1
|
York JR, Rao A, Huber PB, Schock EN, Montequin A, Rigney S, LaBonne C. Shared features of blastula and neural crest stem cells evolved at the base of vertebrates. Nat Ecol Evol 2024; 8:1680-1692. [PMID: 39060477 DOI: 10.1038/s41559-024-02476-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/18/2024] [Indexed: 07/28/2024]
Abstract
The neural crest is a vertebrate-specific stem cell population that helped drive the origin and evolution of vertebrates. A distinguishing feature of these cells is their multi-germ layer potential, which has parallels to another stem cell population-pluripotent stem cells of the vertebrate blastula. Here, we investigate the evolutionary origins of neural crest potential by comparing neural crest and pluripotency gene regulatory networks of a jawed vertebrate, Xenopus, and a jawless vertebrate, lamprey. We reveal an ancient evolutionary origin of shared regulatory factors in these gene regulatory networks that dates to the last common ancestor of extant vertebrates. Focusing on the key pluripotency factor pou5, we show that a lamprey pou5 orthologue is expressed in animal pole cells but is absent from neural crest. Both lamprey and Xenopus pou5 promote neural crest formation, suggesting that pou5 activity was lost from the neural crest of jawless vertebrates or acquired along the jawed vertebrate stem. Finally, we provide evidence that pou5 acquired novel, neural crest-enhancing activity after evolving from an ancestral pou3-like clade. This work provides evidence that both the neural crest and blastula pluripotency networks arose at the base of the vertebrates and that this may be linked to functional evolution of pou5.
Collapse
Affiliation(s)
- Joshua R York
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Anjali Rao
- Research Department, Gilead Sciences, Foster City, CA, USA
| | - Paul B Huber
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Elizabeth N Schock
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Andrew Montequin
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Sara Rigney
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Carole LaBonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- National Institute for Theory and Mathematics in Biology, Chicago, IL, USA.
| |
Collapse
|
2
|
Linneberg-Agerholm M, Sell AC, Redó-Riveiro A, Perera M, Proks M, Knudsen TE, Barral A, Manzanares M, Brickman JM. The primitive endoderm supports lineage plasticity to enable regulative development. Cell 2024; 187:4010-4029.e16. [PMID: 38917790 PMCID: PMC11290322 DOI: 10.1016/j.cell.2024.05.051] [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: 05/19/2023] [Revised: 02/27/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024]
Abstract
Mammalian blastocyst formation involves the specification of the trophectoderm followed by the differentiation of the inner cell mass into embryonic epiblast and extra-embryonic primitive endoderm (PrE). During this time, the embryo maintains a window of plasticity and can redirect its cellular fate when challenged experimentally. In this context, we found that the PrE alone was sufficient to regenerate a complete blastocyst and continue post-implantation development. We identify an in vitro population similar to the early PrE in vivo that exhibits the same embryonic and extra-embryonic potency and can form complete stem cell-based embryo models, termed blastoids. Commitment in the PrE is suppressed by JAK/STAT signaling, collaborating with OCT4 and the sustained expression of a subset of pluripotency-related transcription factors that safeguard an enhancer landscape permissive for multi-lineage differentiation. Our observations support the notion that transcription factor persistence underlies plasticity in regulative development and highlight the importance of the PrE in perturbed development.
Collapse
Affiliation(s)
- Madeleine Linneberg-Agerholm
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Annika Charlotte Sell
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Alba Redó-Riveiro
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Marta Perera
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Martin Proks
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Teresa E Knudsen
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Antonio Barral
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, 28049 Madrid, Spain
| | - Miguel Manzanares
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, 28049 Madrid, Spain
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark.
| |
Collapse
|
3
|
Moratilla A, Martín D, Cadenas-Martín M, Stokking M, Quesada MA, Arnalich F, De Miguel MP. Hypoxia Increases the Efficiencies of Cellular Reprogramming and Oncogenic Transformation in Human Blood Cell Subpopulations In Vitro and In Vivo. Cells 2024; 13:971. [PMID: 38891103 PMCID: PMC11172288 DOI: 10.3390/cells13110971] [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: 05/07/2024] [Revised: 05/31/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Patients with chronic hypoxia show a higher tumor incidence; however, no primary common cause has been recognized. Given the similarities between cellular reprogramming and oncogenic transformation, we directly compared these processes in human cells subjected to hypoxia. Mouse embryonic fibroblasts were employed as controls to compare transfection and reprogramming efficiency; human adipose-derived mesenchymal stem cells were employed as controls in human cells. Easily obtainable human peripheral blood mononuclear cells (PBMCs) were chosen to establish a standard protocol to compare cell reprogramming (into induced pluripotent stem cells (iPSCs)) and oncogenic focus formation efficiency. Cell reprogramming was achieved for all three cell types, generating actual pluripotent cells capable for differentiating into the three germ layers. The efficiencies of the cell reprogramming and oncogenic transformation were similar. Hypoxia slightly increased the reprogramming efficiency in all the cell types but with no statistical significance for PBMCs. Various PBMC types can respond to hypoxia differently; lymphocytes and monocytes were, therefore, reprogrammed separately, finding a significant difference between normoxia and hypoxia in monocytes in vitro. These differences were then searched for in vivo. The iPSCs and oncogenic foci were generated from healthy volunteers and patients with chronic obstructive pulmonary disease (COPD). Although higher iPSC generation efficiency in the patients with COPD was found for lymphocytes, this increase was not statistically significant for oncogenic foci. Remarkably, a higher statistically significant efficiency in COPD monocytes was demonstrated for both processes, suggesting that physiological hypoxia exerts an effect on cell reprogramming and oncogenic transformation in vivo in at least some cell types.
Collapse
Affiliation(s)
- Adrián Moratilla
- Cell Engineering Laboratory, La Paz University Hospital Health Research Institute, IdiPAZ, 28046 Madrid, Spain; (A.M.); (D.M.); (M.C.-M.); (M.S.)
| | - Diana Martín
- Cell Engineering Laboratory, La Paz University Hospital Health Research Institute, IdiPAZ, 28046 Madrid, Spain; (A.M.); (D.M.); (M.C.-M.); (M.S.)
| | - Marta Cadenas-Martín
- Cell Engineering Laboratory, La Paz University Hospital Health Research Institute, IdiPAZ, 28046 Madrid, Spain; (A.M.); (D.M.); (M.C.-M.); (M.S.)
| | - Martha Stokking
- Cell Engineering Laboratory, La Paz University Hospital Health Research Institute, IdiPAZ, 28046 Madrid, Spain; (A.M.); (D.M.); (M.C.-M.); (M.S.)
| | - Maria Angustias Quesada
- Internal Medicine Service, La Paz University Hospital, IdiPAZ, 28046 Madrid, Spain; (M.A.Q.); (F.A.)
| | - Francisco Arnalich
- Internal Medicine Service, La Paz University Hospital, IdiPAZ, 28046 Madrid, Spain; (M.A.Q.); (F.A.)
| | - Maria P. De Miguel
- Cell Engineering Laboratory, La Paz University Hospital Health Research Institute, IdiPAZ, 28046 Madrid, Spain; (A.M.); (D.M.); (M.C.-M.); (M.S.)
| |
Collapse
|
4
|
Magro-Lopez E, Vazquez-Alejo E, Espinar-Buitrago MDLS, Muñoz-Fernández MÁ. Optimizing Nodal, Wnt and BMP signaling pathways for robust and efficient differentiation of human induced pluripotent stem cells to intermediate mesoderm cells. Front Cell Dev Biol 2024; 12:1395723. [PMID: 38887514 PMCID: PMC11182123 DOI: 10.3389/fcell.2024.1395723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/06/2024] [Indexed: 06/20/2024] Open
Abstract
Several differentiation protocols have enabled the generation of intermediate mesoderm (IM)-derived cells from human pluripotent stem cells (hPSC). However, the substantial variability between existing protocols for generating IM cells compromises their efficiency, reproducibility, and overall success, potentially hindering the utility of urogenital system organoids. Here, we examined the role of high levels of Nodal signaling and BMP activity, as well as WNT signaling in the specification of IM cells derived from a UCSD167i-99-1 human induced pluripotent stem cells (hiPSC) line. We demonstrate that precise modulation of WNT and BMP signaling significantly enhances IM differentiation efficiency. Treatment of hPSC with 3 μM CHIR99021 induced TBXT+/MIXL1+ mesoderm progenitor (MP) cells after 48 h of differentiation. Further treatment with a combination of 3 μM CHIR99021 and 4 ng/mL BMP4 resulted in the generation of OSR1+/GATA3+/PAX2+ IM cells within a subsequent 48 h period. Molecular characterization of differentiated cells was confirmed through immunofluorescence staining and RT-qPCR. Hence, this study establishes a consistent and reproducible protocol for differentiating hiPSC into IM cells that faithfully recapitulates the molecular signatures of IM development. This protocol holds promise for improving the success of protocols designed to generate urogenital system organoids in vitro, with potential applications in regenerative medicine, drug discovery, and disease modeling.
Collapse
Affiliation(s)
- Esmeralda Magro-Lopez
- Molecular Immuno-Biology Laboratory, Immunology Section, Hospital General Universitario Gregorio Marañón (HGUGM), Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Elena Vazquez-Alejo
- Molecular Immuno-Biology Laboratory, Immunology Section, Hospital General Universitario Gregorio Marañón (HGUGM), Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María de la Sierra Espinar-Buitrago
- Molecular Immuno-Biology Laboratory, Immunology Section, Hospital General Universitario Gregorio Marañón (HGUGM), Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Ángeles Muñoz-Fernández
- Molecular Immuno-Biology Laboratory, Immunology Section, Hospital General Universitario Gregorio Marañón (HGUGM), Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| |
Collapse
|
5
|
Shen Z, Wu Y, Manna A, Yi C, Cairns BR, Evason KJ, Chandrasekharan MB, Tantin D. Oct4 redox sensitivity potentiates reprogramming and differentiation. Genes Dev 2024; 38:308-321. [PMID: 38719541 PMCID: PMC11146590 DOI: 10.1101/gad.351411.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/17/2024] [Indexed: 05/21/2024]
Abstract
The transcription factor Oct4/Pou5f1 is a component of the regulatory circuitry governing pluripotency and is widely used to induce pluripotency from somatic cells. Here we used domain swapping and mutagenesis to study Oct4's reprogramming ability, identifying a redox-sensitive DNA binding domain, cysteine residue (Cys48), as a key determinant of reprogramming and differentiation. Oct4 Cys48 sensitizes the protein to oxidative inhibition of DNA binding activity and promotes oxidation-mediated protein ubiquitylation. Pou5f1 C48S point mutation has little effect on undifferentiated embryonic stem cells (ESCs) but upon retinoic acid (RA) treatment causes retention of Oct4 expression, deregulated gene expression, and aberrant differentiation. Pou5f1 C48S ESCs also form less differentiated teratomas and contribute poorly to adult somatic tissues. Finally, we describe Pou5f1 C48S (Janky) mice, which in the homozygous condition are severely developmentally restricted after E4.5. Rare animals bypassing this restriction appear normal at birth but are sterile. Collectively, these findings uncover a novel Oct4 redox mechanism involved in both entry into and exit from pluripotency.
Collapse
Affiliation(s)
- Zuolian Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Yifan Wu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Asit Manna
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Chongil Yi
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Bradley R Cairns
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Kimberley J Evason
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Mahesh B Chandrasekharan
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA;
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| |
Collapse
|
6
|
Ye Y, Xie W, Ma Z, Wang X, Wen Y, Li X, Qi H, Wu H, An J, Jiang Y, Lu X, Chen G, Hu S, Blaber EA, Chen X, Chang L, Zhang W. Conserved mechanisms of self-renewal and pluripotency in mouse and human ESCs regulated by simulated microgravity using a 3D clinostat. Cell Death Discov 2024; 10:68. [PMID: 38336777 PMCID: PMC10858198 DOI: 10.1038/s41420-024-01846-2] [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: 11/21/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Embryonic stem cells (ESCs) exhibit unique attributes of boundless self-renewal and pluripotency, making them invaluable for fundamental investigations and clinical endeavors. Previous examinations of microgravity effects on ESC self-renewal and differentiation have predominantly maintained a descriptive nature, constrained by limited experimental opportunities and techniques. In this investigation, we present compelling evidence derived from murine and human ESCs, demonstrating that simulated microgravity (SMG)-induced stress significantly impacts self-renewal and pluripotency through a previously unidentified conserved mechanism. Specifically, SMG induces the upregulation of heat shock protein genes, subsequently enhancing the expression of core pluripotency factors and activating the Wnt and/or LIF/STAT3 signaling pathways, thereby fostering ESC self-renewal. Notably, heightened Wnt pathway activity, facilitated by Tbx3 upregulation, prompts mesoendodermal differentiation in both murine and human ESCs under SMG conditions. Recognizing potential disparities between terrestrial SMG simulations and authentic microgravity, forthcoming space flight experiments are imperative to validate the impact of reduced gravity on ESC self-renewal and differentiation mechanisms.
Collapse
Affiliation(s)
- Ying Ye
- Medical College of Soochow University, Suzhou, China
| | - Wenyan Xie
- Medical College of Soochow University, Suzhou, China
| | - Zhaoru Ma
- Medical College of Soochow University, Suzhou, China
| | - Xuepeng Wang
- Medical College of Soochow University, Suzhou, China
| | - Yi Wen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xuemei Li
- School of Basic Medical Sciences, Binzhou Medical University, Yantai, China
| | - Hongqian Qi
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin, 300350, China
| | - Hao Wu
- Medical College of Soochow University, Suzhou, China
| | - Jinnan An
- Institute of Blood and Marrow Transplantation, Medical College of Soochow University, Suzhou, China
| | - Yan Jiang
- School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou, China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin, 300350, China
| | - Guokai Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, 215000, China.
| | - Elizabeth A Blaber
- Department of Biomedical Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| | - Lei Chang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Jiangsu Province International Joint Laboratory For Regeneration Medicine, Medical College of Soochow University, Suzhou, China.
| | | |
Collapse
|
7
|
Bruno S, Schlaeger TM, Del Vecchio D. Epigenetic OCT4 regulatory network: stochastic analysis of cellular reprogramming. NPJ Syst Biol Appl 2024; 10:3. [PMID: 38184707 PMCID: PMC10771499 DOI: 10.1038/s41540-023-00326-0] [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: 07/12/2023] [Accepted: 12/08/2023] [Indexed: 01/08/2024] Open
Abstract
Experimental studies have shown that chromatin modifiers have a critical effect on cellular reprogramming, i.e., the conversion of differentiated cells to pluripotent stem cells. Here, we develop a model of the OCT4 gene regulatory network that includes genes expressing chromatin modifiers TET1 and JMJD2, and the chromatin modification circuit on which these modifiers act. We employ this model to compare three reprogramming approaches that have been considered in the literature with respect to reprogramming efficiency and latency variability. These approaches are overexpression of OCT4 alone, overexpression of OCT4 with TET1, and overexpression of OCT4 with JMJD2. Our results show more efficient and less variable reprogramming when also JMJD2 and TET1 are overexpressed, consistent with previous experimental data. Nevertheless, TET1 overexpression can lead to more efficient reprogramming compared to JMJD2 overexpression. This is the case when the recruitment of DNA methylation by H3K9me3 is weak and the methyl-CpG-binding domain (MBD) proteins are sufficiently scarce such that they do not hamper TET1 binding to methylated DNA. The model that we developed provides a mechanistic understanding of existing experimental results and is also a tool for designing optimized reprogramming approaches that combine overexpression of cell-fate specific transcription factors (TFs) with targeted recruitment of epigenetic modifiers.
Collapse
Affiliation(s)
- Simone Bruno
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Thorsten M Schlaeger
- Boston Children's Hospital Stem Cell Program, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| |
Collapse
|
8
|
York JR, Rao A, Huber PB, Schock EN, Montequin A, Rigney S, LaBonne C. Shared features of blastula and neural crest stem cells evolved at the base of vertebrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572714. [PMID: 38187687 PMCID: PMC10769357 DOI: 10.1101/2023.12.21.572714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The neural crest is vertebrate-specific stem cell population that helped drive the origin and evolution of the vertebrate clade. A distinguishing feature of these stem cells is their multi-germ layer potential, which has drawn developmental and evolutionary parallels to another stem cell population-pluripotent embryonic stem cells (animal pole cells or ES cells) of the vertebrate blastula. Here, we investigate the evolutionary origins of neural crest potential by comparing neural crest and pluripotency gene regulatory networks (GRNs) in both jawed ( Xenopus ) and jawless (lamprey) vertebrates. Through comparative gene expression analysis and transcriptomics, we reveal an ancient evolutionary origin of shared regulatory factors between neural crest and pluripotency GRNs that dates back to the last common ancestor of extant vertebrates. Focusing on the key pluripotency factor pou5 (formerly oct4), we show that the lamprey genome encodes a pou5 ortholog that is expressed in animal pole cells, as in jawed vertebrates, but is absent from the neural crest. However, gain-of-function experiments show that both lamprey and Xenopus pou5 enhance neural crest formation, suggesting that pou5 was lost from the neural crest of jawless vertebrates. Finally, we show that pou5 is required for neural crest specification in jawed vertebrates and that it acquired novel neural crest-enhancing activity after evolving from an ancestral pou3 -like clade that lacks this functionality. We propose that a pluripotency-neural crest GRN was assembled in stem vertebrates and that the multi-germ layer potential of the neural crest evolved by deploying this regulatory program.
Collapse
|
9
|
Ilia K, Shakiba N, Bingham T, Jones RD, Kaminski MM, Aravera E, Bruno S, Palacios S, Weiss R, Collins JJ, Del Vecchio D, Schlaeger TM. Synthetic genetic circuits to uncover the OCT4 trajectories of successful reprogramming of human fibroblasts. SCIENCE ADVANCES 2023; 9:eadg8495. [PMID: 38019912 PMCID: PMC10686568 DOI: 10.1126/sciadv.adg8495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Reprogramming human fibroblasts to induced pluripotent stem cells (iPSCs) is inefficient, with heterogeneity among transcription factor (TF) trajectories driving divergent cell states. Nevertheless, the impact of TF dynamics on reprogramming efficiency remains uncharted. We develop a system that accurately reports OCT4 protein levels in live cells and use it to reveal the trajectories of OCT4 in successful reprogramming. Our system comprises a synthetic genetic circuit that leverages noise to generate a wide range of OCT4 trajectories and a microRNA targeting endogenous OCT4 to set total cellular OCT4 protein levels. By fusing OCT4 to a fluorescent protein, we are able to track OCT4 trajectories with clonal resolution via live-cell imaging. We discover that a supraphysiological, stable OCT4 level is required, but not sufficient, for efficient iPSC colony formation. Our synthetic genetic circuit design and high-throughput live-imaging pipeline are generalizable for investigating TF dynamics for other cell fate programming applications.
Collapse
Affiliation(s)
- Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3 Canada
| | - Trevor Bingham
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard University, Boston, MA 02115, USA
| | - Ross D. Jones
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3 Canada
| | - Michael M. Kaminski
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz-Association, Berlin 10115, Germany
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Medizinische Klinik m.S. Nephrologie und Intensivmedizin, Berlin 10117, Germany
- Berlin Institute of Health, Berlin 13125, Germany
| | - Eliezer Aravera
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Simone Bruno
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
| | | |
Collapse
|
10
|
Bora J, Dey A, Lyngdoh AR, Dhasmana A, Ranjan A, Kishore S, Rustagi S, Tuli HS, Chauhan A, Rath P, Malik S. A critical review on therapeutic approaches of CRISPR-Cas9 in diabetes mellitus. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2023; 396:3459-3481. [PMID: 37522916 DOI: 10.1007/s00210-023-02631-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023]
Abstract
Diabetes mellitus (D.M.) is a common metabolic disorder caused mainly by combining two primary factors, which are (1) defects in insulin production by the pancreatic β-cells and (2) responsiveness of insulin-sensitive tissues towards insulin. Despite the rapid advancement in medicine to suppress elevated blood glucose levels (hyperglycemia) and insulin resistance associated with this hazard, a demand has undoubtedly emerged to find more effective and curative dimensions in therapeutic approaches against D.M. The administration of diabetes treatment that emphasizes insulin production and sensitivity may result in unfavorable side effects, reduced adherence, and potential treatment ineffectiveness. Recent progressions in genome editing technologies, for instance, in zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeat (CRISPR-Cas)-associated nucleases, have greatly influenced the gene editing technology from concepts to clinical practices. Improvements in genome editing technologies have also opened up the possibility to target and modify specific genome sequences in a cell directly. CRISPR/Cas9 has proven effective in utilizing ex vivo gene editing in embryonic stem cells and stem cells derived from patients. This application has facilitated the exploration of pancreatic beta-cell development and function. Furthermore, CRISPR/Cas9 enables the creation of innovative animal models for diabetes and assesses the effectiveness of different therapeutic strategies in treating the condition. We, therefore, present a critical review of the therapeutic approaches of the genome editing tool CRISPR-Cas9 in treating D.M., discussing the challenges and limitations of implementing this technology.
Collapse
Affiliation(s)
- Jutishna Bora
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, 834001, India
| | - Ankita Dey
- Department of Biochemistry, North Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Antonia R Lyngdoh
- Department of Biochemistry, North Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Archna Dhasmana
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, Rostov-On-Don, 344090, Russia
| | - Shristi Kishore
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, 834001, India
| | - Sarvesh Rustagi
- School of Applied and Life Sciences, Uttaranchal University, 22 Dehradun, Uttarakhand, India
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to Be University), Mullana-Ambala, 133207, India
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Sector 125, Noida, Uttar Pradesh, India
| | - Prangya Rath
- Amity Institute of Environmental Sciences, Amity University, Noida, Uttar Pradesh, 201303, India
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, 834001, India.
- School of Applied and Life Sciences, Uttaranchal University, 22 Dehradun, Uttarakhand, India.
- Guru Nanak College of Pharmaceutical Sciences, Dehradun, Uttarakhand, India.
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Zhou Q, Shu X, Chai Y, Liu W, Li Z, Xi Y. The non-coding competing endogenous RNAs in acute myeloid leukemia: biological and clinical implications. Biomed Pharmacother 2023; 163:114807. [PMID: 37150037 DOI: 10.1016/j.biopha.2023.114807] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematologic carcinoma that has seen a considerable improvement in patient prognosis because of genetic diagnostics and molecularly-targeted therapies. Nevertheless, recurrence and drug resistance remain significant obstacles to leukemia treatment. It is critical to investigate the underlying molecular mechanisms and find solutions. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), circular RNAs, long non-coding RNAs, and pseudogenes, have been found to be crucial components in driving cancer. The competing endogenous RNA (ceRNA) mechanism has expanded the complexity of miRNA-mediated gene regulation. A great deal of literature has shown that ncRNAs are essential to the biological functions of the ceRNA network (ceRNET). NcRNAs can compete for the same miRNA response elements to influence miRNA-target RNA interactions. Recent evidence suggests that ceRNA might be a potential biomarker and therapeutic strategy. So far, however, there have been no comprehensive studies on ceRNET about AML. What is not yet clear is the clinical application of ceRNA in AML. This study attempts to summarize the development of research on the related ceRNAs in AML and the roles of ncRNAs in ceRNET. We also briefly describe the mechanisms of ceRNA and ceRNET. What's more significant is that we explore the clinical value of ceRNAs to provide accurate diagnostic and prognostic biomarkers as well as therapeutic targets. Finally, limitations and prospects are considered.
Collapse
Affiliation(s)
- Qi Zhou
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Xiaojun Shu
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China; Department of Vascular Surgery, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yihong Chai
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Wenling Liu
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Zijian Li
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China; Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yaming Xi
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China; Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.
| |
Collapse
|
13
|
Bruno S, Vecchio DD. The epigenetic Oct4 gene regulatory network: stochastic analysis of different cellular reprogramming approaches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530689. [PMID: 36909486 PMCID: PMC10002722 DOI: 10.1101/2023.03.01.530689] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
In the last decade, several experimental studies have shown how chromatin modifications (histone modifications and DNA methylation) and their effect on DNA compaction have a critical effect on cellular reprogramming, i.e., the conversion of differentiated cells to a pluripotent state. In this paper, we compare three reprogramming approaches that have been considered in the literature: (a) prefixed overexpression of transcription factors (TFs) alone (Oct4), (b) prefixed overexpression of Oct4 and DNA methylation "eraser" TET, and (c) prefixed overexpression of Oct4 and H3K9me3 eraser JMJD2. To this end, we develop a model of the pluritpotency gene regulatory network, that includes, for each gene, a circuit recently published encapsulating the main interactions among chromatin modifications and their effect on gene expression. We then conduct a computational study to evaluate, for each reprogramming approach, latency and variability. Our results show a faster and less stochastic reprogramming process when also eraser enzymes are overexpressed, consistent with previous experimental data. However, TET overexpression leads to a faster and more efficient reprogramming compared to JMJD2 overexpression when the recruitment of DNA methylation by H3K9me3 is weak and the MBD protein level is sufficiently low such that it does not hamper TET binding to methylated DNA. The model developed here provides a mechanistic understanding of the outcomes of former experimental studies and is also a tool for the development of optimized reprogramming approaches that combine TF overexpression with modifiers of chromatin state.
Collapse
Affiliation(s)
- Simone Bruno
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| |
Collapse
|
14
|
Madrigal P, Deng S, Feng Y, Militi S, Goh KJ, Nibhani R, Grandy R, Osnato A, Ortmann D, Brown S, Pauklin S. Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation. Nat Commun 2023; 14:405. [PMID: 36697417 PMCID: PMC9876972 DOI: 10.1038/s41467-023-36116-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Stem cells undergo cellular division during their differentiation to produce daughter cells with a new cellular identity. However, the epigenetic events and molecular mechanisms occurring between consecutive cell divisions have been insufficiently studied due to technical limitations. Here, using the FUCCI reporter we developed a cell-cycle synchronised human pluripotent stem cell (hPSC) differentiation system for uncovering epigenome and transcriptome dynamics during the first two divisions leading to definitive endoderm. We observed that transcription of key differentiation markers occurs before cell division, while chromatin accessibility analyses revealed the early inhibition of alternative cell fates. We found that Activator protein-1 members controlled by p38/MAPK signalling are necessary for inducing endoderm while blocking cell fate shifting toward mesoderm, and that enhancers are rapidly established and decommissioned between different cell divisions. Our study has practical biomedical utility for producing hPSC-derived patient-specific cell types since p38/MAPK induction increased the differentiation efficiency of insulin-producing pancreatic beta-cells.
Collapse
Affiliation(s)
- Pedro Madrigal
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Siwei Deng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Stefania Militi
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Kim Jee Goh
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Rodrigo Grandy
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Anna Osnato
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Daniel Ortmann
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stephanie Brown
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK.
| |
Collapse
|
15
|
Ilia K, Shakiba N, Bingham T, Jones RD, Kaminski MM, Aravera E, Bruno S, Palacios S, Weiss R, Collins JJ, Del Vecchio D, Schlaeger TM. Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525529. [PMID: 36747813 PMCID: PMC9900859 DOI: 10.1101/2023.01.25.525529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Reprogramming human fibroblasts to induced pluripotent stem cells (iPSCs) is inefficient, with heterogeneity among transcription factor (TF) trajectories driving divergent cell states. Nevertheless, the impact of TF dynamics on reprogramming efficiency remains uncharted. Here, we identify the successful reprogramming trajectories of the core pluripotency TF, OCT4, and design a genetic controller that enforces such trajectories with high precision. By combining a genetic circuit that generates a wide range of OCT4 trajectories with live-cell imaging, we track OCT4 trajectories with clonal resolution and find that a distinct constant OCT4 trajectory is required for colony formation. We then develop a synthetic genetic circuit that yields a tight OCT4 distribution around the identified trajectory and outperforms in terms of reprogramming efficiency other circuits that less accurately regulate OCT4. Our synthetic biology approach is generalizable for identifying and enforcing TF dynamics for cell fate programming applications.
Collapse
Affiliation(s)
- Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Trevor Bingham
- Boston Children’s Hospital Stem Cell Program, Boston Children’s Hospital, Boston, MA, 02115, USA
- Harvard University, Boston, MA, 02115, USA
| | - Ross D. Jones
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Michael M. Kaminski
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
| | - Eliezer Aravera
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- College of Engineering and Applied Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Simone Bruno
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Thorsten M. Schlaeger
- Boston Children’s Hospital Stem Cell Program, Boston Children’s Hospital, Boston, MA, 02115, USA
| |
Collapse
|
16
|
Durand S, Bruelle M, Bourdelais F, Bennychen B, Blin-Gonthier J, Isaac C, Huyghe A, Martel S, Seyve A, Vanbelle C, Adrait A, Couté Y, Meyronet D, Catez F, Diaz JJ, Lavial F, Ricci EP, Ducray F, Gabut M. RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells. Nat Commun 2023; 14:356. [PMID: 36690642 PMCID: PMC9870888 DOI: 10.1038/s41467-023-36037-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
Embryonic stem cell (ESC) fate decisions are regulated by a complex circuitry that coordinates gene expression at multiple levels from chromatin to mRNA processing. Recently, ribosome biogenesis and translation have emerged as key pathways that efficiently control stem cell homeostasis, yet the underlying molecular mechanisms remain largely unknown. Here, we identified RSL24D1 as highly expressed in both mouse and human pluripotent stem cells. RSL24D1 is associated with nuclear pre-ribosomes and is required for the biogenesis of 60S subunits in mouse ESCs. Interestingly, RSL24D1 depletion significantly impairs global translation, particularly of key pluripotency factors and of components from the Polycomb Repressive Complex 2 (PRC2). While having a moderate impact on differentiation, RSL24D1 depletion significantly alters ESC self-renewal and lineage commitment choices. Altogether, these results demonstrate that RSL24D1-dependant ribosome biogenesis is both required to sustain the expression of pluripotent transcriptional programs and to silence PRC2-regulated developmental programs, which concertedly dictate ESC homeostasis.
Collapse
Affiliation(s)
- Sébastien Durand
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Marion Bruelle
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
| | - Fleur Bourdelais
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Inovarion, 75005, Paris, France
| | - Bigitha Bennychen
- Dept. of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada
| | - Juliana Blin-Gonthier
- Laboratoire de Biologie et de Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, Inserm U1293, Lyon, France
| | - Caroline Isaac
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Aurélia Huyghe
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Equipe labellisée la Ligue contre le cancer, Lyon, France
| | - Sylvie Martel
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
| | - Antoine Seyve
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Neuro-oncology department, Hospices Civils de Lyon, Lyon, France
| | - Christophe Vanbelle
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
| | - Annie Adrait
- University Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - David Meyronet
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Institut de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Catez
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Jean-Jacques Diaz
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Fabrice Lavial
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Equipe labellisée la Ligue contre le cancer, Lyon, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et de Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, Inserm U1293, Lyon, France
| | - François Ducray
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Neuro-oncology department, Hospices Civils de Lyon, Lyon, France
| | - Mathieu Gabut
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France.
- Institut Convergence Plascan, Lyon, France.
| |
Collapse
|
17
|
Furlan G, Huyghe A, Combémorel N, Lavial F. Molecular versatility during pluripotency progression. Nat Commun 2023; 14:68. [PMID: 36604434 PMCID: PMC9814743 DOI: 10.1038/s41467-022-35775-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
A challenge during development is to ensure lineage segregation while preserving plasticity. Using pluripotency progression as a paradigm, we review how developmental transitions are coordinated by redeployments, rather than global resettings, of cellular components. We highlight how changes in response to extrinsic cues (FGF, WNT, Activin/Nodal, Netrin-1), context- and stoichiometry-dependent action of transcription factors (Oct4, Nanog) and reconfigurations of epigenetic regulators (enhancers, promoters, TrxG, PRC) may confer robustness to naïve to primed pluripotency transition. We propose the notion of Molecular Versatility to regroup mechanisms by which molecules are repurposed to exert different, sometimes opposite, functions in close stem cell configurations.
Collapse
Affiliation(s)
- Giacomo Furlan
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
- Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, ON, Canada
| | - Aurélia Huyghe
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Noémie Combémorel
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Fabrice Lavial
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.
| |
Collapse
|
18
|
Mannully CT, Bruck-Haimson R, Zacharia A, Orih P, Shehadeh A, Saidemberg D, Kogan NM, Alfandary S, Serruya R, Dagan A, Petit I, Moussaieff A. Lipid desaturation regulates the balance between self-renewal and differentiation in mouse blastocyst-derived stem cells. Cell Death Dis 2022; 13:1027. [PMID: 36477438 PMCID: PMC9729213 DOI: 10.1038/s41419-022-05263-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 08/31/2022] [Accepted: 09/13/2022] [Indexed: 12/13/2022]
Abstract
Stem cells are defined by their ability to self-renew and differentiate, both shown in multiple studies to be regulated by metabolic processes. To decipher metabolic signatures of self-renewal in blastocyst-derived stem cells, we compared early differentiating embryonic stem cells (ESCs) and their extra-embryonic counterparts, trophoblast (T)SCs to their self-renewing counterparts. A metabolomics analysis pointed to the desaturation of fatty acyl chains as a metabolic signature of differentiating blastocyst-derived SCs via the upregulation of delta-6 desaturase (D6D; FADS2) and delta-5 desaturase (D5D; FADS1), key enzymes in the biosynthesis of polyunsaturated fatty acids (PUFAs). The inhibition of D6D or D5D by specific inhibitors or SiRNA retained stemness in ESCs and TSCs, and attenuated endoplasmic reticulum (ER) stress-related apoptosis. D6D inhibition in ESCs upregulated stearoyl-CoA desaturase-1 (Scd1), essential to maintain ER homeostasis. In TSCs, however, D6D inhibition downregulated Scd1. TSCs show higher Scd1 mRNA expression and high levels of monounsaturated fatty acyl chain products in comparison to ESCs. The addition of oleic acid, the product of Scd1 (essential for ESCs), to culture medium, was detrimental to TSCs. Interestingly, TSCs express a high molecular mass variant of Scd1 protein, hardly expressed by ESCs. Taken together, our data suggest that lipid desaturation is a metabolic regulator of the balance between differentiation and self-renewal of ESCs and TSCs. They point to lipid polydesaturation as a driver of differentiation in both cell types. Monounsaturated fatty acids (MUFAs), essential for ESCs are detrimental to TSCs.
Collapse
Affiliation(s)
- Chanchal Thomas Mannully
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Reut Bruck-Haimson
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anish Zacharia
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Paul Orih
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alaa Shehadeh
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Saidemberg
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Natalya M. Kogan
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sivan Alfandary
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Raphael Serruya
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Arie Dagan
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabelle Petit
- grid.465261.20000 0004 1793 5929Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Arieh Moussaieff
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
19
|
Barajas C, Del Vecchio D. Synthetic biology by controller design. Curr Opin Biotechnol 2022; 78:102837. [PMID: 36343564 DOI: 10.1016/j.copbio.2022.102837] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/26/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Natural biological systems display complex regulation and synthetic biomolecular systems have been used to understand their natural counterparts and to parse sophisticated regulations into core design principles. At the same time, the engineering of biomolecular systems has unarguable potential to transform current and to enable new, yet-to-be-imagined, biotechnology applications. In this review, we discuss the progression of control systems design in synthetic biology, from the purpose of understanding the function of naturally occurring regulatory motifs to that of creating genetic circuits whose function is sufficiently robust for biotechnology applications.
Collapse
Affiliation(s)
- Carlos Barajas
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
20
|
Sukparangsi W, Morganti E, Lowndes M, Mayeur H, Weisser M, Hammachi F, Peradziryi H, Roske F, Hölzenspies J, Livigni A, Godard BG, Sugahara F, Kuratani S, Montoya G, Frankenberg SR, Mazan S, Brickman JM. Evolutionary origin of vertebrate OCT4/POU5 functions in supporting pluripotency. Nat Commun 2022; 13:5537. [PMID: 36130934 PMCID: PMC9492771 DOI: 10.1038/s41467-022-32481-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 07/30/2022] [Indexed: 12/31/2022] Open
Abstract
The support of pluripotent cells over time is an essential feature of development. In eutherian embryos, pluripotency is maintained from naïve states in peri-implantation to primed pluripotency at gastrulation. To understand how these states emerged, we reconstruct the evolutionary trajectory of the Pou5 gene family, which contains the central pluripotency factor OCT4. By coupling evolutionary sequence analysis with functional studies in mouse embryonic stem cells, we find that the ability of POU5 proteins to support pluripotency originated in the gnathostome lineage, prior to the generation of two paralogues, Pou5f1 and Pou5f3 via gene duplication. In osteichthyans, retaining both genes, the paralogues differ in their support of naïve and primed pluripotency. The specialization of these duplicates enables the diversification of function in self-renewal and differentiation. By integrating sequence evolution, cell phenotypes, developmental contexts and structural modelling, we pinpoint OCT4 regions sufficient for naïve pluripotency and describe their adaptation over evolutionary time.
Collapse
Affiliation(s)
- Woranop Sukparangsi
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark.,Department of Biology, Faculty of Science, Burapha University, Chon Buri, Thailand
| | - Elena Morganti
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Molly Lowndes
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Hélène Mayeur
- CNRS, Sorbonne Université, Biologie Intégrative des Organismes Marins, UMR7232, F-66650, Banyuls sur Mer, France
| | - Melanie Weisser
- Structural Molecular Biology Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Fella Hammachi
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, 5 Little France Drive, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Hanna Peradziryi
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Fabian Roske
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Jurriaan Hölzenspies
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Alessandra Livigni
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, 5 Little France Drive, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Benoit Gilbert Godard
- CNRS, Sorbonne Université, UPMC Univ Paris 06, FR2424, Development and Evolution of Vertebrates Group, Station Biologique, F-29688, Roscoff, France.,CNRS, Sorbonne Université, Laboratoire de Biologie du Développement de Villefranche, UMR7009, F-06234, Villefranche sur Mer, France
| | - Fumiaki Sugahara
- Division of Biology, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | | | - Sylvie Mazan
- CNRS, Sorbonne Université, Biologie Intégrative des Organismes Marins, UMR7232, F-66650, Banyuls sur Mer, France.
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark.
| |
Collapse
|
21
|
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
Collapse
|
22
|
Tiana M, Lopez-Jimenez E, de Aja JS, Barral A, Victorino J, Badia-Careaga C, Rollan I, Rouco R, Santos E, Sanchez-Iranzo H, Acemel RD, Torroja C, Adan J, Andres-Leon E, Gomez-Skarmeta JL, Giovinazzo G, Sanchez-Cabo F, Manzanares M. Pluripotency factors regulate the onset of Hox cluster activation in the early embryo. SCIENCE ADVANCES 2022; 8:eabo3583. [PMID: 35857513 PMCID: PMC9286507 DOI: 10.1126/sciadv.abo3583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Pluripotent cells are a transient population of the mammalian embryo dependent on transcription factors, such as OCT4 and NANOG, which maintain pluripotency while suppressing lineage specification. However, these factors are also expressed during early phases of differentiation, and their role in the transition from pluripotency to lineage specification is largely unknown. We found that pluripotency factors play a dual role in regulating key lineage specifiers, initially repressing their expression and later being required for their proper activation. We show that Oct4 is necessary for activation of HoxB genes during differentiation of embryonic stem cells and in the embryo. In addition, we show that the HoxB cluster is coordinately regulated by OCT4 binding sites located at the 3' end of the cluster. Our results show that core pluripotency factors are not limited to maintaining the precommitted epiblast but are also necessary for the proper deployment of subsequent developmental programs.
Collapse
Affiliation(s)
- María Tiana
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, 28029 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Elena Lopez-Jimenez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Julio Sainz de Aja
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Antonio Barral
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, 28029 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Jesus Victorino
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Claudio Badia-Careaga
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Isabel Rollan
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Raquel Rouco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Elisa Santos
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Hector Sanchez-Iranzo
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Rafael D. Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO, 41013 Seville, Spain
| | - Carlos Torroja
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Javier Adan
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Eduardo Andres-Leon
- Instituto de Parasitología y Biomedicina López Neyra (IPBL), CSIC, 18100 Granada, Spain
| | | | - Giovanna Giovinazzo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Fatima Sanchez-Cabo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Miguel Manzanares
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, 28029 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
- Corresponding author.
| |
Collapse
|
23
|
Abstract
POUV is a relatively newly emerged class of POU transcription factors present in jawed vertebrates (Gnathostomata). The function of POUV-class proteins is inextricably linked to zygotic genome activation (ZGA). A large body of evidence now extends the role of these proteins to subsequent developmental stages. While some functions resemble those of other POU-class proteins and are related to neuroectoderm development, others have emerged de novo. The most notable of the latter functions is pluripotency control by Oct4 in mammals. In this review, we focus on these de novo functions in the best-studied species harbouring POUV proteins-zebrafish, Xenopus (anamniotes) and mammals (amniotes). Despite the broad diversity of their biological functions in vertebrates, POUV proteins exert a common feature related to their role in safeguarding the undifferentiated state of cells. Here we summarize numerous pieces of evidence for these specific functions of the POUV-class proteins and recap available loss-of-function data.
Collapse
Affiliation(s)
- Evgeny I. Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - Alexey N. Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| |
Collapse
|
24
|
Xiong L, Tolen EA, Choi J, Velychko S, Caizzi L, Velychko T, Adachi K, MacCarthy CM, Lidschreiber M, Cramer P, Schöler HR. Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells. eLife 2022; 11:71533. [PMID: 35621159 PMCID: PMC9142147 DOI: 10.7554/elife.71533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 05/17/2022] [Indexed: 12/21/2022] Open
Abstract
The transcription factor Oct4 is essential for the maintenance and induction of stem cell pluripotency, but its functional roles are not fully understood. Here, we investigate the functions of Oct4 by depleting and subsequently recovering it in mouse embryonic stem cells (ESCs) and conducting a time-resolved multiomics analysis. Oct4 depletion leads to an immediate loss of its binding to enhancers, accompanied by a decrease in mRNA synthesis from its target genes that are part of the transcriptional network that maintains pluripotency. Gradual decrease of Oct4 binding to enhancers does not immediately change the chromatin accessibility but reduces transcription of enhancers. Conversely, partial recovery of Oct4 expression results in a rapid increase in chromatin accessibility, whereas enhancer transcription does not fully recover. These results indicate different concentration-dependent activities of Oct4. Whereas normal ESC levels of Oct4 are required for transcription of pluripotency enhancers, low levels of Oct4 are sufficient to retain chromatin accessibility, likely together with other factors such as Sox2.
Collapse
Affiliation(s)
- Le Xiong
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Erik A Tolen
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Jinmi Choi
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Sergiy Velychko
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Livia Caizzi
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Taras Velychko
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Kenjiro Adachi
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Caitlin M MacCarthy
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Michael Lidschreiber
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| |
Collapse
|
25
|
OCT4-induced oligodendrocyte progenitor cells promote remyelination and ameliorate disease. NPJ Regen Med 2022; 7:4. [PMID: 35027563 PMCID: PMC8758684 DOI: 10.1038/s41536-021-00199-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 11/30/2021] [Indexed: 12/23/2022] Open
Abstract
The generation of human oligodendrocyte progenitor cells (OPCs) may be therapeutically valuable for human demyelinating diseases such as multiple sclerosis. Here, we report the direct reprogramming of human somatic cells into expandable induced OPCs (iOPCs) using a combination of OCT4 and a small molecule cocktail. This method enables generation of A2B5+ (an early marker for OPCs) iOPCs within 2 weeks retaining the ability to differentiate into MBP-positive mature oligodendrocytes. RNA-seq analysis revealed that the transcriptome of O4+ iOPCs was similar to that of O4+ OPCs and ChIP-seq analysis revealed that putative OCT4-binding regions were detected in the regulatory elements of CNS development-related genes. Notably, engrafted iOPCs remyelinated the brains of adult shiverer mice and experimental autoimmune encephalomyelitis mice with MOG-induced 14 weeks after transplantation. In conclusion, our study may contribute to the development of therapeutic approaches for neurological disorders, as well as facilitate the understanding of the molecular mechanisms underlying glial development.
Collapse
|
26
|
Gordeev MN, Bakhmet EI, Tomilin AN. Pluripotency Dynamics during Embryogenesis and in Cell Culture. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421060059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
27
|
Bakhmet EI, Tomilin AN. Key features of the POU transcription factor Oct4 from an evolutionary perspective. Cell Mol Life Sci 2021; 78:7339-7353. [PMID: 34698883 PMCID: PMC11072838 DOI: 10.1007/s00018-021-03975-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 01/06/2023]
Abstract
Oct4, a class V POU-domain protein that is encoded by the Pou5f1 gene, is thought to be a key transcription factor in the early development of mammals. This transcription factor plays indispensable roles in pluripotent stem cells as well as in the acquisition of pluripotency during somatic cell reprogramming. Oct4 has also been shown to play a role as a pioneer transcription factor during zygotic genome activation (ZGA) from zebrafish to human. However, during the past decade, several studies have brought these conclusions into question. It was clearly shown that the first steps in mouse development are not affected by the loss of Oct4. Subsequently, the role of Oct4 as a genome activator was brought into doubt. It was also found that the reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) could proceed without Oct4. In this review, we summarize recent findings, reassess the role of Oct4 in reprogramming and ZGA, and point to structural features that may underlie this role. We speculate that pluripotent stem cells resemble neural stem cells more closely than previously thought. Oct4 orthologs within the POUV class hold key roles in genome activation during early development of species with late ZGA. However, in Placentalia, eutherian-specific proteins such as Dux overtake Oct4 in ZGA and endow them with the formation of an evolutionary new tissue-the placenta.
Collapse
Affiliation(s)
- Evgeny I Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.
| | - Alexey N Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| |
Collapse
|
28
|
Kulus M, Sibiak R, Stefańska K, Zdun M, Wieczorkiewicz M, Piotrowska-Kempisty H, Jaśkowski JM, Bukowska D, Ratajczak K, Zabel M, Mozdziak P, Kempisty B. Mesenchymal Stem/Stromal Cells Derived from Human and Animal Perinatal Tissues-Origins, Characteristics, Signaling Pathways, and Clinical Trials. Cells 2021; 10:cells10123278. [PMID: 34943786 PMCID: PMC8699543 DOI: 10.3390/cells10123278] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/13/2021] [Accepted: 11/19/2021] [Indexed: 12/15/2022] Open
Abstract
Mesenchymal stem/stromal cells (MSCs) are currently one of the most extensively researched fields due to their promising opportunity for use in regenerative medicine. There are many sources of MSCs, of which cells of perinatal origin appear to be an invaluable pool. Compared to embryonic stem cells, they are devoid of ethical conflicts because they are derived from tissues surrounding the fetus and can be safely recovered from medical waste after delivery. Additionally, perinatal MSCs exhibit better self-renewal and differentiation properties than those derived from adult tissues. It is important to consider the anatomy of perinatal tissues and the general description of MSCs, including their isolation, differentiation, and characterization of different types of perinatal MSCs from both animals and humans (placenta, umbilical cord, amniotic fluid). Ultimately, signaling pathways are essential to consider regarding the clinical applications of MSCs. It is important to consider the origin of these cells, referring to the anatomical structure of the organs of origin, when describing the general and specific characteristics of the different types of MSCs as well as the pathways involved in differentiation.
Collapse
Affiliation(s)
- Magdalena Kulus
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.K.); (K.R.)
| | - Rafał Sibiak
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (R.S.); (K.S.)
- Division of Reproduction, Department of Obstetrics, Gynecology, and Gynecologic Oncology, Poznan University of Medical Sciences, 60-535 Poznan, Poland
| | - Katarzyna Stefańska
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (R.S.); (K.S.)
| | - Maciej Zdun
- Department of Basic and Preclinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.Z.); (M.W.); (H.P.-K.)
| | - Maria Wieczorkiewicz
- Department of Basic and Preclinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.Z.); (M.W.); (H.P.-K.)
| | - Hanna Piotrowska-Kempisty
- Department of Basic and Preclinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.Z.); (M.W.); (H.P.-K.)
- Department of Toxicology, Poznan University of Medical Sciences, 60-631 Poznan, Poland
| | - Jędrzej M. Jaśkowski
- Department of Diagnostics and Clinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (J.M.J.); (D.B.)
| | - Dorota Bukowska
- Department of Diagnostics and Clinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (J.M.J.); (D.B.)
| | - Kornel Ratajczak
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.K.); (K.R.)
| | - Maciej Zabel
- Division of Anatomy and Histology, University of Zielona Gora, 65-046 Zielona Gora, Poland;
| | - Paul Mozdziak
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA;
| | - Bartosz Kempisty
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland; (M.K.); (K.R.)
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (R.S.); (K.S.)
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA;
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland
- Correspondence:
| |
Collapse
|
29
|
Bend family proteins mark chromatin boundaries and synergistically promote early germ cell differentiation. Protein Cell 2021; 13:721-741. [PMID: 34731408 PMCID: PMC9233729 DOI: 10.1007/s13238-021-00884-1] [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: 07/13/2021] [Accepted: 09/19/2021] [Indexed: 12/30/2022] Open
Abstract
Understanding the regulatory networks for germ cell fate specification is necessary to developing strategies for improving the efficiency of germ cell production in vitro. In this study, we developed a coupled screening strategy that took advantage of an arrayed bi-molecular fluorescence complementation (BiFC) platform for protein-protein interaction screens and epiblast-like cell (EpiLC)-induction assays using reporter mouse embryonic stem cells (mESCs). Investigation of candidate interaction partners of core human pluripotent factors OCT4, NANOG, KLF4 and SOX2 in EpiLC differentiation assays identified novel primordial germ cell (PGC)-inducing factors including BEN-domain (BEND/Bend) family members. Through RNA-seq, ChIP-seq, and ATAC-seq analyses, we showed that Bend5 worked together with Bend4 and helped mark chromatin boundaries to promote EpiLC induction in vitro. Our findings suggest that BEND/Bend proteins represent a new family of transcriptional modulators and chromatin boundary factors that participate in gene expression regulation during early germline development.
Collapse
|
30
|
Choudhury S, Surendran N, Das A. Recent advances in the induced pluripotent stem cell-based skin regeneration. Wound Repair Regen 2021; 29:697-710. [PMID: 33970525 DOI: 10.1111/wrr.12925] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/30/2021] [Accepted: 04/27/2021] [Indexed: 01/05/2023]
Abstract
Skin regeneration has been a challenging clinical problem especially in cases of chronic wounds such as diabetic foot ulcers, and epidermolysis bullosa-related skin blisters. Prolonged non-healing wounds often lead to bacterial infections increasing the severity of wounds. Current treatment strategies for chronic wounds include debridement of wounds along with antibiotics, growth factors, and stem cell transplantation therapies. However, the compromised nature of autologous stem cells in patients with comorbidities such as diabetes limits the efficacy of the therapy. The discovery of induced pluripotent stem cell (iPSC) technology has immensely influenced the field of regenerative therapy. Enormous efforts have been made to develop integration-free iPSCs suitable for clinical therapies. This review focuses on recent advances in the methods and reprogramming factors for generating iPSCs along with the existing challenges such as genetic alterations, tumorigenicity, immune rejection, and regulatory hurdles for the clinical application of iPSCs. Furthermore, this review also highlights the benefits of using iPSCs for the generation of skin cells and skin disease modeling over the existing clinical therapies for skin regeneration in chronic wounds and skin diseases.
Collapse
Affiliation(s)
- Subholakshmi Choudhury
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India
- Academy of Science and Innovative Research (AcSIR), Ghaziabad, India
| | - Nidhi Surendran
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India
| | - Amitava Das
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India
- Academy of Science and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
31
|
Auxin-degron system identifies immediate mechanisms of OCT4. Stem Cell Reports 2021; 16:1818-1831. [PMID: 34143975 PMCID: PMC8282470 DOI: 10.1016/j.stemcr.2021.05.016] [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: 09/29/2020] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/11/2022] Open
Abstract
The pluripotency factor OCT4 is essential for the maintenance of naive pluripotent stem cells in vitro and in vivo. However, the specific role of OCT4 in this process remains unknown. Here, we developed a rapid protein-level OCT4 depletion system that demonstrates that the immediate downstream response to loss of OCT4 is reduced expression of key pluripotency factors. Our data show a requirement for OCT4 for the efficient transcription of several key pluripotency factors and suggest that expression of trophectoderm markers is a subsequent event. In addition, we find that NANOG is able to bind to the genome in the absence of OCT4, and this binding is in fact enhanced. Globally, however, the active enhancer-associated histone mark H3K27ac is depleted. Our work establishes that, while OCT4 is required for the maintenance of the naive transcription factor network, at a normal embryonic stem cell levels it antagonizes this network through inhibition of NANOG binding.
Collapse
|
32
|
Wang L, Xiong X, Yao Z, Zhu J, Lin Y, Lin W, Li K, Xu X, Guo Y, Chen Y, Pan Y, Zhou F, Fan J, Chen Y, Gao S, Jim Yeung SC, Zhang H. Chimeric RNA ASTN2-PAPPA as aggravates tumor progression and metastasis in human esophageal cancer. Cancer Lett 2021; 501:1-11. [PMID: 33388371 DOI: 10.1016/j.canlet.2020.10.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 02/05/2023]
Abstract
Transcription-induced chimeric RNAs are an emerging area of research into molecular signatures for disease biomarker and therapeutic target development. Despite their importance, little is known for chimeric RNAs-relevant roles and the underlying mechanisms for cancer pathogenesis and progression. Here we describe a unique ASTN2-PAPPAantisense chimeric RNA (A-PaschiRNA) that could be the first reported chimeric RNA derived from the splicing of exons and intron antisense of two neighboring genes, respectively. Aberrant A-PaschiRNA level in ESCC tissues was associated with tumor progression and patients' outcome. In vitro and in vivo studies demonstrated that A-PaschiRNA aggravated ESCC metastasis and enhanced stemness through modulating OCT4. Mechanistic studies demonstrated that ERK5-mediated non-canonical PAF1 activity was required for A-PaschiRNA-induced cancer malignancy. The study defined an undocumented function of chimeric RNAs in aggravating cancer stemness and metastasis.
Collapse
Affiliation(s)
- Lu Wang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Xiao Xiong
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Zhimeng Yao
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Jianlin Zhu
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Yusheng Lin
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China; Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Wan Lin
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, 515041, China
| | - Kai Li
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Xiaozheng Xu
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yi Guo
- Endoscopy Center, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yuping Chen
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yunlong Pan
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Fuyou Zhou
- The Fourth Affiliated Hospital of Henan University of Science and Technology, Anyang, Henan, 455001, China; Department of Thoracic Surgery, Anyang Tumor Hospital, Anyang, Henan, 455001, China
| | - Jun Fan
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yan Chen
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Shegan Gao
- College of Clinical Medicine, The First Affiliated Hospital of Henan University of Science and Technology, Henan Key Laboratory of Cancer Epigenetics, Luoyang, 471003, China.
| | - Sai-Ching Jim Yeung
- Department of Emergency Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hao Zhang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China.
| |
Collapse
|
33
|
Madsen RR, Longden J, Knox RG, Robin X, Völlmy F, Macleod KG, Moniz LS, Carragher NO, Linding R, Vanhaesebroeck B, Semple RK. NODAL/TGFβ signalling mediates the self-sustained stemness induced by PIK3CAH1047R homozygosity in pluripotent stem cells. Dis Model Mech 2021; 14:dmm048298. [PMID: 33514588 PMCID: PMC7969366 DOI: 10.1242/dmm.048298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
Activating PIK3CA mutations are known 'drivers' of human cancer and developmental overgrowth syndromes. We recently demonstrated that the 'hotspot' PIK3CAH1047R variant exerts unexpected allele dose-dependent effects on stemness in human pluripotent stem cells (hPSCs). In this study, we combine high-depth transcriptomics, total proteomics and reverse-phase protein arrays to reveal potentially disease-related alterations in heterozygous cells, and to assess the contribution of activated TGFβ signalling to the stemness phenotype of homozygous PIK3CAH1047R cells. We demonstrate signalling rewiring as a function of oncogenic PI3K signalling strength, and provide experimental evidence that self-sustained stemness is causally related to enhanced autocrine NODAL/TGFβ signalling. A significant transcriptomic signature of TGFβ pathway activation in heterozygous PIK3CAH1047R was observed but was modest and was not associated with the stemness phenotype seen in homozygous mutants. Notably, the stemness gene expression in homozygous PIK3CAH1047R hPSCs was reversed by pharmacological inhibition of NODAL/TGFβ signalling, but not by pharmacological PI3Kα pathway inhibition. Altogether, this provides the first in-depth analysis of PI3K signalling in hPSCs and directly links strong PI3K activation to developmental NODAL/TGFβ signalling. This work illustrates the importance of allele dosage and expression when artificial systems are used to model human genetic disease caused by activating PIK3CA mutations. This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Ralitsa R. Madsen
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - James Longden
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, 10115Berlin, Germany
| | - Rachel G. Knox
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Xavier Robin
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Franziska Völlmy
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kenneth G. Macleod
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Larissa S. Moniz
- University College London Cancer Institute, Paul O'Gorman Building, University College London, London WC1E 6BT, UK
| | - Neil O. Carragher
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Rune Linding
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, 10115Berlin, Germany
| | - Bart Vanhaesebroeck
- University College London Cancer Institute, Paul O'Gorman Building, University College London, London WC1E 6BT, UK
| | - Robert K. Semple
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| |
Collapse
|
34
|
Sox2 modulation increases naïve pluripotency plasticity. iScience 2021; 24:102153. [PMID: 33665571 PMCID: PMC7903329 DOI: 10.1016/j.isci.2021.102153] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/31/2020] [Accepted: 02/02/2021] [Indexed: 12/21/2022] Open
Abstract
Induced pluripotency provides a tool to explore mechanisms underlying establishment, maintenance, and differentiation of naive pluripotent stem cells (nPSCs). Here, we report that self-renewal of nPSCs requires minimal Sox2 expression (Sox2-low). Sox2-low nPSCs do not show impaired neuroectoderm specification and differentiate efficiently in vitro into all embryonic germ lineages. Strikingly, upon the removal of self-renewing cues Sox2-low nPSCs differentiate into both embryonic and extraembryonic cell fates in vitro and in vivo. This differs from previous studies which only identified conditions that allowed cells to differentiate to one fate or the other. At the single-cell level self-renewing Sox2-low nPSCs exhibit a naive molecular signature. However, they display a nearer trophoblast identity than controls and decreased ability of Oct4 to bind naïve-associated regulatory sequences. In sum, this work defines wild-type levels of Sox2 as a restrictor of developmental potential and suggests perturbation of naive network as a mechanism to increase cell plasticity. Low Sox2 expression is sufficient for naive pluripotent stem cell self-renewal Low Sox2 expression does not impair neurectoderm differentiation in vitro Low Sox2 expression impairs Oct4 genomic occupancy Low Sox2 increases naive pluripotent stem cell plasticity in vitro and in vivo
Collapse
|
35
|
Optimized Approaches for the Induction of Putative Canine Induced Pluripotent Stem Cells from Old Fibroblasts Using Synthetic RNAs. Animals (Basel) 2020; 10:ani10101848. [PMID: 33050577 PMCID: PMC7601034 DOI: 10.3390/ani10101848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary A non-integrating and self-replicating Venezuelan equine encephalitis RNA replicon system can potentially make a great contribution to the generation of clinically applicable canine induced pluripotent stem cells. Our study shows a new method to utilize the synthetic RNA-based approach for canine somatic cell reprogramming regarding transfection and reprogramming efficiency. Abstract Canine induced pluripotent stem cells (ciPSCs) can provide great potential for regenerative veterinary medicine. Several reports have described the generation of canine somatic cell-derived iPSCs; however, none have described the canine somatic cell reprogramming using a non-integrating and self-replicating RNA transfection method. The purpose of this study was to investigate the optimal strategy using this approach and characterize the transition stage of ciPSCs. In this study, fibroblasts obtained from a 13-year-old dog were reprogrammed using a non-integrating Venezuelan equine encephalitis (VEE) RNA virus replicon, which has four reprogramming factors (collectively referred to as T7-VEE-OKS-iG and comprised of hOct4, hKlf4, hSox2, and hGlis1) and co-transfected with the T7-VEE-OKS-iG RNA and B18R mRNA for 4 h. One day after the final transfection, the cells were selected with puromycin (0.5 µg/mL) until day 10. After about 25 days, putative ciPSC colonies were identified showing TRA-1-60 expression and alkaline phosphatase activity. To determine the optimal culture conditions, the basic fibroblast growth factor in the culture medium was replaced with a modified medium supplemented with murine leukemia inhibitory factor (mLIF) and two kinase inhibitors (2i), PD0325901(MEK1/2 inhibitor) and CHIR99021 (GSK3β inhibitor). The derived colonies showed resemblance to naïve iPSCs in their morphology (dome-shaped) and are dependent on mLIF and 2i condition to maintain an undifferentiated phenotype. The expression of endogenous pluripotency markers such as Oct4, Nanog, and Rex1 transcripts were confirmed, suggesting that induced ciPSCs were in the late intermediate stage of reprogramming. In conclusion, the non-integrating and self-replicating VEE RNA replicon system can potentially make a great contribution to the generation of clinically applicable ciPSCs, and the findings of this study suggest a new method to utilize the VEE RNA approach for canine somatic cell reprogramming.
Collapse
|
36
|
Capp JP, Laforge B. A Darwinian and Physical Look at Stem Cell Biology Helps Understanding the Role of Stochasticity in Development. Front Cell Dev Biol 2020; 8:659. [PMID: 32793600 PMCID: PMC7391792 DOI: 10.3389/fcell.2020.00659] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/01/2020] [Indexed: 11/27/2022] Open
Abstract
Single-cell analysis allows biologists to gain huge insight into cell differentiation and tissue structuration. Randomness of differentiation, both in vitro and in vivo, of pluripotent (multipotent) stem cells is now demonstrated to be mainly based on stochastic gene expression. Nevertheless, it remains necessary to incorporate this inherent stochasticity of developmental processes within a coherent scheme. We argue here that the theory called ontophylogenesis is more relevant and better fits with experimental data than alternative theories which have been suggested based on the notions of self-organization and attractor states. The ontophylogenesis theory considers the generation of a differentiated state as a constrained random process: randomness is provided by the stochastic dynamics of biochemical reactions while the environmental constraints, including cell inner structures and cell-cell interactions, drive the system toward a stabilized state of equilibrium. In this conception, biological organization during development can be seen as the result of multiscale constraints produced by the dynamical organization of the biological system which retroacts on the stochastic dynamics at lower scales. This scheme makes it possible to really understand how the generation of reproducible structures at higher organization levels can be fully compatible with probabilistic behavior at the lower levels. It is compatible with the second law of thermodynamics but allows the overtaking of the limitations exhibited by models only based on entropy exchanges which cannot cope with the description nor the dynamics of the mesoscopic and macroscopic organization of biological systems.
Collapse
Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, Toulouse, France
| | - Bertrand Laforge
- LPNHE, UMR 7585, Sorbonne Université, CNRS/IN2P3, Université de Paris, Paris, France
| |
Collapse
|
37
|
Cheng MB, Wang X, Huang Y, Zhang Y. Hyperthermia depletes Oct4 in mouse blastocysts and stem cells. Stem Cell Res Ther 2020; 11:195. [PMID: 32448390 PMCID: PMC7245852 DOI: 10.1186/s13287-020-01715-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/17/2020] [Accepted: 05/07/2020] [Indexed: 11/17/2022] Open
Abstract
Temperature is an important microenvironmental factor that functions epigenetically in normal embryonic development. However, the effect of hyperthermia in the stem cells is not fully understood. Oct4 is a tightly regulated master regulator of pluripotency maintenance in stem cells and during early embryonic development. We report here that Oct4 protein level was significantly reduced under hyperthermia in mouse blastocysts and embryonic stem cells. The reduction in Oct4 in the mouse embryonic stem cells under hyperthermia was mediated by a ubiquitin-proteasome pathway that was dependent on the activity of death-associated protein kinase 1 (Dapk1) to phosphorylate its substrate, Pin1. Our results imply that the depletion of Oct4 via brief hyperthermia, such as a high fever, during early pregnancy might severely impair the growth of the mammalian embryo or even cause its death.
Collapse
Affiliation(s)
- Mo-Bin Cheng
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, 5 Dongdan Santiao, Beijing, 100005, China
| | - Xue Wang
- State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yue Huang
- State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
| | - Ye Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, 5 Dongdan Santiao, Beijing, 100005, China.
| |
Collapse
|
38
|
Gzara C, Dallmann-Sauer M, Orlova M, Van Thuc N, Thai VH, Fava VM, Bihoreau MT, Boland A, Abel L, Alcaïs A, Schurr E, Cobat A. Family-based genome-wide association study of leprosy in Vietnam. PLoS Pathog 2020; 16:e1008565. [PMID: 32421744 PMCID: PMC7259797 DOI: 10.1371/journal.ppat.1008565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/29/2020] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
Leprosy is a chronic infectious disease of the skin and peripheral nerves with a strong genetic predisposition. Recent genome-wide approaches have identified numerous common variants associated with leprosy, almost all in the Chinese population. We conducted the first family-based genome-wide association study of leprosy in 622 affected offspring from Vietnam, followed by replication in an independent sample of 1181 leprosy cases and 668 controls of the same ethnic origin. The most significant results were observed within the HLA region, in which six SNPs displayed genome-wide significant associations, all of which were replicated in the independent case/control sample. We investigated the signal in the HLA region in more detail, by conducting a multivariate analysis on the case/control sample of 319 GWAS-suggestive HLA hits for which evidence for replication was obtained. We identified three independently associated SNPs, two located in the HLA class I region (rs1265048: OR = 0.69 [0.58-0.80], combined p-value = 5.53x10-11; and rs114598080: OR = 1.47 [1.46-1.48], combined p-value = 8.77x10-13), and one located in the HLA class II region (rs3187964 (OR = 1.67 [1.55-1.80], combined p-value = 8.35x10-16). We also validated two previously identified risk factors for leprosy: the missense variant rs3764147 in the LACC1 gene (OR = 1.52 [1.41-1.63], combined p-value = 5.06x10-14), and the intergenic variant rs6871626 located close to the IL12B gene (OR = 0.73 [0.61-0.84], combined p-value = 6.44x10-8). These results shed new light on the genetic control of leprosy, by dissecting the influence of HLA SNPs, and validating the independent role of two additional variants in a large Vietnamese sample.
Collapse
Affiliation(s)
- Chaima Gzara
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France
- Université de Paris, Imagine Institute, Paris, France
| | - Monica Dallmann-Sauer
- McGill International TB Centre, Montreal, QC, Canada
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine and Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Marianna Orlova
- McGill International TB Centre, Montreal, QC, Canada
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine and Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Nguyen Van Thuc
- Hospital for Dermato-Venereology, District, Ho Chi Minh City, Vietnam
| | - Vu Hong Thai
- Hospital for Dermato-Venereology, District, Ho Chi Minh City, Vietnam
| | - Vinicius M. Fava
- McGill International TB Centre, Montreal, QC, Canada
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Marie-Thérèse Bihoreau
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France
- Université de Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, United States of America
| | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France
- Université de Paris, Imagine Institute, Paris, France
| | - Erwin Schurr
- McGill International TB Centre, Montreal, QC, Canada
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine and Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France
- Université de Paris, Imagine Institute, Paris, France
- * E-mail:
| |
Collapse
|
39
|
Luo X, van der Veer BK, Sun L, Bartoccetti M, Boretto M, Vankelecom H, Khoueiry R, Koh KP. Coordination of germ layer lineage choice by TET1 during primed pluripotency. Genes Dev 2020; 34:598-618. [PMID: 32115407 PMCID: PMC7111260 DOI: 10.1101/gad.329474.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/27/2020] [Indexed: 01/23/2023]
Abstract
Here, Luo et al. show how the DNA dioxygenase Tet1 plays a pivotal role upstream of germ layer lineage bifurcation. A permissive role for Tet1 in neural fate induction is identified, and involves Zic2-dependent engagement at neural target genes at lineage priming, is dependent on the signaling environment during gastrulation, and impacts neural tube closure after gastrulation. Gastrulation in the early postimplantation stage mammalian embryo begins when epiblast cells ingress to form the primitive streak or develop as the embryonic ectoderm. The DNA dioxygenase Tet1 is highly expressed in the epiblast and yet continues to regulate lineage specification during gastrulation when its expression is diminished. Here, we show how Tet1 plays a pivotal role upstream of germ layer lineage bifurcation. During the transition from naive pluripotency to lineage priming, a global reconfiguration redistributes Tet1 from Oct4-cobound promoters to distal regulatory elements at lineage differentiation genes, which are distinct from high-affinity sites engaged by Oct4. An altered chromatin landscape in Tet1-deficient primed epiblast-like cells is associated with enhanced Oct4 expression and binding to Nodal and Wnt target genes, resulting in collaborative signals that enhance mesendodermal and inhibit neuroectodermal gene expression during lineage segregation. A permissive role for Tet1 in neural fate induction involves Zic2-dependent engagement at neural target genes at lineage priming, is dependent on the signaling environment during gastrulation, and impacts neural tube closure after gastrulation. Our findings provide mechanistic information for epigenetic integration of pluripotency and signal-induced differentiation cues.
Collapse
Affiliation(s)
- Xinlong Luo
- Laboratory for Stem Cell and Developmental Epigenetics, Department of Development and Regeneration, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Bernard K van der Veer
- Laboratory for Stem Cell and Developmental Epigenetics, Department of Development and Regeneration, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Lei Sun
- Laboratory for Stem Cell and Developmental Epigenetics, Department of Development and Regeneration, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Michela Bartoccetti
- Laboratory for Stem Cell and Developmental Epigenetics, Department of Development and Regeneration, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Matteo Boretto
- Laboratory of Tissue Plasticity in Health and Disease, Department of Development and Regeneration, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Hugo Vankelecom
- Laboratory of Tissue Plasticity in Health and Disease, Department of Development and Regeneration, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Rita Khoueiry
- Laboratory for Stem Cell and Developmental Epigenetics, Department of Development and Regeneration, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Kian Peng Koh
- Laboratory for Stem Cell and Developmental Epigenetics, Department of Development and Regeneration, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| |
Collapse
|
40
|
Chen SH, Lu CH, Tsai MJ. TCTP is Essential for Cell Proliferation and Survival during CNS Development. Cells 2020; 9:cells9010133. [PMID: 31935927 PMCID: PMC7017002 DOI: 10.3390/cells9010133] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/31/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023] Open
Abstract
Translationally controlled tumor-associated protein (TCTP) has been implicated in cell growth, proliferation, and apoptosis through interacting proteins. Although TCTP is expressed abundantly in the mouse brain, little is known regarding its role in the neurogenesis of the nervous system. We used Nestin-cre-driven gene-mutated mice to investigate the function of TCTP in the nervous system. The mice carrying disrupted TCTP in neuronal and glial progenitor cells died at the perinatal stage. The NestinCre/+; TCTPf/f pups displayed reduced body size at postnatal day 0.5 (P0.5) and a lack of milk in the stomach compared with littermate controls. In addition to decreased cell proliferation, terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) and caspase assay revealed that apoptosis was increased in newly committed TCTP-disrupted cells as they migrated away from the ventricular zone. The mechanism may be that the phenotype from specific deletion of TCTP in neural progenitor cells is correlated with the decreased expression of cyclins D2, E2, Mcl-1, Bcl-xL, hax-1, and Octamer-binding transcription factor 4 (Oct4) in conditional knockout mice. Our results demonstrate that TCTP is a critical protein for cell survival during early neuronal and glial differentiation. Thus, enhanced neuronal loss and functional defect in Tuj1 and doublecortin-positive neurons mediated through increased apoptosis and decreased proliferation during central nervous system (CNS) development may contribute to the perinatal death of TCTP mutant mice.
Collapse
Affiliation(s)
- Sung-Ho Chen
- Department of Pharmacology, College of Medicine, Tzu Chi University, Hualien 97004, Taiwan
- Master Program in Pharmacology and Toxicology, College of Medicine, Tzu Chi University, Hualien 97004, Taiwan;
- Correspondence: ; Tel.: +886-3-8565301 (ext. 2452); Fax: +886-3-8561465
| | - Chin-Hung Lu
- Master Program in Pharmacology and Toxicology, College of Medicine, Tzu Chi University, Hualien 97004, Taiwan;
| | - Ming-Jen Tsai
- Department of Emergency Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City 600, Taiwan;
| |
Collapse
|
41
|
Xu Z, Liu C, Zhao Q, Lü J, Ding X, Luo A, He J, Wang G, Li Y, Cai Z, Wang Z, Liu J, Liu S, Li W, Yu Z. Long non-coding RNA CCAT2 promotes oncogenesis in triple-negative breast cancer by regulating stemness of cancer cells. Pharmacol Res 2020; 152:104628. [PMID: 31904506 DOI: 10.1016/j.phrs.2020.104628] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/22/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023]
Abstract
Triple-negative breast cancers (TNBC) are more aggressive due to lacking receptors for hormone therapy and maintaining stemness features in cancer cells. Herein we found long non-coding RNA CCAT2 overexpressed specially in TNBC, and in breast cancer stem cells (BCSC) as well. Enforced overexpression and targeted knockdown demonstrated the oncogenic function of CCAT2 both in vitro and in vivo. CCAT2 promoted the expression of stemness markers including OCT4, Nanog and KLF4, increased mammosphere formation and induced ALDH+ cancer stem cell population in TNBC. A chromosomally adjacent gene OCT4-PG1, as a pseudogene of OCT4, was upregulated by CCAT2, and positively regulated the stemness features of TNBC cells. miR-205 was identified as a target gene of CCAT2 in TNBC. Point-mutation in CCAT2 impaired the sponge inhibition of miR-205. Overexpression of miR-205 rescued the oncogenic phenotypes induced by CCAT2. In addition, Notch2, as a target gene of miR-205, was downregulated by miR-205 and upregulated by CCAT2 in TNBC. Collectively, the current study revealed a novel function of CCAT2 in promoting tumor initiation and progression in TNBC through upregulating OCT4-PG1 expression and activating Notch signaling. These findings not only demonstrated a lncRNA-based therapeutic strategy in treatment of TNBC, but also added a node to the regulatory network of CCAT2 that controls aggressiveness of breast cancer stem cells.
Collapse
Affiliation(s)
- Zhen Xu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China; Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Cuiui Liu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China; Shanghai Cancer Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qian Zhao
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Jinhui Lü
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Xin Ding
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - An Luo
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Jia He
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Guangxue Wang
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Yuan Li
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Zhaoqing Cai
- Tongji University School of Life Science and Technology, Shanghai, China
| | - Zhongrui Wang
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China; Department of Medical Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Junjun Liu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China; Department of Medical Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Suling Liu
- Shanghai Cancer Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wenshu Li
- Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Zuoren Yu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
| |
Collapse
|
42
|
Harbuzariu A, Pitts S, Cespedes JC, Harp KO, Nti A, Shaw AP, Liu M, Stiles JK. Modelling heme-mediated brain injury associated with cerebral malaria in human brain cortical organoids. Sci Rep 2019; 9:19162. [PMID: 31844087 PMCID: PMC6914785 DOI: 10.1038/s41598-019-55631-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/26/2019] [Indexed: 01/09/2023] Open
Abstract
Human cerebral malaria (HCM), a severe encephalopathy associated with Plasmodium falciparum infection, has a 20-30% mortality rate and predominantly affects African children. The mechanisms mediating HCM-associated brain injury are difficult to study in human subjects, highlighting the urgent need for non-invasive ex vivo human models. HCM elevates the systemic levels of free heme, which damages the blood-brain barrier and neurons in distinct regions of the brain. We determined the effects of heme on induced pluripotent stem cells (iPSCs) and a three-dimensional cortical organoid system and assessed apoptosis and differentiation. We evaluated biomarkers associated with heme-induced brain injury, including a pro-inflammatory chemokine, CXCL-10, and its receptor, CXCR3, brain-derived neurotrophic factor (BDNF) and a receptor tyrosine-protein kinase, ERBB4, in the organoids. We then tested the neuroprotective effect of neuregulin-1 (NRG-1) against heme treatment in organoids. Neural stem and mature cells differentially expressed CXCL-10, CXCR3, BDNF and ERBB4 in the developing organoids and in response to heme-induced neuronal injury. The organoids underwent apoptosis and structural changes that were attenuated by NRG-1. Thus, cortical organoids can be used to model heme-induced cortical brain injury associated with HCM pathogenesis as well as for testing agents that reduce brain injury and neurological sequelae.
Collapse
Affiliation(s)
- Adriana Harbuzariu
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr, Atlanta, GA, 30310, USA.
| | - Sidney Pitts
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr, Atlanta, GA, 30310, USA
| | - Juan Carlos Cespedes
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr, Atlanta, GA, 30310, USA
| | - Keri Oxendine Harp
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr, Atlanta, GA, 30310, USA
| | - Annette Nti
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr, Atlanta, GA, 30310, USA
| | - Andrew P Shaw
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA, 30332, USA
| | - Mingli Liu
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr, Atlanta, GA, 30310, USA
| | - Jonathan K Stiles
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr, Atlanta, GA, 30310, USA.
| |
Collapse
|
43
|
Friman ET, Deluz C, Meireles-Filho ACA, Govindan S, Gardeux V, Deplancke B, Suter DM. Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle. eLife 2019; 8:e50087. [PMID: 31794382 PMCID: PMC6890464 DOI: 10.7554/elife.50087] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewing cell divisions and across the cell cycle is poorly understood. Here we assessed the interplay between OCT4 and SOX2 in controlling chromatin accessibility of mouse embryonic stem cells. We found that OCT4 and SOX2 operate in a largely independent manner even at co-occupied sites, and that their cooperative binding is mostly mediated indirectly through regulation of chromatin accessibility. Controlled protein degradation strategies revealed that the uninterrupted presence of OCT4 is required for post-mitotic re-establishment and interphase maintenance of chromatin accessibility, and that highly OCT4-bound enhancers are particularly vulnerable to transient loss of OCT4 expression. Our study sheds light on the constant pioneer activity required to maintain the dynamic pluripotency regulatory landscape in an accessible state.
Collapse
Affiliation(s)
- Elias T Friman
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Cédric Deluz
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Antonio CA Meireles-Filho
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Subashika Govindan
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Vincent Gardeux
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - David M Suter
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| |
Collapse
|
44
|
Barral A, Rollan I, Sanchez-Iranzo H, Jawaid W, Badia-Careaga C, Menchero S, Gomez MJ, Torroja C, Sanchez-Cabo F, Göttgens B, Manzanares M, Sainz de Aja J. Nanog regulates Pou3f1 expression at the exit from pluripotency during gastrulation. Biol Open 2019; 8:bio046367. [PMID: 31791948 PMCID: PMC6899006 DOI: 10.1242/bio.046367] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Pluripotency is regulated by a network of transcription factors that maintain early embryonic cells in an undifferentiated state while allowing them to proliferate. NANOG is a critical factor for maintaining pluripotency and its role in primordial germ cell differentiation has been well described. However, Nanog is expressed during gastrulation across all the posterior epiblast, and only later in development is its expression restricted to primordial germ cells. In this work, we unveiled a previously unknown mechanism by which Nanog specifically represses genes involved in anterior epiblast lineage. Analysis of transcriptional data from both embryonic stem cells and gastrulating mouse embryos revealed Pou3f1 expression to be negatively correlated with that of Nanog during the early stages of differentiation. We have functionally demonstrated Pou3f1 to be a direct target of NANOG by using a dual transgene system for the controlled expression of Nanog Use of Nanog null ES cells further demonstrated a role for Nanog in repressing a subset of anterior neural genes. Deletion of a NANOG binding site (BS) located nine kilobases downstream of the transcription start site of Pou3f1 revealed this BS to have a specific role in the regionalization of the expression of this gene in the embryo. Our results indicate an active role of Nanog inhibiting neural regulatory networks by repressing Pou3f1 at the onset of gastrulation.This article has an associated First Person interview with the joint first authors of the paper.
Collapse
Affiliation(s)
- Antonio Barral
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Isabel Rollan
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Hector Sanchez-Iranzo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Wajid Jawaid
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0AW, UK
| | - Claudio Badia-Careaga
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Sergio Menchero
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Manuel J Gomez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Carlos Torroja
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Fatima Sanchez-Cabo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Berthold Göttgens
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0AW, UK
| | - Miguel Manzanares
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Madrid 28049, Spain
| | - Julio Sainz de Aja
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| |
Collapse
|
45
|
Choi KA, Park HK, Hwang I, Jeong H, Park HS, Jang AY, Namkung Y, Hyun D, Lee S, Yoo BM, Kwon HJ, Seol KC, Kim JO, Hong S. Tissue inhibitor of metalloproteinase proteins inhibit teratoma growth in mice transplanted with pluripotent stem cells. Stem Cells 2019; 38:516-529. [PMID: 31778275 DOI: 10.1002/stem.3132] [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: 06/21/2019] [Accepted: 10/25/2019] [Indexed: 11/11/2022]
Abstract
Pluripotent stem cells (PSCs) can serve as an unlimited cell source for transplantation therapies for treating various devastating diseases, such as cardiovascular diseases, diabetes, and Parkinson's disease. However, PSC transplantation has some associated risks, including teratoma formation from the remaining undifferentiated PSCs. Thus, for successful clinical application, it is essential to ablate the proliferative PSCs before or after transplantation. In this study, neural stem cell-derived conditioned medium (NSC-CM) inhibited the proliferation of PSCs and PSC-derived neural precursor (NP) cells without influencing the potential of PSC-NP cells to differentiate into neurons in vitro and prevented teratoma growth in vivo. Moreover, we found that the NSC-CM remarkably decreased the expression levels of Oct4 and cyclin D1 that Oct4 directly binds to and increased the cleaved-caspase 3-positive cell death through the DNA damage response in PSCs and PSC-NPs. Interestingly, we found that NSCs distinctly secreted the tissue inhibitor of metalloproteinase (TIMP)-1 and TIMP-2 proteins. These proteins suppressed not only the proliferation of PSCs in cell culture but also teratoma growth in mice transplanted with PSCs through inhibition of matrix metalloproteinase (MMP)-2 and MMP-9 activity. Taken together, these results suggest that the TIMP proteins may improve the efficacy and safety of the PSC-based transplantation therapy.
Collapse
Affiliation(s)
- Kyung-Ah Choi
- School of Biosystems and Biomedical Sciences, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Han-Kyul Park
- School of Biosystems and Biomedical Sciences, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Insik Hwang
- School of Biosystems and Biomedical Sciences, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Hyesun Jeong
- School of Biosystems and Biomedical Sciences, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Hang-Soo Park
- School of Biosystems and Biomedical Sciences, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Ah-Young Jang
- School of Biosystems and Biomedical Sciences, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Yong Namkung
- School of Biosystems and Biomedical Sciences, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Donghun Hyun
- School of Biosystems and Biomedical Sciences, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Seulbee Lee
- School of Biosystems and Biomedical Sciences, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Byung Min Yoo
- Medical College of Seoul National University, Seoul, Republic of Korea
| | | | - Ki-Cheon Seol
- Institute of Stem Cell Research, Future Cell Therapy, Ahnyang, Republic of Korea
| | - Jeong-Ok Kim
- Institute of Stem Cell Research, Future Cell Therapy, Ahnyang, Republic of Korea
| | - Sunghoi Hong
- School of Biosystems and Biomedical Sciences, College of Health Science, Korea University, Seoul, Republic of Korea
| |
Collapse
|
46
|
Yiangou L, Grandy RA, Osnato A, Ortmann D, Sinha S, Vallier L. Cell cycle regulators control mesoderm specification in human pluripotent stem cells. J Biol Chem 2019; 294:17903-17914. [PMID: 31515269 PMCID: PMC6879335 DOI: 10.1074/jbc.ra119.008251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 09/09/2019] [Indexed: 12/20/2022] Open
Abstract
The mesoderm is one of the three germ layers produced during gastrulation from which muscle, bones, kidneys, and the cardiovascular system originate. Understanding the mechanisms that control mesoderm specification could inform many applications, including the development of regenerative medicine therapies to manage diseases affecting these tissues. Here, we used human pluripotent stem cells to investigate the role of cell cycle in mesoderm formation. To this end, using small molecules or conditional gene knockdown, we inhibited proteins controlling G1 and G2/M cell cycle phases during the differentiation of human pluripotent stem cells into lateral plate, cardiac, and presomitic mesoderm. These loss-of-function experiments revealed that regulators of the G1 phase, such as cyclin-dependent kinases and pRb (retinoblastoma protein), are necessary for efficient mesoderm formation in a context-dependent manner. Further investigations disclosed that inhibition of the G2/M regulator cyclin-dependent kinase 1 decreases BMP (bone morphogenetic protein) signaling activity specifically during lateral plate mesoderm formation while reducing fibroblast growth factor/extracellular signaling-regulated kinase 1/2 activity in all mesoderm subtypes. Taken together, our findings reveal that cell cycle regulators direct mesoderm formation by controlling the activity of key developmental pathways.
Collapse
Affiliation(s)
- Loukia Yiangou
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
- Wellcome Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Rodrigo A Grandy
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Anna Osnato
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Daniel Ortmann
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Sanjay Sinha
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Ludovic Vallier
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
- Wellcome Sanger Institute, Hinxton CB10 1SA, United Kingdom
| |
Collapse
|
47
|
Abstract
Cancer stem cells (CSC) are a subpopulation of tumor cells that have superior capacities of self-renewal, metastatic dissemination, and chemoresistance. These characteristics resemble, to some extent, the outcome of certain biological processes, including epithelial-mesenchymal transition (EMT), autophagy, and cellular stress response. Indeed, it has been shown that the stimuli that induce these processes and CSC are overlapping, and CSC and tumor cells that underwent EMT or autophagy are much alike. However, as the cross talk between CSC, EMT, autophagy, and cellular stress is further explored, these processes are also found to have an opposing role in CSC, depending on the condition and status of cells. This contextual effect is likely due to overwhelming reliance on CSC markers for their identification, and/or discrepancies in recognition of CSC as a particular cell population or cellular state. In this review, we summarize how EMT, autophagy, and cellular stress response are tied or unwound with CSC. We also discuss the current view of CSC theory evolved from the emphasis of heterogenicity and plasticity of CSC.
Collapse
Affiliation(s)
- Kai-Feng Hung
- Department of Medical Research, Division of Translational Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Department of Dentistry, School of Dentistry, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Ting Yang
- Department of Medical Research, Division of Translational Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Shou-Yen Kao
- Department of Dentistry, School of Dentistry, National Yang-Ming University, Taipei, Taiwan, ROC
- Department of Stomatology, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| |
Collapse
|
48
|
Sharma P, Gupta S, Chaudhary M, Mitra S, Chawla B, Khursheed MA, Ramachandran R. Oct4 mediates Müller glia reprogramming and cell cycle exit during retina regeneration in zebrafish. Life Sci Alliance 2019; 2:2/5/e201900548. [PMID: 31594822 PMCID: PMC6784428 DOI: 10.26508/lsa.201900548] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 12/21/2022] Open
Abstract
The rapid induction of pluripotency-inducing factor Oct4 in the injured retina necessitates the de novo induction of stem cells and their subsequent cell cycle exit. Octamer-binding transcription factor 4 (Oct4, also known as Pou5F3) is an essential pluripotency-inducing factor, governing a plethora of biological functions during cellular reprogramming. Retina regeneration in zebrafish involves reprogramming of Müller glia (MG) into a proliferating population of progenitors (MGPCs) with stem cell–like characteristics, along with up-regulation of pluripotency-inducing factors. However, the significance of Oct4 during retina regeneration remains elusive. In this study, we show an early panretinal induction of Oct4, which is essential for MG reprogramming through the regulation of several regeneration-associated factors such as Ascl1a, Lin28a, Sox2, Zeb, E-cadherin, and various miRNAs, namely, let-7a, miR-200a/miR-200b, and miR-143/miR-145. We also show the crucial roles played by Oct4 during cell cycle exit of MGPCs in collaboration with members of nucleosome remodeling and deacetylase complex such as Hdac1. Notably, Oct4 regulates Tgf-β signaling negatively during MG reprogramming, and positively to cause cycle exit of MGPCs. Our study reveals unique mechanistic involvement of Oct4, during MG reprogramming and cell cycle exit in zebrafish, which may also account for the inefficient retina regeneration in mammals.
Collapse
Affiliation(s)
- Poonam Sharma
- Indian Institute of Science Education and Research, Mohali, India
| | - Shivangi Gupta
- Indian Institute of Science Education and Research, Mohali, India
| | - Mansi Chaudhary
- Indian Institute of Science Education and Research, Mohali, India
| | - Soumitra Mitra
- Indian Institute of Science Education and Research, Mohali, India
| | - Bindia Chawla
- Indian Institute of Science Education and Research, Mohali, India
| | | | | |
Collapse
|
49
|
Strebinger D, Deluz C, Friman ET, Govindan S, Alber AB, Suter DM. Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions. Mol Syst Biol 2019; 15:e9002. [PMID: 31556488 PMCID: PMC6759502 DOI: 10.15252/msb.20199002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 12/20/2022] Open
Abstract
SOX2 and OCT4 are pioneer transcription factors playing a key role in embryonic stem (ES) cell self-renewal and differentiation. How temporal fluctuations in their expression levels bias lineage commitment is unknown. Here, we generated knock-in reporter fusion ES cell lines allowing to monitor endogenous SOX2 and OCT4 protein fluctuations in living cells and to determine their impact on mesendodermal and neuroectodermal commitment. We found that small differences in SOX2 and OCT4 levels impact cell fate commitment in G1 but not in S phase. Elevated SOX2 levels modestly increased neuroectodermal commitment and decreased mesendodermal commitment upon directed differentiation. In contrast, elevated OCT4 levels strongly biased ES cells towards both neuroectodermal and mesendodermal fates in undirected differentiation. Using ATAC-seq on ES cells gated for different endogenous SOX2 and OCT4 levels, we found that high OCT4 levels increased chromatin accessibility at differentiation-associated enhancers. This suggests that small endogenous fluctuations of pioneer transcription factors can bias cell fate decisions by concentration-dependent priming of differentiation-associated enhancers.
Collapse
Affiliation(s)
- Daniel Strebinger
- Sponsored Stem Cells Research Chair (UPSUTER)The Institute of Bioengineering (IBI)School of Life SciencesSwiss Federal Institute of TechnologyLausanneSwitzerland
| | - Cédric Deluz
- Sponsored Stem Cells Research Chair (UPSUTER)The Institute of Bioengineering (IBI)School of Life SciencesSwiss Federal Institute of TechnologyLausanneSwitzerland
| | - Elias T Friman
- Sponsored Stem Cells Research Chair (UPSUTER)The Institute of Bioengineering (IBI)School of Life SciencesSwiss Federal Institute of TechnologyLausanneSwitzerland
| | - Subashika Govindan
- Sponsored Stem Cells Research Chair (UPSUTER)The Institute of Bioengineering (IBI)School of Life SciencesSwiss Federal Institute of TechnologyLausanneSwitzerland
| | - Andrea B Alber
- Sponsored Stem Cells Research Chair (UPSUTER)The Institute of Bioengineering (IBI)School of Life SciencesSwiss Federal Institute of TechnologyLausanneSwitzerland
| | - David M Suter
- Sponsored Stem Cells Research Chair (UPSUTER)The Institute of Bioengineering (IBI)School of Life SciencesSwiss Federal Institute of TechnologyLausanneSwitzerland
| |
Collapse
|
50
|
Distinct Molecular Trajectories Converge to Induce Naive Pluripotency. Cell Stem Cell 2019; 25:388-406.e8. [PMID: 31422912 PMCID: PMC6731995 DOI: 10.1016/j.stem.2019.07.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/20/2019] [Accepted: 07/18/2019] [Indexed: 02/06/2023]
Abstract
Understanding how cell identity transitions occur and whether there are multiple paths between the same beginning and end states are questions of wide interest. Here we show that acquisition of naive pluripotency can follow transcriptionally and mechanistically distinct routes. Starting from post-implantation epiblast stem cells (EpiSCs), one route advances through a mesodermal state prior to naive pluripotency induction, whereas another transiently resembles the early inner cell mass and correspondingly gains greater developmental potency. These routes utilize distinct signaling networks and transcription factors but subsequently converge on the same naive endpoint, showing surprising flexibility in mechanisms underlying identity transitions and suggesting that naive pluripotency is a multidimensional attractor state. These route differences are reconciled by precise expression of Oct4 as a unifying, essential, and sufficient feature. We propose that fine-tuned regulation of this “transition factor” underpins multidimensional access to naive pluripotency, offering a conceptual framework for understanding cell identity transitions. Reprogramming routes differ transcriptionally and mechanistically Reprogramming intermediates resemble different developmental stages Distinct routes converge on precise Oct4 regulation to permit identity transition Precise Oct4 expression is sufficient for reprogramming of EpiSCs and fibroblasts
Collapse
|