tuning of endogenous gene expression. Nat Commun 2023; 14:3225. [PMID: 37270532 DOI: 10.1038/s41467-023-38909-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/22/2023] [Indexed: 06/05/2023] Open
Abstract
Certain cellular processes are dose-dependent, requiring specific quantities or stoichiometries of gene products, as exemplified by haploinsufficiency and sex-chromosome dosage compensation. Understanding dosage-sensitive processes requires tools to quantitatively modulate protein abundance. Here we present CasTuner, a CRISPR-based toolkit for analog tuning of endogenous gene expression. The system exploits Cas-derived repressors that are quantitatively tuned by ligand titration through a FKBP12F36V degron domain. CasTuner can be applied at the transcriptional or post-transcriptional level using a histone deacetylase (hHDAC4) fused to dCas9, or the RNA-targeting CasRx, respectively. We demonstrate analog tuning of gene expression homogeneously across cells in mouse and human cells, as opposed to KRAB-dependent CRISPR-interference systems, which exhibit digital repression. Finally, we quantify the system's dynamics and use it to measure dose-response relationships of NANOG and OCT4 with their target genes and with the cellular phenotype. CasTuner thus provides an easy-to-implement tool to study dose-responsive processes in their physiological context.
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Affiliation(s)
- Gemma Noviello
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Rutger A F Gjaltema
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Edda G Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.
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11
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Carbognin E, Carlini V, Panariello F, Chieregato M, Guerzoni E, Benvegnù D, Perrera V, Malucelli C, Cesana M, Grimaldi A, Mutarelli M, Carissimo A, Tannenbaum E, Kugler H, Hackett JA, Cacchiarelli D, Martello G. Esrrb guides naive pluripotent cells through the formative transcriptional programme. Nat Cell Biol 2023; 25:643-657. [PMID: 37106060 PMCID: PMC7614557 DOI: 10.1038/s41556-023-01131-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/15/2023] [Indexed: 04/29/2023]
Abstract
During embryonic development, naive pluripotent epiblast cells transit to a formative state. The formative epiblast cells form a polarized epithelium, exhibit distinct transcriptional and epigenetic profiles and acquire competence to differentiate into all somatic and germline lineages. However, we have limited understanding of how the transition to a formative state is molecularly controlled. Here we used murine embryonic stem cell models to show that ESRRB is both required and sufficient to activate formative genes. Genetic inactivation of Esrrb leads to illegitimate expression of mesendoderm and extra-embryonic markers, impaired formative expression and failure to self-organize in 3D. Functionally, this results in impaired ability to generate formative stem cells and primordial germ cells in the absence of Esrrb. Computational modelling and genomic analyses revealed that ESRRB occupies key formative genes in naive cells and throughout the formative state. In so doing, ESRRB kickstarts the formative transition, leading to timely and unbiased capacity for multi-lineage differentiation.
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Affiliation(s)
- Elena Carbognin
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Valentina Carlini
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL)-Rome, Adriano Buzzati-Traverso Campus, Rome, Italy
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | | | - Elena Guerzoni
- Department of Biology, University of Padua, Padua, Italy
| | | | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Cristina Malucelli
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Marcella Cesana
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Advanced Biomedical Sciences, University of Naples 'Federico II', Naples, Italy
| | - Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Margherita Mutarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Istituto di Scienze Applicate e Sistemi Intelligenti 'Eduardo Caianiello', Consiglio Nazionale delle Ricerche, Pozzuoli, Italy
| | - Annamaria Carissimo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Istituto per le Applicazioni del Calcolo 'Mauro Picone,' Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Eitan Tannenbaum
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Hillel Kugler
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Jamie A Hackett
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL)-Rome, Adriano Buzzati-Traverso Campus, Rome, Italy.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.
- Department of Translational Medicine, University of Naples 'Federico II', Naples, Italy.
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples 'Federico II', Naples, Italy.
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12
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Schnirman RE, Kuo SJ, Kelly RC, Yamaguchi TP. The role of Wnt signaling in the development of the epiblast and axial progenitors. Curr Top Dev Biol 2023; 153:145-180. [PMID: 36967193 DOI: 10.1016/bs.ctdb.2023.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Understanding how the body plan is established during embryogenesis remains a fundamental biological question. The Wnt/β-catenin signaling pathway plays a crucial and highly conserved role in body plan formation, functioning to polarize the primary anterior-posterior (AP) or head-to-tail body axis in most metazoans. In this chapter, we focus on the roles that the mammalian Wnt/β-catenin pathway plays to prepare the pluripotent epiblast for gastrulation, and to elicit the emergence of multipotent axial progenitors from the caudal epiblast. Interactions between Wnt and retinoic acid (RA), another powerful family of developmental signaling molecules, in axial progenitors will also be discussed. Gastrulation movements and somitogenesis result in the anterior displacement of the RA source (the rostral somites and lateral plate mesoderm (LPM)), from the posterior Wnt source (the primitive streak (PS)), leading to the establishment of antiparallel gradients of RA and Wnt that control the self-renewal and successive differentiation of neck, trunk and tail progenitors.
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Affiliation(s)
| | - Samuel J Kuo
- NCI-Frederick, NIH, Frederick, MD, United States
| | - Ryan C Kelly
- NCI-Frederick, NIH, Frederick, MD, United States
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13
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Endoh M, Niwa H. Stepwise pluripotency transitions in mouse stem cells. EMBO Rep 2022; 23:e55010. [PMID: 35903955 PMCID: PMC9442314 DOI: 10.15252/embr.202255010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/13/2022] [Accepted: 07/01/2022] [Indexed: 07/31/2023] Open
Abstract
Pluripotent cells in mouse embryos, which first emerge in the inner cell mass of the blastocyst, undergo gradual transition marked by changes in gene expression, developmental potential, polarity, and morphology as they develop from the pre-implantation until post-implantation gastrula stage. Recent studies of cultured mouse pluripotent stem cells (PSCs) have clarified the presence of intermediate pluripotent stages between the naïve pluripotent state represented by embryonic stem cells (ESCs-equivalent to the pre-implantation epiblast) and the primed pluripotent state represented by epiblast stem cells (EpiSCs-equivalent to the late post-implantation gastrula epiblast). In this review, we discuss these recent findings in light of our knowledge on peri-implantation mouse development and consider the implications of these new PSCs to understand their temporal sequence and the feasibility of using them as model system for pluripotency.
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Affiliation(s)
- Mitsuhiro Endoh
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics (IMEG)Kumamoto UniversityKumamotoJapan
| | - Hitoshi Niwa
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics (IMEG)Kumamoto UniversityKumamotoJapan
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14
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Roodgar M, Suchy FP, Nguyen LH, Bajpai VK, Sinha R, Vilches-Moure JG, Van Bortle K, Bhadury J, Metwally A, Jiang L, Jian R, Chiang R, Oikonomopoulos A, Wu JC, Weissman IL, Mankowski JL, Holmes S, Loh KM, Nakauchi H, VandeVoort CA, Snyder MP. Chimpanzee and pig-tailed macaque iPSCs: Improved culture and generation of primate cross-species embryos. Cell Rep 2022; 40:111264. [PMID: 36044843 PMCID: PMC10075238 DOI: 10.1016/j.celrep.2022.111264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/06/2022] [Accepted: 08/04/2022] [Indexed: 12/26/2022] Open
Abstract
As our closest living relatives, non-human primates uniquely enable explorations of human health, disease, development, and evolution. Considerable effort has thus been devoted to generating induced pluripotent stem cells (iPSCs) from multiple non-human primate species. Here, we establish improved culture methods for chimpanzee (Pan troglodytes) and pig-tailed macaque (Macaca nemestrina) iPSCs. Such iPSCs spontaneously differentiate in conventional culture conditions, but can be readily propagated by inhibiting endogenous WNT signaling. As a unique functional test of these iPSCs, we injected them into the pre-implantation embryos of another non-human species, rhesus macaques (Macaca mulatta). Ectopic expression of gene BCL2 enhances the survival and proliferation of chimpanzee and pig-tailed macaque iPSCs within the pre-implantation embryo, although the identity and long-term contribution of the transplanted cells warrants further investigation. In summary, we disclose transcriptomic and proteomic data, cell lines, and cell culture resources that may be broadly enabling for non-human primate iPSCs research.
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Affiliation(s)
- Morteza Roodgar
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Fabian P Suchy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lan H Nguyen
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Vivek K Bajpai
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jose G Vilches-Moure
- Department of Comparative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kevin Van Bortle
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joydeep Bhadury
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Biomedicine, Sahlgrenska University Hospital, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Ahmed Metwally
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Rosaria Chiang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Angelos Oikonomopoulos
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph L Mankowski
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Kyle M Loh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Catherine A VandeVoort
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California, Davis, Davis, CA, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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15
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Andersson E, Sjö M, Kaji K, Olariu V. CELLoGeNe - An energy landscape framework for logical networks controlling cell decisions. iScience 2022; 25:104743. [PMID: 35942105 PMCID: PMC9356104 DOI: 10.1016/j.isci.2022.104743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/01/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Experimental and computational efforts are constantly made to elucidate mechanisms controlling cell fate decisions during development and reprogramming. One powerful computational method is to consider cell commitment and reprogramming as movements in an energy landscape. Here, we develop Computation of Energy Landscapes of Logical Gene Networks (CELLoGeNe), which maps Boolean implementation of gene regulatory networks (GRNs) into energy landscapes. CELLoGeNe removes inadvertent symmetries in the energy landscapes normally arising from standard Boolean operators. Furthermore, CELLoGeNe provides tools to visualize and stochastically analyze the shapes of multi-dimensional energy landscapes corresponding to epigenetic landscapes for development and reprogramming. We demonstrate CELLoGeNe on two GRNs governing different aspects of induced pluripotent stem cells, identifying experimentally validated attractors and revealing potential reprogramming roadblocks. CELLoGeNe is a general framework that can be applied to various biological systems offering a broad picture of intracellular dynamics otherwise inaccessible with existing methods. CELLoGeNe – Computation of Energy Landscapes of Logical Gene Networks Cell states as landscape attractors Maintenance and acquisition of cell pluripotency applications Single cell stochastic landscape navigation and visualization tool
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16
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Kim KT, Oh JY, Park S, Kim SM, Benjamin P, Park IH, Chun KH, Chang YT, Cha HJ. Live isolation of naïve ESCs via distinct glucose metabolism and stored glycogen. Metab Eng 2022; 72:97-106. [DOI: 10.1016/j.ymben.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
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17
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Quan Y, Wang M, Xu C, Wang X, Wu Y, Qin D, Lin Y, Lu X, Lu F, Li L. Cnot8 eliminates naïve regulation networks and is essential for naïve-to-formative pluripotency transition. Nucleic Acids Res 2022; 50:4414-4435. [PMID: 35390160 PMCID: PMC9071485 DOI: 10.1093/nar/gkac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 03/11/2022] [Accepted: 03/26/2022] [Indexed: 11/14/2022] Open
Abstract
Mammalian early epiblasts at different phases are characterized by naïve, formative, and primed pluripotency states, involving extensive transcriptome changes. Here, we report that deadenylase Cnot8 of Ccr4-Not complex plays essential roles during the transition from naïve to formative state. Knock out (KO) Cnot8 resulted in early embryonic lethality in mice, but Cnot8 KO embryonic stem cells (ESCs) could be established. Compared with the cells differentiated from normal ESCs, Cnot8 KO cells highly expressed a great many genes during their differentiation into the formative state, including several hundred naïve-like genes enriched in lipid metabolic process and gene expression regulation that may form the naïve regulation networks. Knockdown expression of the selected genes of naïve regulation networks partially rescued the differentiation defects of Cnot8 KO ESCs. Cnot8 depletion led to the deadenylation defects of its targets, increasing their poly(A) tail lengths and half-life, eventually elevating their expression levels. We further found that Cnot8 was involved in the clearance of targets through its deadenylase activity and the binding of Ccr4-Not complex, as well as the interacting with Tob1 and Pabpc1. Our results suggest that Cnot8 eliminates naïve regulation networks through mRNA clearance, and is essential for naïve-to-formative pluripotency transition.
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Affiliation(s)
- Yujun Quan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meijiao Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengpeng Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dandan Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuxuan Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xukun Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Cai J, Chen H, Xie S, Hu Z, Bai Y. Research Progress of Totipotent Stem Cells. Stem Cells Dev 2022; 31:335-345. [PMID: 35502477 DOI: 10.1089/scd.2022.0061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Totipotent stem cells (TSCs), can develop into complete organisms, used in biological fields such as regenerative medicine, mammalian breeding, and conservation. However, cells from early-stage embryos cultured are hard to self-renew and maintain developmental totipotency, which becomes a key factor limiting the research of TSCs. Fortunately, a break-through in the study of induced pluripotent stem cells returning to their totipotent state has been made, resulting in the establishment of multiple TSCs and igniting a new wave of stem cell research. Furthermore, the blastocyst-like structures can be generated by the established TSCs, which lays a foundation for synthetic embryos in vitro. In this review, we summarize the totipotent stage of the early embryos, the establishment and cultivation of TSCs, and the developmental ability exploration of TSCs to promote further research of TSCs.
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Affiliation(s)
- Jianfeng Cai
- Foshan University School of Life Science and Engineering, 118208, Foshan, China, 528000;
| | - Huifang Chen
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
| | - Shiting Xie
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
| | - Zhichao Hu
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
| | - Yinshan Bai
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
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19
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β-catenin links cell seeding density to global gene expression during mouse embryonic stem cell differentiation. iScience 2022; 25:103541. [PMID: 34977504 PMCID: PMC8689156 DOI: 10.1016/j.isci.2021.103541] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/05/2021] [Accepted: 11/25/2021] [Indexed: 11/21/2022] Open
Abstract
Although cell density is known to affect numerous biological processes including gene expression and cell fate specification, mechanistic understanding of what factors link cell density to global gene regulation is lacking. Here, we reveal that the expression of thousands of genes in mouse embryonic stem cells (mESCs) is affected by cell seeding density and that low cell density enhances the efficiency of differentiation. Mechanistically, β-catenin is localized primarily to adherens junctions during both self-renewal and differentiation at high density. However, when mESCs differentiate at low density, β-catenin translocates to the nucleus and associates with Tcf7l1, inducing co-occupied lineage markers. Meanwhile, Esrrb sustains the expression of pluripotency-associated genes while repressing lineage markers at high density, and its association with DNA decreases at low density. Our results provide new insights into the previously neglected but pervasive phenomenon of density-dependent gene regulation.
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20
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Abuhashem A, Garg V, Hadjantonakis AK. RNA polymerase II pausing in development: orchestrating transcription. Open Biol 2022; 12:210220. [PMID: 34982944 PMCID: PMC8727152 DOI: 10.1098/rsob.210220] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/08/2021] [Indexed: 01/09/2023] Open
Abstract
The coordinated regulation of transcriptional networks underpins cellular identity and developmental progression. RNA polymerase II promoter-proximal pausing (Pol II pausing) is a prevalent mechanism by which cells can control and synchronize transcription. Pol II pausing regulates the productive elongation step of transcription at key genes downstream of a variety of signalling pathways, such as FGF and Nodal. Recent advances in our understanding of the Pol II pausing machinery and its role in transcription call for an assessment of these findings within the context of development. In this review, we discuss our current understanding of the molecular basis of Pol II pausing and its function during organismal development. By critically assessing the tools used to study this process we conclude that combining recently developed genomics approaches with refined perturbation systems has the potential to expand our understanding of Pol II pausing mechanistically and functionally in the context of development and beyond.
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Affiliation(s)
- Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
- Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medical College, New York, NY 10021, USA
| | - Vidur Garg
- 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
- Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medical College, New York, NY 10021, USA
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21
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Yeh CY, Huang WH, Chen HC, Meir YJJ. Capturing Pluripotency and Beyond. Cells 2021; 10:cells10123558. [PMID: 34944066 PMCID: PMC8700150 DOI: 10.3390/cells10123558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
During the development of a multicellular organism, the specification of different cell lineages originates in a small group of pluripotent cells, the epiblasts, formed in the preimplantation embryo. The pluripotent epiblast is protected from premature differentiation until exposure to inductive cues in strictly controlled spatially and temporally organized patterns guiding fetus formation. Epiblasts cultured in vitro are embryonic stem cells (ESCs), which recapitulate the self-renewal and lineage specification properties of their endogenous counterparts. The characteristics of totipotency, although less understood than pluripotency, are becoming clearer. Recent studies have shown that a minor ESC subpopulation exhibits expanded developmental potential beyond pluripotency, displaying a characteristic reminiscent of two-cell embryo blastomeres (2CLCs). In addition, reprogramming both mouse and human ESCs in defined media can produce expanded/extended pluripotent stem cells (EPSCs) similar to but different from 2CLCs. Further, the molecular roadmaps driving the transition of various potency states have been clarified. These recent key findings will allow us to understand eutherian mammalian development by comparing the underlying differences between potency network components during development. Using the mouse as a paradigm and recent progress in human PSCs, we review the epiblast's identity acquisition during embryogenesis and their ESC counterparts regarding their pluripotent fates and beyond.
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Affiliation(s)
- Chih-Yu Yeh
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
| | - Wei-Han Huang
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
| | - Hung-Chi Chen
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Correspondence: (H.-C.C.); (Y.-J.J.M.)
| | - Yaa-Jyuhn James Meir
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: (H.-C.C.); (Y.-J.J.M.)
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22
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Abdulhasan M, Ruden X, Rappolee B, Dutta S, Gurdziel K, Ruden DM, Awonuga AO, Korzeniewski SJ, Puscheck EE, Rappolee DA. Stress Decreases Host Viral Resistance and Increases Covid Susceptibility in Embryonic Stem Cells. Stem Cell Rev Rep 2021; 17:2164-2177. [PMID: 34155611 PMCID: PMC8216586 DOI: 10.1007/s12015-021-10188-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 12/13/2022]
Abstract
Stress-induced changes in viral receptor and susceptibility gene expression were measured in embryonic stem cells (ESC) and differentiated progeny. Rex1 promoter-Red Fluorescence Protein reporter ESC were tested by RNAseq after 72hr exposures to control stress hyperosmotic sorbitol under stemness culture (NS) to quantify stress-forced differentiation (SFD) transcriptomic programs. Control ESC cultured with stemness factor removal produced normal differentiation (ND). Bulk RNAseq transcriptomic analysis showed significant upregulation of two genes involved in Covid-19 cell uptake, Vimentin (VIM) and Transmembrane Serine Protease 2 (TMPRSS2). SFD increased the hepatitis A virus receptor (Havcr1) and the transplacental Herpes simplex 1 (HSV1) virus receptor (Pvrl1) compared with ESC undergoing ND. Several other coronavirus receptors, Glutamyl Aminopeptidase (ENPEP) and Dipeptidyl Peptidase 4 (DPP4) were upregulated significantly in SFD>ND. Although stressed ESC are more susceptible to infection due to increased expression of viral receptors and decreased resistance, the necessary Covid-19 receptor, angiotensin converting enzyme (ACE)2, was not expressed in our experiments. TMPRSS2, ENPEP, and DPP4 mediate Coronavirus uptake, but are also markers of extra-embryonic endoderm (XEN), which arise from ESC undergoing ND or SFD. Mouse and human ESCs differentiated to XEN increase TMPRSS2 and other Covid-19 uptake-mediating gene expression, but only some lines express ACE2. Covid-19 susceptibility appears to be genotype-specific and not ubiquitous. Of the 30 gene ontology (GO) groups for viral susceptibility, 15 underwent significant stress-forced changes. Of these, 4 GO groups mediated negative viral regulation and most genes in these increase in ND and decrease with SFD, thus suggesting that stress increases ESC viral susceptibility. Taken together, the data suggest that a control hyperosmotic stress can increase Covid-19 susceptibility and decrease viral host resistance in mouse ESC. However, this limited pilot study should be followed with studies in human ESC, tests of environmental, hormonal, and pharmaceutical stressors and direct tests for infection of stressed, cultured ESC and embryos by Covid-19.
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Affiliation(s)
- Mohammed Abdulhasan
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
- Reproductive Stress 3M Inc, Grosse Pointe Farms, MI, 48236, USA
| | - Ximena Ruden
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
| | | | - Sudipta Dutta
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
- Reproductive Endocrinology and Cell Signaling LaboratoryDepartment of Integrative BiosciencesCollege of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, USA
| | - Katherine Gurdziel
- Genome Sciences Center, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Douglas M Ruden
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
- Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, 48202, USA
| | - Awoniyi O Awonuga
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
| | - Steve J Korzeniewski
- Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, 48202, USA
| | - Elizabeth E Puscheck
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
- Reproductive Stress 3M Inc, Grosse Pointe Farms, MI, 48236, USA
- Invia Fertility Clinics, Hoffman Estates, Illinois, 60169, USA
| | - Daniel A Rappolee
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA.
- Reproductive Stress 3M Inc, Grosse Pointe Farms, MI, 48236, USA.
- Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, 48202, USA.
- Program for Reproductive Sciences and Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Department of Biology, University of Windsor, Windsor, ON, N9B 3P4, Canada.
- CS Mott Center for Human Growth and Development, Wayne State University School of Medicine, 275 East Hancock, Detroit, MI, 48201, USA.
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Luo M, Liu Q, Ye S, Liu S, Hu Y, Lv D, Wang G, Li M, Jian C, Huang B. RNA-seq of buffalo fibroblasts over-expressed pluripotent-related genes to investigate characteristics of its preliminarily reprogrammed stage. Res Vet Sci 2021; 144:164-174. [PMID: 34839950 DOI: 10.1016/j.rvsc.2021.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/19/2021] [Accepted: 11/16/2021] [Indexed: 01/10/2023]
Abstract
Induced pluripotent stem cells (iPSCs) can enhance the efficiency of buffalo genetic improvements because of their differentiation potential and proliferation ability, which are similar to those of embryonic stem cells. However, very few studies have focussed on buffalo iPSCs, and a stable induction system has not been established for buffalo somatic cell reprogramming. In this study, we constructed a PiggyBac transposon vector co-expressing buffalo OCT4, C-MYC, KLF4 and SOX2 genes (PB_OMKS) separated by the nucleotide sequence of three 2A peptides and established the buffalo foetal skin fibroblast (BFSF) cell line BFSF_OMKS. RNA-seq technology and bioinformatics analysis methods were mainly employed to perform a transcriptome analysis between BFSF and BFSF_OMKS. The results revealed that over-expression of OCT4, C-MYC, KLF4 and SOX2 in BFSFs led to the activation of reprogramming-related LIF, activin, BMP4, SMAD1/5/9 and Wnt signals. These results increased our understanding of buffalo somatic cell reprogramming mechanisms and could provide a possible theory for the selection of small-molecule cocktails to promote reprogramming.
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Affiliation(s)
- Man Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China; College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Quanhui Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China; College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Sheng Ye
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China; College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Shulin Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China; College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Yanan Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China; College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Danwei Lv
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China; College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Guodong Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China; College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Mengmei Li
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China.
| | - Chongdong Jian
- Department of Neurology, The Affiliated Hospital of Youjiang Medical for Nationalities, Baise, Guangxi 533000, China.
| | - Ben Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, China; College of Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China.
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Pluripotency Stemness and Cancer: More Questions than Answers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1376:77-100. [PMID: 34725790 DOI: 10.1007/5584_2021_663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Embryonic stem cells and induced pluripotent stem cells provided us with fascinating new knowledge in recent years. Mechanistic insight into intricate regulatory circuitry governing pluripotency stemness and disclosing parallels between pluripotency stemness and cancer instigated numerous studies focusing on roles of pluripotency transcription factors, including Oct4, Sox2, Klf4, Nanog, Sall4 and Tfcp2L1, in cancer. Although generally well substantiated as tumour-promoting factors, oncogenic roles of pluripotency transcription factors and their clinical impacts are revealing themselves as increasingly complex. In certain tumours, both Oct4 and Sox2 behave as genuine oncogenes, and reporter genes driven by composite regulatory elements jointly recognized by both the factors can identify stem-like cells in a proportion of tumours. On the other hand, cancer stem cells seem to be biologically very heterogeneous both among different tumour types and among and even within individual tumours. Pluripotency transcription factors are certainly implicated in cancer stemness, but do not seem to encompass its entire spectrum. Certain cancer stem cells maintain their stemness by biological mechanisms completely different from pluripotency stemness, sometimes even by engaging signalling pathways that promote differentiation of pluripotent stem cells. Moreover, while these signalling pathways may well be antithetical to stemness in pluripotent stem cells, they may cooperate with pluripotency factors in cancer stem cells - a paradigmatic example is provided by the MAPK-AP-1 pathway. Unexpectedly, forced expression of pluripotency transcription factors in cancer cells frequently results in loss of their tumour-initiating ability, their phenotypic reversion and partial epigenetic normalization. Besides the very different signalling contexts operating in pluripotent and cancer stem cells, respectively, the pronounced dose dependency of reprogramming pluripotency factors may also contribute to the frequent loss of tumorigenicity observed in induced pluripotent cancer cells. Finally, contradictory cell-autonomous and non-cell-autonomous effects of various signalling molecules operate during pluripotency (cancer) reprogramming. The effects of pluripotency transcription factors in cancer are thus best explained within the concept of cancer stem cell heterogeneity.
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Inhibition of ubiquitin-specific protease 13-mediated degradation of Raf1 kinase by Spautin-1 has opposing effects in naïve and primed pluripotent stem cells. J Biol Chem 2021; 297:101332. [PMID: 34688658 PMCID: PMC8577099 DOI: 10.1016/j.jbc.2021.101332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/10/2021] [Accepted: 10/19/2021] [Indexed: 11/20/2022] Open
Abstract
Embryonic stem cells (ESCs) are progenitor cells that retain the ability to differentiate into various cell types and are necessary for tissue repair. Improving cell culture conditions to maintain the pluripotency of ESCs in vitro is an urgent problem in the field of regenerative medicine. Here, we reveal that Spautin-1, a specific small-molecule inhibitor of ubiquitin-specific protease (USP) family members USP10 and USP13, promotes the maintenance of self-renewal and pluripotency of mouse ESCs in vitro. Functional studies reveal that only knockdown of USP13, but not USP10, is capable of mimicking the function of Spautin-1. Mechanistically, we demonstrate that USP13 physically interacts with, deubiquitinates, and stabilizes serine/threonine kinase Raf1 and thereby sustains Raf1 protein at the posttranslational level to activate the FGF/MEK/ERK prodifferentiation signaling pathway in naïve mouse ESCs. In contrast, in primed mouse epiblast stem cells and human induced pluripotent stem cells, the addition of Spautin-1 had an inhibitory effect on Raf1 levels, but USP13 overexpression promoted self-renewal. The addition of an MEK inhibitor impaired the effect of USP13 upregulation in these cells. These findings provide new insights into the regulatory network of naïve and primed pluripotency.
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Duan K, Si CY, Zhao SM, Ai ZY, Niu BH, Yin Y, Xiang LF, Ding H, Zheng Y. The Long Terminal Repeats of ERV6 Are Activated in Pre-Implantation Embryos of Cynomolgus Monkey. Cells 2021; 10:cells10102710. [PMID: 34685690 PMCID: PMC8534818 DOI: 10.3390/cells10102710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
Precise gene regulation is critical during embryo development. Long terminal repeat elements (LTRs) of endogenous retroviruses (ERVs) are dynamically expressed in blastocysts of mammalian embryos. However, the expression pattern of LTRs in monkey blastocyst is still unknown. By single-cell RNA-sequencing (seq) data of cynomolgus monkeys, we found that LTRs of several ERV families, including MacERV6, MacERV3, MacERV2, MacERVK1, and MacERVK2, were highly expressed in pre-implantation embryo cells including epiblast (EPI), trophectoderm (TrB), and primitive endoderm (PrE), but were depleted in post-implantation. We knocked down MacERV6-LTR1a in cynomolgus monkeys with a short hairpin RNA (shRNA) strategy to examine the potential function of MacERV6-LTR1a in the early development of monkey embryos. The silence of MacERV6-LTR1a mainly postpones the differentiation of TrB, EPI, and PrE cells in embryos at day 7 compared to control. Moreover, we confirmed MacERV6-LTR1a could recruit Estrogen Related Receptor Beta (ESRRB), which plays an important role in the maintenance of self-renewal and pluripotency of embryonic and trophoblast stem cells through different signaling pathways including FGF and Wnt signaling pathways. In summary, these results suggest that MacERV6-LTR1a is involved in gene regulation of the pre-implantation embryo of the cynomolgus monkeys.
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Affiliation(s)
- Kui Duan
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Chen-Yang Si
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Shu-Mei Zhao
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Zong-Yong Ai
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Bao-Hua Niu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Yu Yin
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Li-Feng Xiang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Hao Ding
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Yun Zheng
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
- Correspondence:
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Gadd45g initiates embryonic stem cell differentiation and inhibits breast cell carcinogenesis. Cell Death Discov 2021; 7:271. [PMID: 34601500 PMCID: PMC8487429 DOI: 10.1038/s41420-021-00667-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 11/24/2022] Open
Abstract
Many self-renewal-promoting factors of embryonic stem cells (ESCs) have been implicated in carcinogenesis, while little known about the genes that direct ESCs exit from pluripotency and regulate tumor development. Here, we show that the transcripts of Gadd45 family genes, including Gadd45a, Gadd45b, and Gadd45g, are gradually increased upon mouse ESC differentiation. Upregulation of Gadd45 members decreases cell proliferation and induces endodermal and trophectodermal lineages. In contrast, knockdown of Gadd45 genes can delay mouse ESC differentiation. Mechanistic studies reveal that Gadd45g activates MAPK signaling by increasing expression levels of the positive modulators of this pathway, such as Csf1r, Igf2, and Fgfr3. Therefore, inhibition of MAPK signaling with a MEK specific inhibitor is capable of eliminating the differentiation phenotype caused by Gadd45g upregulation. Meanwhile, GADD45G functions as a suppressor in human breast cancers. Enforced expression of GADD45G significantly inhibits tumor formation and breast cancer metastasis in mice through limitation of the propagation and invasion of breast cancer cells. These results not only expand our understanding of the regulatory network of ESCs, but also help people better treatment of cancers by manipulating the prodifferentiation candidates.
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Zhang M, Ji J, Wang X, Zhang X, Zhang Y, Li Y, Wang X, Li X, Ban Q, Ye SD. The transcription factor Tfcp2l1 promotes primordial germ cell-like cell specification of pluripotent stem cells. J Biol Chem 2021; 297:101217. [PMID: 34555410 PMCID: PMC8517209 DOI: 10.1016/j.jbc.2021.101217] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 12/17/2022] Open
Abstract
Primordial germ cells (PGCs) are common ancestors of all germline cells. However, mechanistic understanding of how PGC specification occurs is limited. Here, we identified transcription factor CP2-like 1 (Tfcp2l1), an important pluripotency factor, as a pivotal factor for PGC-like cell (PGCLC) specification. High-throughput sequencing and quantitative real-time PCR analysis showed that Tfcp2l1 expression is gradually increased during mouse and human epiblast differentiation into PGCLCs in vivo and in vitro. Consequently, overexpression of Tfcp2l1 can enhance the specification efficiency even without inductive cytokines in mouse epiblast-like cells derived from embryonic stem cells, while knockdown of Tfcp2l1 significantly inhibits PGCLC generation. Mechanistic studies revealed that Tfcp2l1 exerts its function partially through the direct induction of PR domain zinc finger protein 14, a key PGC marker, as downregulation of the PR domain zinc finger protein 14 transcript can impair the ability of Tfcp2l1 to direct PGCLC commitment. Importantly, we finally demonstrated that the crucial role of the human homolog Tfcp2l1 in promoting PGCLC specification is conserved in human pluripotent stem cells. Together, our data uncover a novel function of Tfcp2l1 in PGCLC fate determination and facilitate a better understanding of germ cell development.
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Affiliation(s)
- Meng Zhang
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Junxiang Ji
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xiaoxiao Wang
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Xinbao Zhang
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Yan Zhang
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Yuting Li
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xin Wang
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xiaofeng Li
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Qian Ban
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Shou-Dong Ye
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, China; Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China.
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Doumpas N, Söderholm S, Narula S, Moreira S, Doble BW, Cantù C, Basler K. TCF/LEF regulation of the topologically associated domain ADI promotes mESCs to exit the pluripotent ground state. Cell Rep 2021; 36:109705. [PMID: 34525377 DOI: 10.1016/j.celrep.2021.109705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/10/2021] [Accepted: 08/23/2021] [Indexed: 11/19/2022] Open
Abstract
Mouse embryonic stem cells (mESCs) can be maintained in vitro in defined N2B27 medium supplemented with two chemical inhibitors for GSK3 and MEK (2i) and the cytokine leukemia inhibitory factor (LIF), which act synergistically to promote self-renewal and pluripotency. Here, we find that genetic deletion of the four genes encoding the TCF/LEF transcription factors confers mESCs with the ability to self-renew in N2B27 medium alone. TCF/LEF quadruple knockout (qKO) mESCs display dysregulation of several genes, including Aire, Dnmt3l, and IcosL, located adjacent to each other within a topologically associated domain (TAD). Aire, Dnmt3l, and IcosL appear to be regulated by TCF/LEF in a β-catenin independent manner. Moreover, downregulation of Aire and Dnmt3l in wild-type mESCs mimics the loss of TCF/LEF and increases mESC survival in the absence of 2iL. Hence, this study identifies TCF/LEF effectors that mediate exit from the pluripotent state.
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Affiliation(s)
- Nikolaos Doumpas
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Simon Söderholm
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Smarth Narula
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Steven Moreira
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Bradley W Doble
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Departments of Biochemistry and Medical Genetics & Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3E 0W2, Canada
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
| | - Konrad Basler
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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Festuccia N, Owens N, Chervova A, Dubois A, Navarro P. The combined action of Esrrb and Nr5a2 is essential for murine naïve pluripotency. Development 2021; 148:271840. [PMID: 34397088 PMCID: PMC8451941 DOI: 10.1242/dev.199604] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022]
Abstract
The maintenance of pluripotency in mouse embryonic stem cells (ESCs) is governed by the action of an interconnected network of transcription factors. Among them, only Oct4 and Sox2 have been shown to be strictly required for the self-renewal of ESCs and pluripotency, particularly in culture conditions in which differentiation cues are chemically inhibited. Here, we report that the conjunct activity of two orphan nuclear receptors, Esrrb and Nr5a2, parallels the importance of that of Oct4 and Sox2 in naïve mouse ESCs. By occupying a large common set of regulatory elements, these two factors control the binding of Oct4, Sox2 and Nanog to DNA. Consequently, in their absence the pluripotency network collapses and the transcriptome is substantially deregulated, leading to the differentiation of ESCs. Altogether, this work identifies orphan nuclear receptors, previously thought to be performing supportive functions, as a set of core regulators of naïve pluripotency. Summary: Esrrb and Nr5a2, two orphan nuclear receptors, are identified as essential regulators of pluripotency in mouse embryonic stem cells.
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Affiliation(s)
- Nicola Festuccia
- Regulatory Dynamics and Cell Identity, MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK.,Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France
| | - Nick Owens
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Almira Chervova
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France
| | - Agnès Dubois
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France
| | - Pablo Navarro
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France
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31
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Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons. Sci Rep 2021; 11:16977. [PMID: 34417498 PMCID: PMC8379280 DOI: 10.1038/s41598-021-96263-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 08/04/2021] [Indexed: 12/15/2022] Open
Abstract
Chromatin architecture influences transcription by modulating the physical access of regulatory factors to DNA, playing fundamental roles in cell identity. Studies on dopaminergic differentiation have identified coding genes, but the relationship with non-coding genes or chromatin accessibility remains elusive. Using RNA-Seq and ATAC-Seq we profiled differentially expressed transcripts and open chromatin regions during early dopaminergic neuron differentiation. Hierarchical clustering of differentially expressed genes, resulted in 6 groups with unique characteristics. Surprisingly, the abundance of long non-coding RNAs (lncRNAs) was high in the most downregulated transcripts, and depicted positive correlations with target mRNAs. We observed that open chromatin regions decrease upon differentiation. Enrichment analyses of accessibility depict an association between open chromatin regions and specific functional pathways and gene-sets. A bioinformatic search for motifs allowed us to identify transcription factors and structural nuclear proteins that potentially regulate dopaminergic differentiation. Interestingly, we also found changes in protein and mRNA abundance of the CCCTC-binding factor, CTCF, which participates in genome organization and gene expression. Furthermore, assays demonstrated co-localization of CTCF with Polycomb-repressed chromatin marked by H3K27me3 in pluripotent cells, progressively decreasing in neural precursor cells and differentiated neurons. Our work provides a unique resource of transcription factors and regulatory elements, potentially involved in the acquisition of human dopaminergic neuron cell identity.
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32
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Olivieri D, Paramanathan S, Bardet AF, Hess D, Smallwood SA, Elling U, Betschinger J. The BTB-domain transcription factor ZBTB2 recruits chromatin remodelers and a histone chaperone during the exit from pluripotency. J Biol Chem 2021; 297:100947. [PMID: 34270961 PMCID: PMC8350017 DOI: 10.1016/j.jbc.2021.100947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/21/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Transcription factors (TFs) harboring broad-complex, tramtrack, and bric-a-brac (BTB) domains play important roles in development and disease. These BTB domains are thought to recruit transcriptional modulators to target DNA regions. However, a systematic molecular understanding of the mechanism of action of this TF family is lacking. Here, we identify the zinc finger BTB-TF Zbtb2 from a genetic screen for regulators of exit from pluripotency and demonstrate that its absence perturbs embryonic stem cell differentiation and the gene expression dynamics underlying peri-implantation development. We show that ZBTB2 binds the chromatin remodeler Ep400 to mediate downstream transcription. Independently, the BTB domain directly interacts with nucleosome remodeling and deacetylase and histone chaperone histone regulator A. Nucleosome remodeling and deacetylase recruitment is a common feature of BTB TFs, and based on phylogenetic analysis, we propose that this is a conserved evolutionary property. Binding to UBN2, in contrast, is specific to ZBTB2 and requires a C-terminal extension of the BTB domain. Taken together, this study identifies a BTB-domain TF that recruits chromatin modifiers and a histone chaperone during a developmental cell state transition and defines unique and shared molecular functions of the BTB-domain TF family.
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Affiliation(s)
- Daniel Olivieri
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | | | - Anaïs F Bardet
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; CNRS, University of Strasbourg, UMR7242 Biotechnology and Cell Signaling, Illkirch, France
| | - Daniel Hess
- 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
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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33
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Liu Y, Yamane J, Tanaka A, Fujibuchi W, Yamashita JK. AMPK activation reverts mouse epiblast stem cells to naive state. iScience 2021; 24:102783. [PMID: 34308289 PMCID: PMC8283141 DOI: 10.1016/j.isci.2021.102783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 05/01/2021] [Accepted: 06/23/2021] [Indexed: 12/25/2022] Open
Abstract
Despite increasing knowledge on primed and naive pluripotency, the cell signaling that regulates the pluripotency type in stem cells remains not fully understood. Here we show that AMP kinase (AMPK) activators can induce the reversion of primed mouse epiblast stem cells (mEpiSCs) to the naive pluripotent state. The addition of AMPK activators alone or together with leukemia inhibitory factor to primed mEpiSCs induced the appearance of naive-like cells. After passaging in naive culture conditions, the colony morphology, protein expression, and global gene expression profiles indicated the naive state, as did germline transmission ability. Loss-of-function and gain-of-function studies suggested that p38 is a critical downstream target in AMPK activation. Finally, single-cell RNA sequencing analysis revealed that the reversion process through AMPK signaling passes an intermediate naive-like population. In conclusion, the AMPK pathway is a critical driving force in the reversion of primed to naive pluripotency.
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Affiliation(s)
- Yajing Liu
- The Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Junko Yamane
- The Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Akito Tanaka
- The Department of Animal Research Facility, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Wataru Fujibuchi
- The Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Jun K. Yamashita
- The Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
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34
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Mao Y, Wang L, Zhong B, Yang N, Li Z, Cui T, Feng G, Li W, Zhang Y, Zhou Q. Continuous expression of reprogramming factors induces and maintains mouse pluripotency without specific growth factors and signaling inhibitors. Cell Prolif 2021; 54:e13090. [PMID: 34197016 PMCID: PMC8349648 DOI: 10.1111/cpr.13090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/06/2021] [Accepted: 06/09/2021] [Indexed: 12/11/2022] Open
Abstract
Objectives Derivation and maintenance of pluripotent stem cells (PSCs) generally require optimized and complex culture media, which hinders the derivation of PSCs from various species. Expression of Oct4, Sox2, Klf4, and c‐Myc (OSKM) can reprogram somatic cells into induced PSCs (iPSCs), even for species possessing no optimal culture condition. Herein, we explored whether expression of OSKM could induce and maintain pluripotency without PSC‐specific growth factors and signaling inhibitors. Methods The culture medium of Tet‐On‐OSKM/Oct4‐GFP mouse embryonic stem cells (ESCs) was switched from N2B27 with MEK inhibitor, GSK3β inhibitor, and leukemia inhibitory factor (LIF) (2iL) to N2B27 with doxycycline. Tet‐On‐OSKM mouse embryonic fibroblast (MEF) cells were reprogrammed in N2B27 with doxycycline. Cell proliferation was traced. Pluripotency was assessed by expression of ESC marker genes, teratoma, and chimera formation. RNA‐Seq was conducted to analyze gene expression. Results Via continuous expression of OSKM, mouse ESCs (OSKM‐ESCs) and the resulting iPSCs (OSKM‐iPSCs) reprogrammed from MEF cells propagated stably, expressed pluripotency marker genes, and formed three germ layers in teratomas. Transcriptional landscapes of OSKM‐iPSCs resembled those of ESCs cultured in 2iL and were more similar to those of ESCs cultured in serum/LIF. Furthermore, OSKM‐iPSCs contributed to germline transmission. Conclusions Expression of OSKM could induce and maintain mouse pluripotency without specific culturing factors. Importantly, OSKM‐iPSCs could produce gene‐modified animals through germline transmission, with potential applications in other species.
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Affiliation(s)
- Yihuan Mao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Libin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Bei Zhong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Ning Yang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhikun Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Tongtong Cui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
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35
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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] [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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36
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Mnatsakanyan H, Salmeron-Sanchez M, Rico P. Lithium Directs Embryonic Stem Cell Differentiation Into Hemangioblast-Like Cells. Adv Biol (Weinh) 2021; 5:e2000569. [PMID: 33969645 DOI: 10.1002/adbi.202000569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/20/2021] [Indexed: 11/08/2022]
Abstract
Definitive hematopoietic stem cells (HSCs) derive from specialized regions of the endothelium known as the hemogenic endothelium (HE) during embryonic developmental processes. This knowledge opens up new possibilities for designing new strategies to obtain HSCs in vitro from pluripotent stem cells (PSCs). Previous advances in this field show that the Wnt/β-catenin signaling pathway plays a crucial role in PSC-derived HSC formation. In this work, lithium, a GSK3 inhibitor, is identified as an element capable of stabilizing β-catenin and inducing embryonic stem cells (ESCs) differentiation in hemangioblast-like cells, highly consistent with the role of Wnt agonists on ESC differentiation. ESCs treated with 10 mm lithium express CD31+, SCA-1+, Nkx2-5+, CD34+, and FLK1+ cells characteristic of the hemangioblast cells that precede HE development. However, 10 mm Li treated cells remain arrested in a hemangioblast-like phase, which switched into the expression of HE markers after stimulation with maturation medium. The ability of lithium-treated ESCs to further derive into HE is confirmed after defined maturation, resulting in a rapid increase in cells positive for the HE markers RUNX1 and SOX17. The results represent a novel strategy for generating HSC precursors in vitro as a multipotent source of stem cells for blood disease therapies.
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Affiliation(s)
- Hayk Mnatsakanyan
- Center for Biomaterials and Tissue Engineering (CBIT), Universitat Politècnica de València, Camino de Vera s/n, Valencia, 46022, Spain
| | - Manuel Salmeron-Sanchez
- Center for Biomaterials and Tissue Engineering (CBIT), Universitat Politècnica de València, Camino de Vera s/n, Valencia, 46022, Spain.,Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5 Pabellón 11, Madrid, 28029, Spain.,Centre for the Cellular Microenvironment, University of Glasgow, Glasgow, G12 8LT, United Kingdom
| | - Patricia Rico
- Center for Biomaterials and Tissue Engineering (CBIT), Universitat Politècnica de València, Camino de Vera s/n, Valencia, 46022, Spain.,Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5 Pabellón 11, Madrid, 28029, Spain
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37
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Kang X, Li C. A Dimension Reduction Approach for Energy Landscape: Identifying Intermediate States in Metabolism-EMT Network. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003133. [PMID: 34026435 PMCID: PMC8132071 DOI: 10.1002/advs.202003133] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/18/2020] [Indexed: 05/08/2023]
Abstract
Dimension reduction is a challenging problem in complex dynamical systems. Here, a dimension reduction approach of landscape (DRL) for complex dynamical systems is proposed, by mapping a high-dimensional system on a low-dimensional energy landscape. The DRL approach is applied to three biological networks, which validates that new reduced dimensions preserve the major information of stability and transition of original high-dimensional systems. The consistency of barrier heights calculated from the low-dimensional landscape and transition actions calculated from the high-dimensional system further shows that the landscape after dimension reduction can quantify the global stability of the system. The epithelial-mesenchymal transition (EMT) and abnormal metabolism are two hallmarks of cancer. With the DRL approach, a quadrastable landscape for metabolism-EMT network is identified, including epithelial (E), abnormal metabolic (A), hybrid E/M (H), and mesenchymal (M) cell states. The quantified energy landscape and kinetic transition paths suggest that for the EMT process, the cells at E state need to first change their metabolism, then enter the M state. The work proposes a general framework for the dimension reduction of a stochastic dynamical system, and advances the mechanistic understanding of the underlying relationship between EMT and cellular metabolism.
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Affiliation(s)
- Xin Kang
- School of Mathematical SciencesFudan UniversityShanghai200433China
- Shanghai Center for Mathematical SciencesFudan UniversityShanghai200433China
| | - Chunhe Li
- Shanghai Center for Mathematical SciencesFudan UniversityShanghai200433China
- Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
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38
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Bayerl J, Ayyash M, Shani T, Manor YS, Gafni O, Massarwa R, Kalma Y, Aguilera-Castrejon A, Zerbib M, Amir H, Sheban D, Geula S, Mor N, Weinberger L, Naveh Tassa S, Krupalnik V, Oldak B, Livnat N, Tarazi S, Tawil S, Wildschutz E, Ashouokhi S, Lasman L, Rotter V, Hanna S, Ben-Yosef D, Novershtern N, Viukov S, Hanna JH. Principles of signaling pathway modulation for enhancing human naive pluripotency induction. Cell Stem Cell 2021; 28:1549-1565.e12. [PMID: 33915080 PMCID: PMC8423434 DOI: 10.1016/j.stem.2021.04.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 02/05/2021] [Accepted: 03/31/2021] [Indexed: 12/21/2022]
Abstract
Isolating human MEK/ERK signaling-independent pluripotent stem cells (PSCs) with naive pluripotency characteristics while maintaining differentiation competence and (epi)genetic integrity remains challenging. Here, we engineer reporter systems that allow the screening for defined conditions that induce molecular and functional features of human naive pluripotency. Synergistic inhibition of WNT/β-CATENIN, protein kinase C (PKC), and SRC signaling consolidates the induction of teratoma-competent naive human PSCs, with the capacity to differentiate into trophoblast stem cells (TSCs) and extraembryonic naive endodermal (nEND) cells in vitro. Divergent signaling and transcriptional requirements for boosting naive pluripotency were found between mouse and human. P53 depletion in naive hPSCs increased their contribution to mouse-human cross-species chimeric embryos upon priming and differentiation. Finally, MEK/ERK inhibition can be substituted with the inhibition of NOTCH/RBPj, which induces alternative naive-like hPSCs with a diminished risk for deleterious global DNA hypomethylation. Our findings set a framework for defining the signaling foundations of human naive pluripotency. Inhibition of SRC, PKC, and WNT consolidates human naive pluripotency induction Competitiveness of p53 depleted human PSCs in cross-species chimeric embryos Opposing net effect for ACTIVIN and WNT on mouse versus human naive pluripotency 2i and ERKi independent alternative human naive-like PSC conditions
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Affiliation(s)
- Jonathan Bayerl
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Muneef Ayyash
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tom Shani
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yair Shlomo Manor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ohad Gafni
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rada Massarwa
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yael Kalma
- Wolfe PGD‑Stem Cell Laboratory, Racine IVF Unit, Lis Maternity Hospital, Tel-Aviv Sourasky Medical Center, Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel‑Aviv, Israel
| | | | - Mirie Zerbib
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hadar Amir
- Wolfe PGD‑Stem Cell Laboratory, Racine IVF Unit, Lis Maternity Hospital, Tel-Aviv Sourasky Medical Center, Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel‑Aviv, Israel
| | - Daoud Sheban
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shay Geula
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nofar Mor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Leehee Weinberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Segev Naveh Tassa
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Vladislav Krupalnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Bernardo Oldak
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nir Livnat
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shadi Tarazi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shadi Tawil
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Emilie Wildschutz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shahd Ashouokhi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lior Lasman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Varda Rotter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Suhair Hanna
- Department of Pediatrics, Rambam Hospital, Haifa, Israel
| | - Dalit Ben-Yosef
- Wolfe PGD‑Stem Cell Laboratory, Racine IVF Unit, Lis Maternity Hospital, Tel-Aviv Sourasky Medical Center, Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel‑Aviv, Israel.
| | - Noa Novershtern
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Sergey Viukov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Aquaporins implicated in the cell proliferation and the signaling pathways of cell stemness. Biochimie 2021; 188:52-60. [PMID: 33894294 DOI: 10.1016/j.biochi.2021.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/11/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022]
Abstract
Aquaporins (AQPs) are water channel proteins facilitating passive transport of water and other small molecules across biomembranes. Regulation of osmotic homeostasis via AQPs is accompanied by dynamic participation of various cellular signaling pathways. Recently emerging evidence reveals that functional roles of AQPs are further extended from the osmotic regulation via water permeation into the cell proliferation and differentiation. In particular, anomalous expression of AQPs has been demonstrated in various types of cancer cells and cancer stem-like cells and it has been proposed as markers for proliferation and progression of cancer cells. Thus, a more comprehensive view on AQPs could bring a great interest in the cell stemness accompanied by the expression of AQPs. AQPs are broadly expressed across tissues and cells in a cell type- and lineage-specific manner during development via spatiotemporal transcriptional regulation. Moreover, AQPs are expressed in various adult stem cells and cells associated with a stem cell niche as well as cancer stem-like cells. However, the expression and regulatory mechanisms of AQP expression in stem cells have not been well understood. This review highlighted the AQPs expression in stem cell niches/stem cells and the involvement of AQPs in the cell proliferation and signaling pathways associated with cell stemness.
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40
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Dissection of two routes to naïve pluripotency using different kinase inhibitors. Nat Commun 2021; 12:1863. [PMID: 33767186 PMCID: PMC7994667 DOI: 10.1038/s41467-021-22181-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 03/04/2021] [Indexed: 01/31/2023] Open
Abstract
Embryonic stem cells (ESCs) can be maintained in the naïve state through inhibition of Mek1/2 and Gsk3 (2i). A relevant effect of 2i is the inhibition of Cdk8/19, which are negative regulators of the Mediator complex, responsible for the activity of enhancers. Inhibition of Cdk8/19 (Cdk8/19i) stimulates enhancers and, similar to 2i, stabilizes ESCs in the naïve state. Here, we use mass spectrometry to describe the molecular events (phosphoproteome, proteome, and metabolome) triggered by 2i and Cdk8/19i on ESCs. Our data reveal widespread commonalities between these two treatments, suggesting overlapping processes. We find that post-transcriptional de-repression by both 2i and Cdk8/19i might support the mitochondrial capacity of naive cells. However, proteome reprogramming in each treatment is achieved by different mechanisms. Cdk8/19i acts directly on the transcriptional machinery, activating key identity genes to promote the naïve program. In contrast, 2i stabilizes the naïve circuitry through, in part, de-phosphorylation of downstream transcriptional effectors.
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41
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Sevilla A, Papatsenko D, Mazloom AR, Xu H, Vasileva A, Unwin RD, LeRoy G, Chen EY, Garrett-Bakelman FE, Lee DF, Trinite B, Webb RL, Wang Z, Su J, Gingold J, Melnick A, Garcia BA, Whetton AD, MacArthur BD, Ma'ayan A, Lemischka IR. An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. Front Cell Dev Biol 2021; 9:630067. [PMID: 33816475 PMCID: PMC8017264 DOI: 10.3389/fcell.2021.630067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/17/2021] [Indexed: 01/02/2023] Open
Abstract
Cell fate decisions during development are governed by multi-factorial regulatory mechanisms including chromatin remodeling, DNA methylation, binding of transcription factors to specific loci, RNA transcription and protein synthesis. However, the mechanisms by which such regulatory “dimensions” coordinate cell fate decisions are currently poorly understood. Here we quantified the multi-dimensional molecular changes that occur in mouse embryonic stem cells (mESCs) upon depletion of Estrogen related receptor beta (Esrrb), a key pluripotency regulator. Comparative analyses of expression changes subsequent to depletion of Esrrb or Nanog, indicated that a system of interlocked feed-forward loops involving both factors, plays a central part in regulating the timing of mESC fate decisions. Taken together, our meta-analyses support a hierarchical model in which pluripotency is maintained by an Oct4-Sox2 regulatory module, while the timing of differentiation is regulated by a Nanog-Esrrb module.
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Affiliation(s)
- Ana Sevilla
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Departament de Biología Cellular, Fisiología i Immunología, Facultat de Biología, Universitat de Barcelona, Barcelona, Spain
| | - Dimitri Papatsenko
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Amin R Mazloom
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Huilei Xu
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ana Vasileva
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Richard D Unwin
- Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom.,Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester, United Kingdom.,Centre for Advanced Discovery and Experimental Therapeutics, Central Manchester University Hospitals NHS Foundation Trust, Institute of Human Development, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Gary LeRoy
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Edward Y Chen
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Francine E Garrett-Bakelman
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, United States
| | - Dung-Fang Lee
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Benjamin Trinite
- Institut de Recerca de La Sida, IrsiCaixa AIDS Research Institute, Germans Trias I Pujol Research Institute, Hospital Universitari Germans Trias I Pujol, Catalonia, Spain
| | - Ryan L Webb
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Zichen Wang
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jie Su
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Julian Gingold
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ari Melnick
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, United States
| | - Benjamin A Garcia
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Anthony D Whetton
- Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom.,Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester, United Kingdom
| | - Ben D MacArthur
- The Centre for Human Development, Stem Cells and Regeneration, Institute of Developmental Sciences, University of Southampton, Southampton, United Kingdom
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ihor R Lemischka
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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42
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Lackner A, Sehlke R, Garmhausen M, Giuseppe Stirparo G, Huth M, Titz-Teixeira F, van der Lelij P, Ramesmayer J, Thomas HF, Ralser M, Santini L, Galimberti E, Sarov M, Stewart AF, Smith A, Beyer A, Leeb M. Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency. EMBO J 2021; 40:e105776. [PMID: 33687089 PMCID: PMC8047444 DOI: 10.15252/embj.2020105776] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
In the mammalian embryo, epiblast cells must exit the naïve state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditions in vitro. However, our understanding of the molecular cascades and gene networks involved in the exit from naïve pluripotency remains fragmentary. Here, we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large‐scale transcriptomics and computational systems biology to delineate the regulatory circuits governing naïve state exit. Transcriptome profiles for 73 ESC lines deficient for regulators of the exit from naïve pluripotency predominantly manifest delays on the trajectory from naïve to formative epiblast. We find that gene networks operative in ESCs are also active during transition from pre‐ to post‐implantation epiblast in utero. We identified 496 naïve state‐associated genes tightly connected to the in vivo epiblast state transition and largely conserved in primate embryos. Integrated analysis of mutant transcriptomes revealed funnelling of multiple gene activities into discrete regulatory modules. Finally, we delineate how intersections with signalling pathways direct this pivotal mammalian cell state transition.
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Affiliation(s)
- Andreas Lackner
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Robert Sehlke
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Marius Garmhausen
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Giuliano Giuseppe Stirparo
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.,Living Systems Institute, University of Exeter, Exeter, UK
| | - Michelle Huth
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Fabian Titz-Teixeira
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Petra van der Lelij
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Julia Ramesmayer
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Henry F Thomas
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Meryem Ralser
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Laura Santini
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Elena Galimberti
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - A Francis Stewart
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Austin Smith
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.,Living Systems Institute, University of Exeter, Exeter, UK
| | - Andreas Beyer
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Martin Leeb
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
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43
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Abstract
Organoids are three-dimensional structures that are derived from the self-organization of stem cells as they differentiate in vitro. The plasticity of stem cells is one of the major criteria for generating organoids most similar to the tissue structures they intend to mimic. Stem cells are cells with unique properties of self-renewal and differentiation. Depending on their origin, a distinction is made between pluripotent (embryonic) stem cells (PSCs), adult (or tissue) stem cells (ASCs), and those obtained by somatic reprogramming, so-called induced pluripotent stem cells (iPSCs). While most data since the 1980s have been acquired in the mouse model, and then from the late 1990s in humans, the process of somatic reprogammation has revolutionized the field of stem cell research. For domestic animals, numerous attempts have been made to obtain PSCs and iPSCs, an approach that makes it possible to omit the use of embryos to derive the cells. Even if the plasticity of the cells obtained is not always optimal, the recent progress in obtaining reprogrammed cells is encouraging. Along with PSCs and iPSCs, many organoid derivations in animal species are currently obtained from ASCs. In this study, we present state-of-the-art stem cell research according to their origins in the various animal models developed.
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Affiliation(s)
- Bertrand Pain
- Univ Lyon, Université Lyon 1, INSERM, INRAE, Stem Cell and Brain Research Institute, U1208, CSC USC1361, Bron, France.
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44
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C3G Regulates STAT3, ERK, Adhesion Signaling, and Is Essential for Differentiation of Embryonic Stem Cells. Stem Cell Rev Rep 2021; 17:1465-1477. [PMID: 33624208 PMCID: PMC8372029 DOI: 10.1007/s12015-021-10136-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2021] [Indexed: 02/06/2023]
Abstract
C3G (RAPGEF1), engaged in multiple signaling pathways, is essential for the early development of the mouse. In this study, we have examined its role in mouse embryonic stem cell self-renewal and differentiation. C3G null cells generated by CRISPR mediated knock-in of a targeting vector exhibited enhanced clonogenicity and long-term self-renewal. They did not differentiate in response to LIF withdrawal when compared to the wild type ES cells and were defective for lineage commitment upon teratoma formation in vivo. Gene expression analysis of C3G KO cells showed misregulated expression of a large number of genes compared with WT cells. They express higher levels of self-renewal factors like KLF4 and ESRRB and show high STAT3 activity, and very low ERK activity compared to WT cells. Reintroduction of C3G expression in a KO line partially reverted expression of ESRRB, and KLF4, and ERK activity similar to that seen in WT cells. The expression of self-renewal factors was persistent for a longer time, and induction of lineage-specific markers was not seen when C3G KO cells were induced to form embryoid bodies. C3G KO cells showed poor adhesion and significantly reduced levels of pFAK, pPaxillin, and Integrin-β1, in addition to downregulation of the cluster of genes involved in cell adhesion, compared to WT cells. Our results show that C3G is essential for the regulation of STAT3, ERK, and adhesion signaling, to maintain pluripotency of mouse embryonic stem cells and enable their lineage commitment for differentiation. ![]()
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45
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Shahsavari A, Weeratunga P, Ovchinnikov DA, Whitworth DJ. Pluripotency and immunomodulatory signatures of canine induced pluripotent stem cell-derived mesenchymal stromal cells are similar to harvested mesenchymal stromal cells. Sci Rep 2021; 11:3486. [PMID: 33568729 PMCID: PMC7875972 DOI: 10.1038/s41598-021-82856-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 01/25/2021] [Indexed: 01/30/2023] Open
Abstract
With a view towards harnessing the therapeutic potential of canine mesenchymal stromal cells (cMSCs) as modulators of inflammation and the immune response, and to avoid the issues of the variable quality and quantity of harvested cMSCs, we examined the immunomodulatory properties of cMSCs derived from canine induced pluripotent stem cells (ciMSCs), and compared them to cMSCs harvested from adipose tissue (cAT-MSC) and bone marrow (cBM-MSC). A combination of deep sequencing and quantitative RT-PCR of the ciMSC transcriptome confirmed that ciMSCs express more genes in common with cBM-MSCs and cAT-MSCs than with the ciPSCs from which they were derived. Both ciMSCs and harvested cMSCs express a range of pluripotency factors in common with the ciPSCs including NANOG, POU5F1 (OCT-4), SOX-2, KLF-4, LIN-28A, MYC, LIF, LIFR, and TERT. However, ESRRB and PRDM-14, both factors associated with naïve, rather than primed, pluripotency were expressed only in the ciPSCs. CXCR-4, which is essential for the homing of MSCs to sites of inflammation, is also detectable in ciMSCs, cAT- and cBM-MSCs, but not ciPSCs. ciMSCs constitutively express the immunomodulatory factors iNOS, GAL-9, TGF-β1, PTGER-2α and VEGF, and the pro-inflammatory mediators COX-2, IL-1β and IL-8. When stimulated with the canine pro-inflammatory cytokines tumor necrosis factor-α (cTNF-α), interferon-γ (cIFN-γ), or a combination of both, ciMSCs upregulated their expression of IDO, iNOS, GAL-9, HGF, TGF-β1, PTGER-2α, VEGF, COX-2, IL-1β and IL-8. When co-cultured with mitogen-stimulated lymphocytes, ciMSCs downregulated their expression of iNOS, HGF, TGF-β1 and PTGER-2α, while increasing their expression of COX-2, IDO and IL-1β. Taken together, these findings suggest that ciMSCs possess similar immunomodulatory capabilities as harvested cMSCs and support further investigation into their potential use for the management of canine immune-mediated and inflammatory disorders.
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Affiliation(s)
- Arash Shahsavari
- grid.1003.20000 0000 9320 7537School of Veterinary Science, University of Queensland, Gatton, QLD 4343 Australia
| | - Prasanna Weeratunga
- grid.1003.20000 0000 9320 7537School of Veterinary Science, University of Queensland, Gatton, QLD 4343 Australia
| | - Dmitry A. Ovchinnikov
- grid.1003.20000 0000 9320 7537Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4067 Australia
| | - Deanne J. Whitworth
- grid.1003.20000 0000 9320 7537School of Veterinary Science, University of Queensland, Gatton, QLD 4343 Australia ,grid.1003.20000 0000 9320 7537Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4067 Australia
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46
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Betto RM, Diamante L, Perrera V, Audano M, Rapelli S, Lauria A, Incarnato D, Arboit M, Pedretti S, Rigoni G, Guerineau V, Touboul D, Stirparo GG, Lohoff T, Boroviak T, Grumati P, Soriano ME, Nichols J, Mitro N, Oliviero S, Martello G. Metabolic control of DNA methylation in naive pluripotent cells. Nat Genet 2021; 53:215-229. [PMID: 33526924 PMCID: PMC7116828 DOI: 10.1038/s41588-020-00770-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/17/2020] [Indexed: 12/31/2022]
Abstract
Naive epiblast and embryonic stem cells (ESCs) give rise to all cells of adults. Such developmental plasticity is associated with genome hypomethylation. Here, we show that LIF-Stat3 signaling induces genomic hypomethylation via metabolic reconfiguration. Stat3-/- ESCs show decreased α-ketoglutarate production from glutamine, leading to increased Dnmt3a and Dnmt3b expression and DNA methylation. Notably, genome methylation is dynamically controlled through modulation of α-ketoglutarate availability or Stat3 activation in mitochondria. Alpha-ketoglutarate links metabolism to the epigenome by reducing the expression of Otx2 and its targets Dnmt3a and Dnmt3b. Genetic inactivation of Otx2 or Dnmt3a and Dnmt3b results in genomic hypomethylation even in the absence of active LIF-Stat3. Stat3-/- ESCs show increased methylation at imprinting control regions and altered expression of cognate transcripts. Single-cell analyses of Stat3-/- embryos confirmed the dysregulated expression of Otx2, Dnmt3a and Dnmt3b as well as imprinted genes. Several cancers display Stat3 overactivation and abnormal DNA methylation; therefore, the molecular module that we describe might be exploited under pathological conditions.
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Affiliation(s)
- Riccardo M Betto
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Linda Diamante
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
- Neuroscience Sector, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Matteo Audano
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Stefania Rapelli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy
| | - Andrea Lauria
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy
| | - Danny Incarnato
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Mattia Arboit
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Silvia Pedretti
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Giovanni Rigoni
- Department of Biology, University of Padua, Padua, Italy
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Vincent Guerineau
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | - David Touboul
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | | | - Tim Lohoff
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Thorsten Boroviak
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Jennifer Nichols
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Nico Mitro
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy.
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.
| | - Graziano Martello
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy.
- Department of Biology, University of Padua, Padua, Italy.
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47
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Kim J, T. Jakobsen S, Natarajan KN, Won KJ. TENET: gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data. Nucleic Acids Res 2021; 49:e1. [PMID: 33170214 PMCID: PMC7797076 DOI: 10.1093/nar/gkaa1014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/05/2020] [Accepted: 10/14/2020] [Indexed: 12/22/2022] Open
Abstract
Accurate prediction of gene regulatory rules is important towards understanding of cellular processes. Existing computational algorithms devised for bulk transcriptomics typically require a large number of time points to infer gene regulatory networks (GRNs), are applicable for a small number of genes and fail to detect potential causal relationships effectively. Here, we propose a novel approach 'TENET' to reconstruct GRNs from single cell RNA sequencing (scRNAseq) datasets. Employing transfer entropy (TE) to measure the amount of causal relationships between genes, TENET predicts large-scale gene regulatory cascades/relationships from scRNAseq data. TENET showed better performance than other GRN reconstructors, in identifying key regulators from public datasets. Specifically from scRNAseq, TENET identified key transcriptional factors in embryonic stem cells (ESCs) and during direct cardiomyocytes reprogramming, where other predictors failed. We further demonstrate that known target genes have significantly higher TE values, and TENET predicted higher TE genes were more influenced by the perturbation of their regulator. Using TENET, we identified and validated that Nme2 is a culture condition specific stem cell factor. These results indicate that TENET is uniquely capable of identifying key regulators from scRNAseq data.
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Affiliation(s)
- Junil Kim
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen N, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Simon T. Jakobsen
- Functional Genomics and Metabolism Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
| | - Kedar N Natarajan
- Functional Genomics and Metabolism Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
- Danish Institute of Advanced Study (D-IAS), University of Southern Denmark, Denmark
| | - Kyoung-Jae Won
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen N, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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48
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Garbutt TA, Konganti K, Konneker T, Hillhouse A, Phelps D, Jones A, Aylor D, Threadgill DW. Derivation of stable embryonic stem cell-like, but transcriptionally heterogenous, induced pluripotent stem cells from non-permissive mouse strains. Mamm Genome 2020; 31:263-286. [PMID: 33015751 PMCID: PMC9113365 DOI: 10.1007/s00335-020-09849-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 09/22/2020] [Indexed: 11/26/2022]
Abstract
Genetic background is known to play a role in the ability to derive pluripotent, embryonic stem cells (ESC), a trait referred to as permissiveness. Previously we demonstrated that induced pluripotent stem cells (iPSC) can be readily derived from non-permissive mouse strains by addition of serum-based media supplemented with GSK3B and MEK inhibitors, termed 2iS media, 3 days into reprogramming. Here, we describe the derivation of second type of iPSC colony from non-permissive mouse strains that can be stably maintained independently of 2iS media. The resulting cells display transcriptional heterogeneity similar to that observed in ESC from permissive genetic backgrounds derived in conventional serum containing media supplemented with leukemia inhibitor factor. However, unlike previous studies that report exclusive subpopulations, we observe both exclusive and simultaneous expression of naive and primed cell surface markers. Herein, we explore shifts in pluripotency in the presence of 2iS and characterize heterogenous subpopulations to determine their pluripotent state and role in heterogenous iPSCs derived from the non-permissive NOD/ShiLtJ strain. We conclude that heterogeneity is a naturally occurring, necessary quality of stem cells that allows for the maintenance of pluripotency. This study further demonstrates the efficacy of the 2iS reprogramming technique. It is also the first study to derive stable ESC-like stem cells from the non-permissive NOD/ShiLtJ and WSB/EiJ strains, enabling easier and broader research possibilities into pluripotency for these and similar non-permissive mouse strains and species.
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Affiliation(s)
- Tiffany A Garbutt
- Program in Genetics, Department of Biological Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Kranti Konganti
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, 77843, USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Thomas Konneker
- Program in Genetics, Department of Biological Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Andrew Hillhouse
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, 77843, USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Drake Phelps
- Program in Genetics, Department of Biological Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alexis Jones
- Program in Genetics, Department of Biological Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - David Aylor
- Program in Genetics, Department of Biological Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - David W Threadgill
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, 77843, USA.
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, 77843, USA.
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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Wnt/Beta-catenin/Esrrb signalling controls the tissue-scale reorganization and maintenance of the pluripotent lineage during murine embryonic diapause. Nat Commun 2020; 11:5499. [PMID: 33127892 PMCID: PMC7603494 DOI: 10.1038/s41467-020-19353-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022] Open
Abstract
The epiblast, which provides the foundation of the future body, is actively reshaped during early embryogenesis, but the reshaping mechanisms are poorly understood. Here, using a 3D in vitro model of early epiblast development, we identify the canonical Wnt/β-catenin pathway and its central downstream factor Esrrb as the key signalling cascade regulating the tissue-scale organization of the murine pluripotent lineage. Although in vivo the Wnt/β-catenin/Esrrb circuit is dispensable for embryonic development before implantation, autocrine Wnt activity controls the morphogenesis and long-term maintenance of the epiblast when development is put on hold during diapause. During this phase, the progressive changes in the epiblast architecture and Wnt signalling response show that diapause is not a stasis but instead is a dynamic process with underlying mechanisms that can appear redundant during transient embryogenesis. Embryonic diapause is a state of dormancy with poorly understood mechanisms of embryo intrinsic regulation. Here, the authors show that murine diapause is a dynamic process, where tissue-scale reorganization of the pluripotent lineage is controlled in an autocrine manner by the Wnt/b-catenin/Esrrb signalling cascade.
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Taei A, Kiani T, Taghizadeh Z, Moradi S, Samadian A, Mollamohammadi S, Sharifi‐Zarchi A, Guenther S, Akhlaghpour A, Asgari Abibeiglou B, Najar‐Asl M, Karamzadeh R, Khalooghi K, Braun T, Hassani S, Baharvand H. Temporal activation of LRH-1 and RAR-γ in human pluripotent stem cells induces a functional naïve-like state. EMBO Rep 2020; 21:e47533. [PMID: 33252195 PMCID: PMC7534641 DOI: 10.15252/embr.201847533] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/13/2020] [Accepted: 07/17/2020] [Indexed: 12/19/2022] Open
Abstract
Naïve pluripotency can be established in human pluripotent stem cells (hPSCs) by manipulation of transcription factors, signaling pathways, or a combination thereof. However, differences exist in the molecular and functional properties of naïve hPSCs generated by different protocols, which include varying similarities with pre-implantation human embryos, differentiation potential, and maintenance of genomic integrity. We show here that short treatment with two chemical agonists (2a) of nuclear receptors, liver receptor homologue-1 (LRH-1) and retinoic acid receptor gamma (RAR-γ), along with 2i/LIF (2a2iL) induces naïve-like pluripotency in human cells during reprogramming of fibroblasts, conversion of pre-established hPSCs, and generation of new cell lines from blastocysts. 2a2iL-hPSCs match several defined criteria of naïve-like pluripotency and contribute to human-mouse interspecies chimeras. Activation of TGF-β signaling is instrumental for acquisition of naïve-like pluripotency by the 2a2iL induction procedure, and transient activation of TGF-β signaling substitutes for 2a to generate naïve-like hPSCs. We reason that 2a2iL-hPSCs are an easily attainable system to evaluate properties of naïve-like hPSCs and for various applications.
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Affiliation(s)
- Adeleh Taei
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
- Department of Developmental BiologyUniversity of Science and CultureTehranIran
| | - Tahereh Kiani
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
| | - Zeinab Taghizadeh
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
| | - Sharif Moradi
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
| | - Azam Samadian
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
| | - Sepideh Mollamohammadi
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
| | - Ali Sharifi‐Zarchi
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
- Computer Engineering DepartmentSharif University of TechnologyTehranIran
| | - Stefan Guenther
- Department of Cardiac Development and RemodelingMax‐Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Azimeh Akhlaghpour
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
| | - Behrouz Asgari Abibeiglou
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
| | - Mostafa Najar‐Asl
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
| | - Razieh Karamzadeh
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
| | - Keynoosh Khalooghi
- Department of Cardiac Development and RemodelingMax‐Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Thomas Braun
- Department of Cardiac Development and RemodelingMax‐Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Seyedeh‐Nafiseh Hassani
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental BiologyCell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECRTehranIran
- Department of Developmental BiologyUniversity of Science and CultureTehranIran
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