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OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human. Nat Commun 2021; 12:5123. [PMID: 34446700 PMCID: PMC8390644 DOI: 10.1038/s41467-021-25107-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). While the protein-protein interactions of core pluripotency factors have been identified in mouse ESCs, their interactome in human ESCs (hESCs) has not to date been explored. Here we mapped the OCT4 interactomes in naïve and primed hESCs, revealing extensive connections to mammalian ATP-dependent nucleosome remodeling complexes. In naïve hESCs, OCT4 is associated with both BRG1 and BRM, the two paralog ATPases of the BAF complex. Genome-wide location analyses and genetic studies reveal that these two enzymes cooperate in a functionally redundant manner in the transcriptional regulation of blastocyst-specific genes. In contrast, in primed hESCs, OCT4 cooperates with BRG1 and SOX2 to promote chromatin accessibility at ectodermal genes. This work reveals how a common transcription factor utilizes differential BAF complexes to control distinct transcriptional programs in naïve and primed hESCs. Although the interactors of pluripotency factors have been identified in mouse embryonic stem cells (ESCs), their interactors in human ESCs remain unexplored. Here the authors map OCT4 protein interactions in naïve and primed human ESCs to find specific interactions with BAF subunits that promote an open chromatin architecture at blastocyst-associated genes and ectodermal genes, respectively.
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52
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Building Pluripotency Identity in the Early Embryo and Derived Stem Cells. Cells 2021; 10:cells10082049. [PMID: 34440818 PMCID: PMC8391114 DOI: 10.3390/cells10082049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
The fusion of two highly differentiated cells, an oocyte with a spermatozoon, gives rise to the zygote, a single totipotent cell, which has the capability to develop into a complete, fully functional organism. Then, as development proceeds, a series of programmed cell divisions occur whereby the arising cells progressively acquire their own cellular and molecular identity, and totipotency narrows until when pluripotency is achieved. The path towards pluripotency involves transcriptome modulation, remodeling of the chromatin epigenetic landscape to which external modulators contribute. Both human and mouse embryos are a source of different types of pluripotent stem cells whose characteristics can be captured and maintained in vitro. The main aim of this review is to address the cellular properties and the molecular signature of the emerging cells during mouse and human early development, highlighting similarities and differences between the two species and between the embryos and their cognate stem cells.
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53
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Divergent roles for KLF4 and TFCP2L1 in naive ground state pluripotency and human primordial germ cell development. Stem Cell Res 2021; 55:102493. [PMID: 34399163 DOI: 10.1016/j.scr.2021.102493] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 01/08/2023] Open
Abstract
During embryo development, human primordial germ cells (hPGCs) express a naive gene expression program with similarities to pre-implantation naive epiblast (EPI) cells and naive human embryonic stem cells (hESCs). Previous studies have shown that TFAP2C is required for establishing naive gene expression in these cell types, however the role of additional naive transcription factors in hPGC biology is not known. Here, we show that unlike TFAP2C, the naive transcription factors KLF4 and TFCP2L1 are not required for induction of hPGC-like cells (hPGCLCs) from hESCs, and they have no role in establishing and maintaining a naive-like gene expression program in hPGCLCs with extended time in culture. Taken together, our results suggest a model whereby the molecular mechanisms that drive naive gene expression in hPGCs/hPGCLCs are distinct from those in the naive EPI/hESCs.
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54
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Khan SA, Park KM, Fischer LA, Dong C, Lungjangwa T, Jimenez M, Casalena D, Chew B, Dietmann S, Auld DS, Jaenisch R, Theunissen TW. Probing the signaling requirements for naive human pluripotency by high-throughput chemical screening. Cell Rep 2021; 35:109233. [PMID: 34133938 PMCID: PMC8272458 DOI: 10.1016/j.celrep.2021.109233] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 03/25/2021] [Accepted: 05/19/2021] [Indexed: 01/04/2023] Open
Abstract
Naive human embryonic stem cells (hESCs) have been isolated that more closely resemble the pre-implantation epiblast compared to conventional “primed” hESCs, but the signaling principles underlying these discrete stem cell states remain incompletely understood. Here, we describe the results from a high-throughput screen using ~3,000 well-annotated compounds to identify essential signaling requirements for naive human pluripotency. We report that MEK1/2 inhibitors can be replaced during maintenance of naive human pluripotency by inhibitors targeting either upstream (FGFR, RAF) or downstream (ERK1/2) kinases. Naive hESCs maintained under these alternative conditions display elevated levels of ERK phosphorylation but retain genome-wide DNA hypomethylation and a transcriptional identity of the pre-implantation epiblast. In contrast, dual inhibition of MEK and ERK promotes efficient primed-to-naive resetting in combination with PKC, ROCK, and TNKS inhibitors and activin A. This work demonstrates that induction and maintenance of naive human pluripotency are governed by distinct signaling requirements. Khan et al. describe a high-throughput chemical screen to identify essential signaling requirements for naive human pluripotency in minimal conditions. They report that naive hESCs can be maintained by blocking distinct nodes in the FGF signaling pathway and that dual MEK/ERK inhibition promotes efficient primed-to-naive resetting in combination with activin A.
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Affiliation(s)
- Shafqat A Khan
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kyoung-Mi Park
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A Fischer
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chen Dong
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tenzin Lungjangwa
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Marta Jimenez
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Dominick Casalena
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Brian Chew
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sabine Dietmann
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Thorold W Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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55
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The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency. PLoS Genet 2021; 17:e1009587. [PMID: 34033652 PMCID: PMC8184003 DOI: 10.1371/journal.pgen.1009587] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/07/2021] [Accepted: 05/06/2021] [Indexed: 12/29/2022] Open
Abstract
Human pluripotent stem cells (PSCs) express human endogenous retrovirus type-H (HERV-H), which exists as more than a thousand copies on the human genome and frequently produces chimeric transcripts as long-non-coding RNAs (lncRNAs) fused with downstream neighbor genes. Previous studies showed that HERV-H expression is required for the maintenance of PSC identity, and aberrant HERV-H expression attenuates neural differentiation potentials, however, little is known about the actual of function of HERV-H. In this study, we focused on ESRG, which is known as a PSC-related HERV-H-driven lncRNA. The global transcriptome data of various tissues and cell lines and quantitative expression analysis of PSCs showed that ESRG expression is much higher than other HERV-Hs and tightly silenced after differentiation. However, the loss of function by the complete excision of the entire ESRG gene body using a CRISPR/Cas9 platform revealed that ESRG is dispensable for the maintenance of the primed and naïve pluripotent states. The loss of ESRG hardly affected the global gene expression of PSCs or the differentiation potential toward trilineage. Differentiated cells derived from ESRG-deficient PSCs retained the potential to be reprogrammed into induced PSCs (iPSCs) by the forced expression of OCT3/4, SOX2, and KLF4. In conclusion, ESRG is dispensable for the maintenance and recapturing of human pluripotency. We have been interested in the role of human endogenous retrovirus (HERVs) in human pluripotent stem cells (PSCs). Although we and others have demonstrated that HERV expression is crucial for somatic cell reprogramming to a pluripotent state and the characteristics of PSCs. Little is known which one of more than 1,000 copies of HERVs is important. Thus, in this study, we focused on a HERV-related gene, ESRG which is expressed strongly and specifically in human PSCs but not in differentiated cells. Using a CRISPR/Cas9 platform, we generated complete knockout cell lines by deleting the entire gene body of ESRG. Our results demonstrate that ESRG is dispensable for the PSC characters such as gene expression, self-renewing capacity, and differentiation potential. In addition, ESRG does not contribute to the reprogramming of differentiated cells to a pluripotent state. Altogether, we concluded that ESRG is an excellent marker of pluripotency but dispensable for the PSC identity.
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56
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Posfai E, Lanner F, Mulas C, Leitch HG. All models are wrong, but some are useful: Establishing standards for stem cell-based embryo models. Stem Cell Reports 2021; 16:1117-1141. [PMID: 33979598 PMCID: PMC8185978 DOI: 10.1016/j.stemcr.2021.03.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
Detailed studies of the embryo allow an increasingly mechanistic understanding of development, which has proved of profound relevance to human disease. The last decade has seen in vitro cultured stem cell-based models of embryo development flourish, which provide an alternative to the embryo for accessible experimentation. However, the usefulness of any stem cell-based embryo model will be determined by how accurately it reflects in vivo embryonic development, and/or the extent to which it facilitates new discoveries. Stringent benchmarking of embryo models is thus an important consideration for this growing field. Here we provide an overview of means to evaluate both the properties of stem cells, the building blocks of most embryo models, as well as the usefulness of current and future in vitro embryo models.
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Affiliation(s)
- Eszter Posfai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Fredrik Lanner
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden; Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden; Ming Wai Lau Center for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Carla Mulas
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Harry G Leitch
- MRC London Institute of Medical Sciences, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK; Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London W2 1PG, UK
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57
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Bayerl J, Ayyash M, Shani T, Manor YS, Gafni O, Massarwa R, Kalma Y, Aguilera-Castrejon A, Zerbib M, Amir H, Sheban D, Geula S, Mor N, Weinberger L, Naveh Tassa S, Krupalnik V, Oldak B, Livnat N, Tarazi S, Tawil S, Wildschutz E, Ashouokhi S, Lasman L, Rotter V, Hanna S, Ben-Yosef D, Novershtern N, Viukov S, Hanna JH. Principles of signaling pathway modulation for enhancing human naive pluripotency induction. Cell Stem Cell 2021; 28:1549-1565.e12. [PMID: 33915080 PMCID: PMC8423434 DOI: 10.1016/j.stem.2021.04.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 02/05/2021] [Accepted: 03/31/2021] [Indexed: 12/21/2022]
Abstract
Isolating human MEK/ERK signaling-independent pluripotent stem cells (PSCs) with naive pluripotency characteristics while maintaining differentiation competence and (epi)genetic integrity remains challenging. Here, we engineer reporter systems that allow the screening for defined conditions that induce molecular and functional features of human naive pluripotency. Synergistic inhibition of WNT/β-CATENIN, protein kinase C (PKC), and SRC signaling consolidates the induction of teratoma-competent naive human PSCs, with the capacity to differentiate into trophoblast stem cells (TSCs) and extraembryonic naive endodermal (nEND) cells in vitro. Divergent signaling and transcriptional requirements for boosting naive pluripotency were found between mouse and human. P53 depletion in naive hPSCs increased their contribution to mouse-human cross-species chimeric embryos upon priming and differentiation. Finally, MEK/ERK inhibition can be substituted with the inhibition of NOTCH/RBPj, which induces alternative naive-like hPSCs with a diminished risk for deleterious global DNA hypomethylation. Our findings set a framework for defining the signaling foundations of human naive pluripotency. Inhibition of SRC, PKC, and WNT consolidates human naive pluripotency induction Competitiveness of p53 depleted human PSCs in cross-species chimeric embryos Opposing net effect for ACTIVIN and WNT on mouse versus human naive pluripotency 2i and ERKi independent alternative human naive-like PSC conditions
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Affiliation(s)
- Jonathan Bayerl
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Muneef Ayyash
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tom Shani
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yair Shlomo Manor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ohad Gafni
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rada Massarwa
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yael Kalma
- Wolfe PGD‑Stem Cell Laboratory, Racine IVF Unit, Lis Maternity Hospital, Tel-Aviv Sourasky Medical Center, Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel‑Aviv, Israel
| | | | - Mirie Zerbib
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hadar Amir
- Wolfe PGD‑Stem Cell Laboratory, Racine IVF Unit, Lis Maternity Hospital, Tel-Aviv Sourasky Medical Center, Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel‑Aviv, Israel
| | - Daoud Sheban
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shay Geula
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nofar Mor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Leehee Weinberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Segev Naveh Tassa
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Vladislav Krupalnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Bernardo Oldak
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nir Livnat
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shadi Tarazi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shadi Tawil
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Emilie Wildschutz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shahd Ashouokhi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lior Lasman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Varda Rotter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Suhair Hanna
- Department of Pediatrics, Rambam Hospital, Haifa, Israel
| | - Dalit Ben-Yosef
- Wolfe PGD‑Stem Cell Laboratory, Racine IVF Unit, Lis Maternity Hospital, Tel-Aviv Sourasky Medical Center, Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel‑Aviv, Israel.
| | - Noa Novershtern
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Sergey Viukov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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58
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Ghosh A, Som A. Decoding molecular markers and transcriptional circuitry of naive and primed states of human pluripotency. Stem Cell Res 2021; 53:102334. [PMID: 33862536 DOI: 10.1016/j.scr.2021.102334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 03/22/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022] Open
Abstract
Pluripotent stem cells (PSCs) have been observed to occur in two distinct states - naive and primed. Both naive and primed state PSCs can give rise to tissues of all the three germ layers in vitro but differ in their potential to generate germline chimera in vivo. Understanding the molecular mechanisms that govern these two states of pluripotency in human can open a plethora of opportunities for studying early embryonic development and in biomedical applications. In this work, we use weighted gene co-expression network analysis (WGCNA) to identify the key molecular makers and their interactions that define the two distinct pluripotency states. Signed hybrid network was reconstructed from transcriptomic data (RNA-seq) of naive and primed state pluripotent samples. Our analysis revealed two sets of genes that are involved in the establishment and maintenance of naive and primed states. The naive state genes were found to be enriched for biological processes and pathways related to metabolic processes while primed state genes were associated with system development. We further filtered these lists to identify the intra-modular hubs and the hub transcription factors (TFs) for each group. Validation of the identified TFs was carried out using independent microarray datasets and we finally present a list of 52 and 33 TFs as the set of core TFs that are responsible for the induction and maintenance of naive and primed states of pluripotency in human, respectively. Among these, the TFs ZNF275, ZNF232, SP4, and MSANTD3 could be of interest as they were not reported in previous studies.
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Affiliation(s)
- Arindam Ghosh
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj 211002, India; Institute of Biomedicine, University of Eastern Finland, FI-70210 Kuopio, Finland
| | - Anup Som
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj 211002, India.
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59
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Cao H, Huang H, Tang H. Zbtb7a and Zbtb7b: Opening naïve loci to reprogram ESCs. Biosci Trends 2021; 15:58-60. [PMID: 33627571 DOI: 10.5582/bst.2020.03429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Bone morphogenetic protein 4 (BMP4) was recently reported to confer reprogramming capability to embryonic stem cells (ESCs) by reactivating naïve pluripotency genes via Zbtb7a and Zbtb7b. A visual reporting system was developed to first identify BMP4 as a driver for the primed-to-naïve transition (PNT). In addition, two specific inhibitors were identified as significantly improving the efficiency of PNT (~80% transition) within 8 days. The Zbtb7 family members were first introduced in the context of PNT and stem cell fate decision-making. These findings provide valuable information on acquiring naïve pluripotent stem cells for regenerative medicine.
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Affiliation(s)
- Hua Cao
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Hong Huang
- Institute of Cardiovascular Disease, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China.,Institute of Clinical Medicine, The First Affiliated Hospital of University of South China, Hengyang, Hunan Province, China
| | - Huifang Tang
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China.,Institute of Cardiovascular Disease, The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
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60
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Semi K, Takashima Y. Pluripotent stem cells for the study of early human embryology. Dev Growth Differ 2021; 63:104-115. [PMID: 33570781 PMCID: PMC8251740 DOI: 10.1111/dgd.12715] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Forty years have passed since the first pluripotent stem cells (PSCs), mouse embryonic stem cells (ESCs), were established. Since then, several PSCs have been reported, including human ESCs in 1998, mouse epiblast stem cells (EpiSCs) in 2007, induced PSCs (iPSCs) in 2006 and 2007, and naïve human PSCs in 2014. Naïve PSCs are thought to correspond to pre-implantation epiblast cells, whereas conventional (or primed) human PSCs correspond to post-implantation epiblast cells. Thus, naïve and primed PSCs are classified by their developmental stages and have stage-specific characteristics, despite sharing the common feature of pluripotency. In this review, we discuss the current status of PSCs and their use to model human peri-implantation development.
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Affiliation(s)
- Katsunori Semi
- Center for iPS Cell Research and ApplicationKyoto UniversityKyotoJapan
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61
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DGK and DZHK position paper on genome editing: basic science applications and future perspective. Basic Res Cardiol 2021; 116:2. [PMID: 33449167 PMCID: PMC7810637 DOI: 10.1007/s00395-020-00839-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022]
Abstract
For a long time, gene editing had been a scientific concept, which was limited to a few applications. With recent developments, following the discovery of TALEN zinc-finger endonucleases and in particular the CRISPR/Cas system, gene editing has become a technique applicable in most laboratories. The current gain- and loss-of function models in basic science are revolutionary as they allow unbiased screens of unprecedented depth and complexity and rapid development of transgenic animals. Modifications of CRISPR/Cas have been developed to precisely interrogate epigenetic regulation or to visualize DNA complexes. Moreover, gene editing as a clinical treatment option is rapidly developing with first trials on the way. This article reviews the most recent progress in the field, covering expert opinions gathered during joint conferences on genome editing of the German Cardiac Society (DGK) and the German Center for Cardiovascular Research (DZHK). Particularly focusing on the translational aspect and the combination of cellular and animal applications, the authors aim to provide direction for the development of the field and the most frequent applications with their problems.
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62
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SETDB1-Mediated Cell Fate Transition between 2C-Like and Pluripotent States. Cell Rep 2021; 30:25-36.e6. [PMID: 31914391 DOI: 10.1016/j.celrep.2019.12.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/29/2019] [Accepted: 12/03/2019] [Indexed: 12/17/2022] Open
Abstract
Known as a histone H3K9 methyltransferase, SETDB1 is essential for embryonic development and pluripotent inner cell mass (ICM) establishment. However, its function in pluripotency regulation remains elusive. In this study, we find that under the "ground state" of pluripotency with two inhibitors (2i) of the MEK and GSK3 pathways, Setdb1-knockout fails to induce trophectoderm (TE) differentiation as in serum/LIF (SL), indicating that TE fate restriction is not the direct target of SETDB1. In both conditions, Setdb1-knockout activates a group of genes targeted by SETDB1-mediated H3K9 methylation, including Dux. Notably, Dux is indispensable for the reactivation of 2C-like state genes upon Setdb1 deficiency, delineating the mechanistic role of SETDB1 in totipotency restriction. Furthermore, Setdb1-null ESCs maintain pluripotent marker (e.g., Nanog) expression in the 2i condition. This "ground state" Setdb1-null population undergoes rapid cell death by activating Ripk3 and, subsequently, RIPK1/RIPK3-dependent necroptosis. These results reveal the essential role of Setdb1 between totipotency and pluripotency transition.
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63
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Panda A, Zylicz JJ, Pasque V. New Insights into X-Chromosome Reactivation during Reprogramming to Pluripotency. Cells 2020; 9:E2706. [PMID: 33348832 PMCID: PMC7766869 DOI: 10.3390/cells9122706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Dosage compensation between the sexes results in one X chromosome being inactivated during female mammalian development. Chromosome-wide transcriptional silencing from the inactive X chromosome (Xi) in mammalian cells is erased in a process termed X-chromosome reactivation (XCR), which has emerged as a paradigm for studying the reversal of chromatin silencing. XCR is linked with germline development and induction of naive pluripotency in the epiblast, and also takes place upon reprogramming somatic cells to induced pluripotency. XCR depends on silencing of the long non-coding RNA (lncRNA) X inactive specific transcript (Xist) and is linked with the erasure of chromatin silencing. Over the past years, the advent of transcriptomics and epigenomics has provided new insights into the transcriptional and chromatin dynamics with which XCR takes place. However, multiple questions remain unanswered about how chromatin and transcription related processes enable XCR. Here, we review recent work on establishing the transcriptional and chromatin kinetics of XCR, as well as discuss a model by which transcription factors mediate XCR not only via Xist repression, but also by direct targeting of X-linked genes.
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Affiliation(s)
- Amitesh Panda
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
| | - Jan J. Zylicz
- The Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Vincent Pasque
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
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Wu L, Zhao G, Xu S, Kuang J, Ming J, Wu G, Wang T, Wang B, Zhu P, Pei D, Liu J. The nuclear factor CECR2 promotes somatic cell reprogramming by reorganizing the chromatin structure. J Biol Chem 2020; 296:100022. [PMID: 33144328 PMCID: PMC7948406 DOI: 10.1074/jbc.ra120.014598] [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: 05/28/2020] [Revised: 10/22/2020] [Accepted: 11/03/2020] [Indexed: 11/24/2022] Open
Abstract
Somatic cells can be reprogrammed into pluripotent stem cells with a minimal set of defined factors, Oct3/4, Sox2, Klf4, and c-Myc, also known as OKSM, although this reprogramming is somewhat inefficient. Recent work has identified other nuclear factors, including SALL4, that can synergize with the OSK factors to improve reprogramming dynamics, but the specific role of each of these factors remains poorly understood. In this study, we sought to learn more about the role of SALL4. We observed that SALL4 was the most significant factor in promoting OKS-induced reprogramming. To look for molecules downstream of SALL4, we screened a set of putative targets to determine whether they could promote OKS-induced reprogramming. We identified CECR2, a multidomain nuclear factor and histone acetyl-lysine reader, as a SALL4 effector. Mechanistically, we determined that SALL4 activates Cecr2 expression by directly binding to its promotor region. CECR2 in turn promotes reprogramming by forming a chromatin remodeling complex; this complex contained the SWI/SNF family member SMARCA1 and was dependent on CECR2’s DTT domain. In combination, our findings suggest that CECR2 is a novel reprogramming factor and works through a protein network to overcome epigenetic barriers during reprogramming.
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Affiliation(s)
- Linlin Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, China; CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Guoqing Zhao
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Joint School of Life Science, Guangzhou Medical University-Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Shuyang Xu
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Junqi Kuang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Science, Beijing, China
| | - Jin Ming
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Science, Beijing, China
| | - Guangmin Wu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Tao Wang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Bo Wang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
| | - Jing Liu
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic and Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
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65
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B3GALT5 knockout alters gycosphingolipid profile and facilitates transition to human naïve pluripotency. Proc Natl Acad Sci U S A 2020; 117:27435-27444. [PMID: 33087559 PMCID: PMC7959494 DOI: 10.1073/pnas.2003155117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
These studies provide systematically characterized glycosphingolipid (GSL) profiles and expression level of glycosyltransferase upon the conversion of human ESCs from primed to naïve state. We identify a switch of GSL profile from globo- and lacto-series to neolacto-series GSLs, accompanied by the downregulation of β-1,3-galactosyltransferase (B3GALT5) during the pluripotency transition. The CRISPR/Cas9-generated B3GALT5 knockout increases the level of intracellular Ca2+, resulting in an intermediate state of pluripotency, which facilitates the primed- to naïve-state transition in human ESCs. In addition, the altered GSL could be rescued through overexpression of B3GALT5. Thus, our results provide a new perspective in the understanding of human pluripotency transition from primed to naïve state, which can be facilitated by changing the expression of single glycosyltransferase, B3GALT5. Conversion of human pluripotent stem cells from primed to naïve state is accompanied by altered transcriptome and methylome, but glycosphingolipid (GSL) profiles in naïve human embryonic stem cells (hESCs) have not been systematically characterized. Here we showed a switch from globo-(SSEA-3, SSEA-4, and Globo H) and lacto-series (fucosyl-Lc4Cer) to neolacto-series GSLs (SSEA-1 and H type 2 antigen), along with marked down-regulation of β-1,3-galactosyltransferase (B3GALT5) upon conversion to naïve state. CRISPR/Cas9-generated B3GALT5-knockout (KO) hESCs displayed an altered GSL profile, increased cloning efficiency and intracellular Ca2+, reminiscent of the naïve state, while retaining differentiation ability. The altered GSLs could be rescued through overexpression of B3GALT5. B3GALT5-KO cells cultured with 2iLAF exhibited naïve-like transcriptome, global DNA hypomethylation, and X-chromosome reactivation. In addition, B3GALT5-KO rendered hESCs more resistant to calcium chelator in blocking entry into naïve state. Thus, loss of B3GALT5 induces a distinctive state of hESCs displaying unique GSL profiling with expression of neolacto-glycans, increased Ca2+, and conducive for transition to naïve pluripotency.
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66
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Rohani L, Borys BS, Razian G, Naghsh P, Liu S, Johnson AA, Machiraju P, Holland H, Lewis IA, Groves RA, Toms D, Gordon PMK, Li JW, So T, Dang T, Kallos MS, Rancourt DE. Stirred suspension bioreactors maintain naïve pluripotency of human pluripotent stem cells. Commun Biol 2020; 3:492. [PMID: 32895477 PMCID: PMC7476926 DOI: 10.1038/s42003-020-01218-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/03/2020] [Indexed: 11/11/2022] Open
Abstract
Due to their ability to standardize key physiological parameters, stirred suspension bioreactors can potentially scale the production of quality-controlled pluripotent stem cells (PSCs) for cell therapy application. Because of differences in bioreactor expansion efficiency between mouse (m) and human (h) PSCs, we investigated if conversion of hPSCs, from the conventional "primed" pluripotent state towards the "naïve" state prevalent in mPSCs, could be used to enhance hPSC production. Through transcriptomic enrichment of mechano-sensing signaling, the expression of epigenetic regulators, metabolomics, and cell-surface protein marker analyses, we show that the stirred suspension bioreactor environment helps maintain a naïve-like pluripotent state. Our research corroborates that converting hPSCs towards a naïve state enhances hPSC manufacturing and indicates a potentially important role for the stirred suspension bioreactor's mechanical environment in maintaining naïve-like pluripotency.
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Affiliation(s)
- Leili Rohani
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Breanna S Borys
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, Calgary, AB, Canada
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, Canada
| | - Golsa Razian
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Pooyan Naghsh
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Shiying Liu
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Pranav Machiraju
- Department of Paediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Heidrun Holland
- Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Ryan A Groves
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Derek Toms
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Paul M K Gordon
- CSM Center for Health Genomic and Informatics, University of Calgary, Calgary, AB, Canada
| | - Joyce W Li
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Tania So
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, Calgary, AB, Canada
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, Canada
| | - Tiffany Dang
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, Calgary, AB, Canada
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, Canada
| | - Michael S Kallos
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, Calgary, AB, Canada
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, Canada
| | - Derrick E Rancourt
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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67
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An C, Feng G, Zhang J, Cao S, Wang Y, Wang N, Lu F, Zhou Q, Wang H. Overcoming Autocrine FGF Signaling-Induced Heterogeneity in Naive Human ESCs Enables Modeling of Random X Chromosome Inactivation. Cell Stem Cell 2020; 27:482-497.e4. [DOI: 10.1016/j.stem.2020.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/27/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
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68
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Abstract
Human pluripotent stem cells harbor the capacity to differentiate into cells from the three embryonic germ layers, and this ability grants them a central role in modeling human disorders and in the field of regenerative medicine. Here, we review pluripotency in human cells with respect to four different aspects: (1) embryonic development, (2) transcriptomes of pluripotent cell stages, (3) genes and pathways that reprogram somatic cells into pluripotent stem cells, and finally (4) the recent identification of the human pluripotent stem cell essentialome. These four aspects of pluripotency collectively culminate in a broader understanding of what makes a cell pluripotent.
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69
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Dodsworth BT, Hatje K, Rostovskaya M, Flynn R, Meyer CA, Cowley SA. Profiling of naïve and primed human pluripotent stem cells reveals state-associated miRNAs. Sci Rep 2020; 10:10542. [PMID: 32601281 PMCID: PMC7324611 DOI: 10.1038/s41598-020-67376-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/08/2020] [Indexed: 12/11/2022] Open
Abstract
Naïve human pluripotent stem cells (hPSC) resemble the embryonic epiblast at an earlier time-point in development than conventional, 'primed' hPSC. We present a comprehensive miRNA profiling of naïve-to-primed transition in hPSC, a process recapitulating aspects of early in vivo embryogenesis. We identify miR-143-3p and miR-22-3p as markers of the naïve state and miR-363-5p, several members of the miR-17 family, miR-302 family as primed markers. We uncover that miR-371-373 are highly expressed in naïve hPSC. MiR-371-373 are the human homologs of the mouse miR-290 family, which are the most highly expressed miRNAs in naïve mouse PSC. This aligns with the consensus that naïve hPSC resemble mouse naive PSC, showing that the absence of miR-371-373 in conventional hPSC is due to cell state rather than a species difference.
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Affiliation(s)
- Benjamin T Dodsworth
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Klas Hatje
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | | | - Rowan Flynn
- Censo Biotechnologies, Roslin Innovation Centre Charnock Bradley Building, Easter Bush Campus, Roslin, EH25 9RG, UK
| | - Claas A Meyer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Sally A Cowley
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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70
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Ma Z, Li Y, Zhang Y, Chen J, Tan T, Fan Y. A lncRNA-miRNA-mRNA network for human primed, naive and extended pluripotent stem cells. PLoS One 2020; 15:e0234628. [PMID: 32544168 PMCID: PMC7297305 DOI: 10.1371/journal.pone.0234628] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 05/30/2020] [Indexed: 11/19/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) represent a promising platform for studying embryonic development, and different states of pluripotency reflect the different stages of embryo development. Here, we successfully converted three in-house-derived primed hPSC lines (H10, H24, and iPS) to a naive state and an expanded pluripotent stem cell (EPS) state. Primed, naive and EPS cells displayed state-specific morphologies and expressed pluripotent markers. The expression of SSEA4 and TRA-1-60 was downregulated in the conversion process. The H3K27me3 expression level also decreased, indicating that global methylation was reduced and that the X chromosome started to reactivate. RNA-sequencing analysis results revealed that differentially expressed genes (DEGs) were significantly enriched in both naive hPSCs and EPS cells when compared to the primed state. However, imprinted gene expression barely changed before and after state reversion. Gene ontology (GO) analyses showed that the upregulated DEGs were mostly enriched in RNA processing, DNA replication and repair, and regulation of cell cycle process, while downregulated DEGs were related to extracellular adhesion and various tissue developmental processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that EPS cells were enriched in the PI3K-Akt and Wnt signaling pathways. Analysis of the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network between primed, naive hPSCs and EPS cells revealed that hsa-miR-424-5p, has-miR-16-5p, has-miR-27b-3p, has-miR-29c-3p, and KCNQ1OT1 were crucial nodes with high degrees of connectivity. Our work may represent new insight into the intrinsic molecular features of different hPSC states.
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Affiliation(s)
- Zhenglai Ma
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanni Li
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yingying Zhang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiaxin Chen
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tao Tan
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- * E-mail: (YF); (TT)
| | - Yong Fan
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- * E-mail: (YF); (TT)
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71
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Dodsworth BT, Hatje K, Meyer CA, Flynn R, Cowley SA. Rates of homology directed repair of CRISPR-Cas9 induced double strand breaks are lower in naïve compared to primed human pluripotent stem cells. Stem Cell Res 2020; 46:101852. [PMID: 32521498 PMCID: PMC7347009 DOI: 10.1016/j.scr.2020.101852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 02/14/2020] [Accepted: 05/20/2020] [Indexed: 11/21/2022] Open
Abstract
Kinetics of Cas9-induced double strand break repair in conventional hPSC. Homology directed repair to resolve Cas9-induced double strand breaks is 40% lower in naïve hPSC compared to conventional hPSC. Naïve hPSC (4iLA) have a higher number of cells in G1 phase of the cell cycle.
Gene editing in human pluripotent stem cells (hPSC) is a powerful tool for understanding biology, for drug discovery and gene therapy. Naïve hPSC have been suggested to be superior for gene editing compared to conventional ‘primed’ hPSC. Using droplet digital PCR, we uncover the kinetics of Cas9-induced double strand break repair in conventional hPSC. Cut but unrepaired alleles reach their maximum after 12–24 h. Homology directed repair plateaus after 24 h, whereas repair by non-homologous end joining continues until 48 h after Cas9 introduction. Using this method, we demonstrate that the rate of homology directed repair to resolve Cas9-induced double strand breaks is 40% lower in naïve hPSC compared to conventional hPSC, correlating with, and feasibly explained by, a higher number of cells in G1 phase of the cell cycle in naïve hPSC. Therefore, naïve hPSC are less efficient for CRISPR/Cas9-mediated homology directed repair.
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Affiliation(s)
- Benjamin T Dodsworth
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, United Kingdom; Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Klas Hatje
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Claas Aiko Meyer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Rowan Flynn
- Censo Biotechnologies, Roslin Innovation Centre Charnock Bradley Building, Easter Bush Campus EH25 9RG, United Kingdom
| | - Sally A Cowley
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, United Kingdom.
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72
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Yu S, Zhou C, Cao S, He J, Cai B, Wu K, Qin Y, Huang X, Xiao L, Ye J, Xu S, Xie W, Kuang J, Chu S, Guo J, Liu H, Pang W, Guo L, Zeng M, Wang X, Luo R, Li C, Zhao G, Wang B, Wu L, Chen J, Liu J, Pei D. BMP4 resets mouse epiblast stem cells to naive pluripotency through ZBTB7A/B-mediated chromatin remodelling. Nat Cell Biol 2020; 22:651-662. [PMID: 32393886 DOI: 10.1038/s41556-020-0516-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 04/03/2020] [Indexed: 01/09/2023]
Abstract
BMP4 regulates a plethora of developmental processes, including the dorsal-ventral axis and neural patterning. Here, we report that BMP4 reconfigures the nuclear architecture during the primed-to-naive transition (PNT). We first established a BMP4-driven PNT and show that BMP4 orchestrates the chromatin accessibility dynamics during PNT. Among the loci opened early by BMP4, we identified Zbtb7a and Zbtb7b (Zbtb7a/b) as targets that drive PNT. ZBTB7A/B in turn facilitate the opening of naive pluripotent chromatin loci and the activation of nearby genes. Mechanistically, ZBTB7A not only binds to chromatin loci near to the genes that are activated, but also strategically occupies those that are silenced, consistent with a role of BMP4 in both activating and suppressing gene expression during PNT at the chromatin level. Our results reveal a previously unknown function of BMP4 in regulating nuclear architecture and link its targets ZBTB7A/B to chromatin remodelling and pluripotent fate control.
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Affiliation(s)
- Shengyong Yu
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Chunhua Zhou
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Shangtao Cao
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Jiangping He
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Baomei Cai
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Kaixin Wu
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Yue Qin
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Xingnan Huang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangzhou Branch of the Supercomputing Center, Chinese Academy of Sciences, Guangzhou, China
| | - Lizhan Xiao
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jing Ye
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Shuyang Xu
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Wenxiu Xie
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Junqi Kuang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Shilong Chu
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Jing Guo
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - He Liu
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Wei Pang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Lin Guo
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Mengying Zeng
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Xiaoshan Wang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.,Guangzhou Branch of the Supercomputing Center, Chinese Academy of Sciences, Guangzhou, China
| | - Rongping Luo
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Chen Li
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Guoqing Zhao
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.,Laboratory of Regenerative Biology, Joint School of Life Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, China
| | - Bo Wang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Linlin Wu
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.,Guangzhou Branch of the Supercomputing Center, Chinese Academy of Sciences, Guangzhou, China.,Laboratory of Regenerative Biology, Joint School of Life Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, China
| | - Jing Liu
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. .,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China. .,Guangzhou Branch of the Supercomputing Center, Chinese Academy of Sciences, Guangzhou, China. .,Laboratory of Regenerative Biology, Joint School of Life Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, China.
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. .,Center for Cell Fate and Lineage, Division of Basic Research and International Corporation, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China. .,Guangzhou Branch of the Supercomputing Center, Chinese Academy of Sciences, Guangzhou, China. .,Laboratory of Regenerative Biology, Joint School of Life Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, China.
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73
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Wojdyla K, Collier AJ, Fabian C, Nisi PS, Biggins L, Oxley D, Rugg-Gunn PJ. Cell-Surface Proteomics Identifies Differences in Signaling and Adhesion Protein Expression between Naive and Primed Human Pluripotent Stem Cells. Stem Cell Reports 2020; 14:972-988. [PMID: 32302559 PMCID: PMC7220956 DOI: 10.1016/j.stemcr.2020.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022] Open
Abstract
Naive and primed human pluripotent stem cells (hPSC) provide valuable models to study cellular and molecular developmental processes. The lack of detailed information about cell-surface protein expression in these two pluripotent cell types prevents an understanding of how the cells communicate and interact with their microenvironments. Here, we used plasma membrane profiling to directly measure cell-surface protein expression in naive and primed hPSC. This unbiased approach quantified over 1,700 plasma membrane proteins, including those involved in cell adhesion, signaling, and cell interactions. Notably, multiple cytokine receptors upstream of JAK-STAT signaling were more abundant in naive hPSC. In addition, functional experiments showed that FOLR1 and SUSD2 proteins are highly expressed at the cell surface in naive hPSC but are not required to establish human naive pluripotency. This study provides a comprehensive stem cell proteomic resource that uncovers differences in signaling pathway activity and has identified new markers to define human pluripotent states.
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Affiliation(s)
- Katarzyna Wojdyla
- Epigenetics Programme, The Babraham Institute, Cambridge, UK; Mass Spectrometry Facility, The Babraham Institute, Cambridge, UK
| | | | - Charlene Fabian
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Paola S Nisi
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Laura Biggins
- Bioinformatics Group, The Babraham Institute, Cambridge, UK
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, UK; Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
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74
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Identification of cell surface markers and establishment of monolayer differentiation to retinal pigment epithelial cells. Nat Commun 2020; 11:1609. [PMID: 32231223 PMCID: PMC7105463 DOI: 10.1038/s41467-020-15326-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 02/27/2020] [Indexed: 11/29/2022] Open
Abstract
In vitro differentiation of human pluripotent stem cells into functional retinal pigment epithelial (RPE) cells provides a potentially unlimited source for cell based reparative therapy of age-related macular degeneration. Although the inherent pigmentation of the RPE cells have been useful to grossly evaluate differentiation efficiency and allowed manual isolation of pigmented structures, accurate quantification and automated isolation has been challenging. To address this issue, here we perform a comprehensive antibody screening and identify cell surface markers for RPE cells. We show that these markers can be used to isolate RPE cells during in vitro differentiation and to track, quantify and improve differentiation efficiency. Finally, these surface markers aided to develop a robust, direct and scalable monolayer differentiation protocol on human recombinant laminin-111 and −521 without the need for manual isolation. Whilst pigmentation has been used to identify retinal pigment epithelial (RPE) cells, surface markers for these cells remain unclear. Here, the authors define surface markers for the RPE including CD140b, which help produce hPSC-derived RPE cells at a large scale following a robust, direct and scalable monolayer differentiation protocol.
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75
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Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution. Cell Rep 2020; 26:815-824.e4. [PMID: 30673604 PMCID: PMC6344340 DOI: 10.1016/j.celrep.2018.12.099] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/26/2018] [Accepted: 12/26/2018] [Indexed: 12/26/2022] Open
Abstract
Conventional human embryonic stem cells are considered to be primed pluripotent but can be induced to enter a naive state. However, the transcriptional features associated with naive and primed pluripotency are still not fully understood. Here we used single-cell RNA sequencing to characterize the differences between these conditions. We observed that both naive and primed populations were mostly homogeneous with no clear lineage-related structure and identified an intermediate subpopulation of naive cells with primed-like expression. We found that the naive-primed pluripotency axis is preserved across species, although the timing of the transition to a primed state is species specific. We also identified markers for distinguishing human naive and primed pluripotency as well as strong co-regulatory relationships between lineage markers and epigenetic regulators that were exclusive to naive cells. Our data provide valuable insights into the transcriptional landscape of human pluripotency at a cellular and genome-wide resolution. A single-cell RNA-seq resource of naive and primed human embryonic stem cells (hESCs) Naive and primed hESCs are homogeneous except for a naive intermediate subpopulation Naive and primed pluripotency signatures are conserved between species Pluripotency and lineage markers correlate with epigenetic machinery in naive hESCs
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76
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Bi Y, Tu Z, Zhang Y, Yang P, Guo M, Zhu X, Zhao C, Zhou J, Wang H, Wang Y, Gao S. Identification of ALPPL2 as a Naive Pluripotent State-Specific Surface Protein Essential for Human Naive Pluripotency Regulation. Cell Rep 2020; 30:3917-3931.e5. [DOI: 10.1016/j.celrep.2020.02.090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/28/2019] [Accepted: 02/25/2020] [Indexed: 10/24/2022] Open
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77
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Dong C, Beltcheva M, Gontarz P, Zhang B, Popli P, Fischer LA, Khan SA, Park KM, Yoon EJ, Xing X, Kommagani R, Wang T, Solnica-Krezel L, Theunissen TW. Derivation of trophoblast stem cells from naïve human pluripotent stem cells. eLife 2020; 9:e52504. [PMID: 32048992 PMCID: PMC7062471 DOI: 10.7554/elife.52504] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 02/11/2020] [Indexed: 12/24/2022] Open
Abstract
Naïve human pluripotent stem cells (hPSCs) provide a unique experimental platform of cell fate decisions during pre-implantation development, but their lineage potential remains incompletely characterized. As naïve hPSCs share transcriptional and epigenomic signatures with trophoblast cells, it has been proposed that the naïve state may have enhanced predisposition for differentiation along this extraembryonic lineage. Here we examined the trophoblast potential of isogenic naïve and primed hPSCs. We found that naïve hPSCs can directly give rise to human trophoblast stem cells (hTSCs) and undergo further differentiation into both extravillous and syncytiotrophoblast. In contrast, primed hPSCs do not support hTSC derivation, but give rise to non-self-renewing cytotrophoblasts in response to BMP4. Global transcriptome and chromatin accessibility analyses indicate that hTSCs derived from naïve hPSCs are similar to blastocyst-derived hTSCs and acquire features of post-implantation trophectoderm. The derivation of hTSCs from naïve hPSCs will enable elucidation of early mechanisms that govern normal human trophoblast development and associated pathologies.
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Affiliation(s)
- Chen Dong
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Mariana Beltcheva
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Paul Gontarz
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Pooja Popli
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of MedicineSt. LouisUnited States
| | - Laura A Fischer
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Shafqat A Khan
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Kyoung-mi Park
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Eun-Ja Yoon
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Xiaoyun Xing
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
- Department of Genetics, Center for Genome Sciences & Systems Biology, Washington University School of MedicineSt. LouisUnited States
| | - Ramakrishna Kommagani
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of MedicineSt. LouisUnited States
| | - Ting Wang
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
- Department of Genetics, Center for Genome Sciences & Systems Biology, Washington University School of MedicineSt. LouisUnited States
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Thorold W Theunissen
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Center of Regenerative Medicine, Washington University School of MedicineSt. LouisUnited States
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78
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Goodwin J, Laslett AL, Rugg-Gunn PJ. The application of cell surface markers to demarcate distinct human pluripotent states. Exp Cell Res 2020; 387:111749. [PMID: 31790696 PMCID: PMC6983944 DOI: 10.1016/j.yexcr.2019.111749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/17/2019] [Accepted: 11/27/2019] [Indexed: 01/24/2023]
Abstract
Recent advances in human pluripotent stem cell (hPSC) research have uncovered different subpopulations within stem cell cultures and have captured a range of pluripotent states that hold distinct molecular and functional properties. At the two ends of the pluripotency spectrum are naïve and primed hPSC, whereby naïve hPSC grown in stringent conditions recapitulate features of the preimplantation human embryo, and the conventionally grown primed hPSC align closer to the early postimplantation embryo. Investigating these cell types will help to define the mechanisms that control early development and should provide new insights into stem cell properties such as cell identity, differentiation and reprogramming. Monitoring cell surface marker expression provides a valuable approach to resolve complex cell populations, to directly compare between cell types, and to isolate viable cells for functional experiments. This review discusses the discovery and applications of cell surface markers to study human pluripotent cell types with a particular focus on the transitions between naïve and primed states. Highlighted areas for future study include the potential functions for the identified cell surface proteins in pluripotency, the production of new high-quality monoclonal antibodies to naïve-specific protein epitopes and the use of cell surface markers to characterise subpopulations within pluripotent states.
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Affiliation(s)
- Jacob Goodwin
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Andrew L Laslett
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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79
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Song B, Lee JM, Park YJ, Kim IK, Kim BS, Shin KS, Jeon I, Koh CH, Bae EA, Seo H, Byun Y, Kang CY. Differentiation of c-Kit + CD24 + natural killer cells into myeloid cells in a GATA-2-dependent manner. FASEB J 2020; 34:4462-4481. [PMID: 31989715 DOI: 10.1096/fj.201902662r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/26/2019] [Accepted: 01/14/2020] [Indexed: 01/09/2023]
Abstract
Myeloid progenitor cells have generally been considered the predominant source of myeloid cells under steady-state conditions. Here we show that NK cells contributed to a myeloid cell lineage pool in naïve and tumor-bearing mice. Using fate tracing of NKp46+ cells, we found that myeloid cells could be derived from NK cells. Notably, among mature CD11b+ CD27+ NK cells, c-Kit+ CD24+ NK cells were capable of differentiating into a range of myeloid lineages in vitro and produced neutrophils and monocytes in vivo. The differentiation was completely inhibited by NK-stimulating cytokines. In addition to the potential for differentiation into myeloid cells, c-Kit+ CD24+ NK cells retained NK cell phenotypes and effector functions. Mechanistically, GATA-2 was necessary for the differentiation of c-Kit+ CD24+ NK cells. Therefore, we discovered that GATA-2-dependent differentiation of c-Kit+ CD24+ NK cells contributes to myeloid cell development and identified a novel pathway for myeloid lineage commitment under physiological conditions.
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Affiliation(s)
- Boyeong Song
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Jeong-Mi Lee
- Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Young-Jun Park
- Laboratory of Immune Regulation, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Il-Kyu Kim
- Laboratory of Immunology, Research Institute of Pharmaceutical Science, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Byung-Seok Kim
- Laboratory of Immune Regulation, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Kwang-Soo Shin
- Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Insu Jeon
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Choong-Hyun Koh
- Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Eun-Ah Bae
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Hyungseok Seo
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea.,Laboratory of Immunology, Research Institute of Pharmaceutical Science, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Youngro Byun
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Chang-Yuil Kang
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea.,Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
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80
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GP130 signaling and the control of naïve pluripotency in humans, monkeys, and pigs. Exp Cell Res 2020; 386:111712. [DOI: 10.1016/j.yexcr.2019.111712] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 12/19/2022]
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81
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McKee C, Brown C, Chaudhry GR. Self-Assembling Scaffolds Supported Long-Term Growth of Human Primed Embryonic Stem Cells and Upregulated Core and Naïve Pluripotent Markers. Cells 2019; 8:cells8121650. [PMID: 31888235 PMCID: PMC6952907 DOI: 10.3390/cells8121650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/13/2019] [Accepted: 12/14/2019] [Indexed: 12/14/2022] Open
Abstract
The maintenance and expansion of human embryonic stem cells (ESCs) in two-dimensional (2-D) culture is technically challenging, requiring routine manipulation and passaging. We developed three-dimensional (3-D) scaffolds to mimic the in vivo microenvironment for stem cell proliferation. The scaffolds were made of two 8-arm polyethylene glycol (PEG) polymers functionalized with thiol (PEG-8-SH) and acrylate (PEG-8-Acr) end groups, which self-assembled via a Michael addition reaction. When primed ESCs (H9 cells) were mixed with PEG polymers, they were encapsulated and grew for an extended period, while maintaining their viability, self-renewal, and differentiation potential both in vitro and in vivo. Three-dimensional (3-D) self-assembling scaffold-grown cells displayed an upregulation of core pluripotency genes, OCT4, NANOG, and SOX2. In addition, the expression of primed markers decreased, while the expression of naïve markers substantially increased. Interestingly, the expression of mechanosensitive genes, YAP and TAZ, was also upregulated. YAP inhibition by Verteporfin abrogated the increased expression of YAP/TAZ as well as core and naïve pluripotent markers. Evidently, the 3-D culture conditions induced the upregulation of makers associated with a naïve state of pluripotency in the primed cells. Overall, our 3-D culture system supported the expansion of a homogenous population of ESCs and should be helpful in advancing their use for cell therapy and regenerative medicine.
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Affiliation(s)
- Christina McKee
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - Christina Brown
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - G. Rasul Chaudhry
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
- Correspondence: ; Tel.: +1-248-370-3350
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82
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Dong C, Fischer LA, Theunissen TW. Recent insights into the naïve state of human pluripotency and its applications. Exp Cell Res 2019; 385:111645. [PMID: 31585117 DOI: 10.1016/j.yexcr.2019.111645] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/12/2019] [Accepted: 09/21/2019] [Indexed: 01/06/2023]
Abstract
The past decade has seen significant interest in the isolation of pluripotent stem cells corresponding to various stages of mammalian embryonic development. Two distinct and well-defined pluripotent states can be derived from mouse embryos: "naïve" pluripotent cells with properties of pre-implantation epiblast, and "primed" pluripotent cells, resembling post-implantation epiblast. Prompted by the successful interconversion between these two stem cell states in the mouse system, several groups have devised strategies for inducing a naïve state of pluripotency in human pluripotent stem cells. Here, we review recent insights into the naïve state of human pluripotency, focusing on two methods that confer defining transcriptomic and epigenomic signatures of the pre-implantation embryo. The isolation of naïve human pluripotent stem cells offers a window into early developmental mechanisms that cannot be adequately modeled in primed cells, such as X chromosome reactivation, metabolic reprogramming, and the regulation of hominid-specific transposable elements. We outline key unresolved questions regarding naïve human pluripotency, including its extrinsic and intrinsic control mechanisms, potential for embryonic and extraembryonic differentiation, and general utility as a model system for human development and disease.
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Affiliation(s)
- Chen Dong
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Laura A Fischer
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Thorold W Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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83
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Liu W, Deng C, Godoy-Parejo C, Zhang Y, Chen G. Developments in cell culture systems for human pluripotent stem cells. World J Stem Cells 2019; 11:968-981. [PMID: 31768223 PMCID: PMC6851012 DOI: 10.4252/wjsc.v11.i11.968] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) are important resources for cell-based therapies and pharmaceutical applications. In order to realize the potential of hPSCs, it is critical to develop suitable technologies required for specific applications. Most hPSC technologies depend on cell culture, and are critically influenced by culture medium composition, extracellular matrices, handling methods, and culture platforms. This review summarizes the major technological advances in hPSC culture, and highlights the opportunities and challenges in future therapeutic applications.
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Affiliation(s)
- Weiwei Liu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Bioimaging and Stem Cell Core Facility, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Chunhao Deng
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Carlos Godoy-Parejo
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Yumeng Zhang
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Guokai Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau 999078, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China.
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84
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Kong Q, Yang X, Zhang H, Liu S, Zhao J, Zhang J, Weng X, Jin J, Liu Z. Lineage specification and pluripotency revealed by transcriptome analysis from oocyte to blastocyst in pig. FASEB J 2019; 34:691-705. [DOI: 10.1096/fj.201901818rr] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Qingran Kong
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province College of Life Science Northeast Agricultural University Harbin China
| | - Xu Yang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province College of Life Science Northeast Agricultural University Harbin China
| | - Heng Zhang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province College of Life Science Northeast Agricultural University Harbin China
- Institute of Biology Westlake University Hangzhou China
| | - Shichao Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province College of Life Science Northeast Agricultural University Harbin China
| | - Jianchao Zhao
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province College of Life Science Northeast Agricultural University Harbin China
| | - Jiaming Zhang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province College of Life Science Northeast Agricultural University Harbin China
| | - Xiaogang Weng
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province College of Life Science Northeast Agricultural University Harbin China
| | - Junxue Jin
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province College of Life Science Northeast Agricultural University Harbin China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province College of Life Science Northeast Agricultural University Harbin China
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85
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Lucchesi S, Nolfi E, Pettini E, Pastore G, Fiorino F, Pozzi G, Medaglini D, Ciabattini A. Computational Analysis of Multiparametric Flow Cytometric Data to Dissect B Cell Subsets in Vaccine Studies. Cytometry A 2019; 97:259-267. [PMID: 31710181 PMCID: PMC7079172 DOI: 10.1002/cyto.a.23922] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 01/03/2023]
Abstract
The generation of the B cell response upon vaccination is characterized by the induction of different functional and phenotypic subpopulations and is strongly dependent on the vaccine formulation, including the adjuvant used. Here, we have profiled the different B cell subsets elicited upon vaccination, using machine learning methods for interpreting high‐dimensional flow cytometry data sets. The B cell response elicited by an adjuvanted vaccine formulation, compared to the antigen alone, was characterized using two automated methods based on clustering (FlowSOM) and dimensional reduction (t‐SNE) approaches. The clustering method identified, based on multiple marker expression, different B cell populations, including plasmablasts, plasma cells, germinal center B cells and their subsets, while this profiling was more difficult with t‐SNE analysis. When undefined phenotypes were detected, their characterization could be improved by integrating the t‐SNE spatial visualization of cells with the FlowSOM clusters. The frequency of some cellular subsets, in particular plasma cells, was significantly higher in lymph nodes of mice primed with the adjuvanted formulation compared to antigen alone. Thanks to this automatic data analysis it was possible to identify, in an unbiased way, different B cell populations and also intermediate stages of cell differentiation elicited by immunization, thus providing a signature of B cell recall response that can be hardly obtained with the classical bidimensional gating analysis. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Simone Lucchesi
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical BiotechnologiesUniversity of SienaSienaItaly
| | - Emanuele Nolfi
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical BiotechnologiesUniversity of SienaSienaItaly
| | - Elena Pettini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical BiotechnologiesUniversity of SienaSienaItaly
| | - Gabiria Pastore
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical BiotechnologiesUniversity of SienaSienaItaly
| | - Fabio Fiorino
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical BiotechnologiesUniversity of SienaSienaItaly
| | - Gianni Pozzi
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical BiotechnologiesUniversity of SienaSienaItaly
| | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical BiotechnologiesUniversity of SienaSienaItaly
| | - Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical BiotechnologiesUniversity of SienaSienaItaly
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86
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Lacombe F, Lechevalier N, Vial JP, Béné MC. An R-Derived FlowSOM Process to Analyze Unsupervised Clustering of Normal and Malignant Human Bone Marrow Classical Flow Cytometry Data. Cytometry A 2019; 95:1191-1197. [PMID: 31577391 DOI: 10.1002/cyto.a.23897] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 01/14/2023]
Abstract
Multiparameter flow cytometry (MFC) is a powerful and versatile tool to accurately analyze cell subsets, notably to explore normal and pathological hematopoiesis. Yet, mostly supervised subjective strategies are used to identify cell subsets in this complex tissue. In the past few years, the implementation of mass cytometry and the big data generated have led to a blossoming of new software solutions. Their application to classical MFC in hematology is however still seldom reported. Here, we show how one of these new tools, the FlowSOM R solution, can be applied, together with the Kaluza® software, to a new delineation of hematopoietic subsets in normal human bone marrow (BM). We thus combined the unsupervised discrimination of cell subsets provided by FlowSOM and their expert-driven node-by-node assignment to known or new hematopoietic subsets. We also show how this new tool could modify the MFC exploration of hematological malignancies both at diagnosis (Dg) and follow-up (FU). This can be achieved by direct comparison of merged listmodes of reference normal BM, Dg, and FU samples of a representative acute myeloblastic case tested with the same immunophenotyping panel. This provides an immediate unsupervised evaluation of minimal residual disease. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- Francis Lacombe
- Flow cytometry department, Hematology Laboratory, Bordeaux University Hospital, Pessac, France
| | - Nicolas Lechevalier
- Flow cytometry department, Hematology Laboratory, Bordeaux University Hospital, Pessac, France
| | - Jean Philippe Vial
- Flow cytometry department, Hematology Laboratory, Bordeaux University Hospital, Pessac, France
| | - Marie C Béné
- Hematology Biology, Nantes University Hospital, CRCINA, Nantes, France
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87
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Avior Y, Eggan K, Benvenisty N. RETRACTED: Cancer-Related Mutations Identified in Primed and Naive Human Pluripotent Stem Cells. Cell Stem Cell 2019; 25:456-461. [DOI: 10.1016/j.stem.2019.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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88
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Talon I, Janiszewski A, Chappell J, Vanheer L, Pasque V. Recent Advances in Understanding the Reversal of Gene Silencing During X Chromosome Reactivation. Front Cell Dev Biol 2019; 7:169. [PMID: 31552244 PMCID: PMC6733891 DOI: 10.3389/fcell.2019.00169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/07/2019] [Indexed: 12/24/2022] Open
Abstract
Dosage compensation between XX female and XY male cells is achieved by a process known as X chromosome inactivation (XCI) in mammals. XCI is initiated early during development in female cells and is subsequently stably maintained in most somatic cells. Despite its stability, the robust transcriptional silencing of XCI is reversible, in the embryo and also in a number of reprogramming settings. Although XCI has been intensively studied, the dynamics, factors, and mechanisms of X chromosome reactivation (XCR) remain largely unknown. In this review, we discuss how new sequencing technologies and reprogramming approaches have enabled recent advances that revealed the timing of transcriptional activation during XCR. We also discuss the factors and chromatin features that might be important to understand the dynamics and mechanisms of the erasure of transcriptional gene silencing on the inactive X chromosome (Xi).
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Affiliation(s)
| | | | | | | | - Vincent Pasque
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
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89
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Fernandes CFDL, Iglesia RP, Melo-Escobar MI, Prado MB, Lopes MH. Chaperones and Beyond as Key Players in Pluripotency Maintenance. Front Cell Dev Biol 2019; 7:150. [PMID: 31428613 PMCID: PMC6688531 DOI: 10.3389/fcell.2019.00150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/17/2019] [Indexed: 12/21/2022] Open
Abstract
Pluripotency is orchestrated by distinct players and chaperones and their partners have emerged as pivotal molecules in proteostasis control to maintain stemness. The proteostasis network consists of diverse interconnected pathways that function dynamically according to the needs of the cell to quality control and maintain protein homeostasis. The proteostasis machinery of pluripotent stem cells (PSCs) is finely adjusted in response to distinct stimuli during cell fate commitment to determine successful organism development. Growing evidence has shown different classes of chaperones regulating crucial cellular processes in PSCs. Histones chaperones promote proper nucleosome assembly and modulate the epigenetic regulation of factors involved in PSCs’ rapid turnover from pluripotency to differentiation. The life cycle of pluripotency proteins from synthesis and folding, transport and degradation is finely regulated by chaperones and co-factors either to maintain the stemness status or to cell fate commitment. Here, we summarize current knowledge of the chaperone network that govern stemness and present the versatile role of chaperones in stem cells resilience. Elucidation of the intricate regulation of pluripotency, dissecting in detail molecular determinants and drivers, is fundamental to understanding the properties of stem cells in order to provide a reliable foundation for biomedical research and regenerative medicine.
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Affiliation(s)
- Camila Felix de Lima Fernandes
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rebeca Piatniczka Iglesia
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria Isabel Melo-Escobar
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mariana Brandão Prado
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marilene Hohmuth Lopes
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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90
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de Souza Lima IM, Schiavinato JLDS, Paulino Leite SB, Sastre D, Bezerra HLDO, Sangiorgi B, Corveloni AC, Thomé CH, Faça VM, Covas DT, Zago MA, Giacca M, Mano M, Panepucci RA. High-content screen in human pluripotent cells identifies miRNA-regulated pathways controlling pluripotency and differentiation. Stem Cell Res Ther 2019; 10:202. [PMID: 31287022 PMCID: PMC6615276 DOI: 10.1186/s13287-019-1318-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 06/11/2019] [Accepted: 06/30/2019] [Indexed: 01/13/2023] Open
Abstract
Background By post-transcriptionally regulating multiple target transcripts, microRNAs (miRNAs or miR) play important biological functions. H1 embryonic stem cells (hESCs) and NTera-2 embryonal carcinoma cells (ECCs) are two of the most widely used human pluripotent model cell lines, sharing several characteristics, including the expression of miRNAs associated to the pluripotent state or with differentiation. However, how each of these miRNAs functionally impacts the biological properties of these cells has not been systematically evaluated. Methods We investigated the effects of 31 miRNAs on NTera-2 and H1 hESCs, by transfecting miRNA mimics. Following 3–4 days of culture, cells were stained for the pluripotency marker OCT4 and the G2 cell-cycle marker Cyclin B1, and nuclei and cytoplasm were co-stained with Hoechst and Cell Mask Blue, respectively. By using automated quantitative fluorescence microscopy (i.e., high-content screening (HCS)), we obtained several morphological and marker intensity measurements, in both cell compartments, allowing the generation of a multiparametric miR-induced phenotypic profile describing changes related to proliferation, cell cycle, pluripotency, and differentiation. Results Despite the overall similarities between both cell types, some miRNAs elicited cell-specific effects, while some related miRNAs induced contrasting effects in the same cell. By identifying transcripts predicted to be commonly targeted by miRNAs inducing similar effects (profiles grouped by hierarchical clustering), we were able to uncover potentially modulated signaling pathways and biological processes, likely mediating the effects of the microRNAs on the distinct groups identified. Specifically, we show that miR-363 contributes to pluripotency maintenance, at least in part, by targeting NOTCH1 and PSEN1 and inhibiting Notch-induced differentiation, a mechanism that could be implicated in naïve and primed pluripotent states. Conclusions We present the first multiparametric high-content microRNA functional screening in human pluripotent cells. Integration of this type of data with similar data obtained from siRNA screenings (using the same HCS assay) could provide a large-scale functional approach to identify and validate microRNA-mediated regulatory mechanisms controlling pluripotency and differentiation. Electronic supplementary material The online version of this article (10.1186/s13287-019-1318-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ildercílio Mota de Souza Lima
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Josiane Lilian Dos Santos Schiavinato
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Sarah Blima Paulino Leite
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Danuta Sastre
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil
| | - Hudson Lenormando de Oliveira Bezerra
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Bruno Sangiorgi
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Amanda Cristina Corveloni
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Carolina Hassibe Thomé
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, Brazil
| | - Vitor Marcel Faça
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, Brazil
| | - Dimas Tadeu Covas
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Marco Antônio Zago
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil.,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic and Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Miguel Mano
- Molecular Medicine Laboratory, International Centre for Genetic and Engineering and Biotechnology (ICGEB), Trieste, Italy.,Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Rodrigo Alexandre Panepucci
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, CEP: 14051-140, Brazil. .,Department of Genetics and Internal Medicine, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil.
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91
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Karagiannis P, Takashima Y. Surface Markers Guide the Journey toward Naive Pluripotency. Cell Stem Cell 2019; 20:737-738. [PMID: 28575685 DOI: 10.1016/j.stem.2017.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Several protocols have managed to reset human primed PSCs to the naive state. In this issue of Cell Stem Cell, Collier et al. (2017) report a set of surface markers that identify which cells are susceptible to resetting and suggest a potential roadmap for the acquisition of naive pluripotency.
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Affiliation(s)
- Peter Karagiannis
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Kyoto Prefecture 606-8501, Japan
| | - Yasuhiro Takashima
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Kyoto Prefecture 606-8501, Japan.
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92
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Yang P, Humphrey SJ, Cinghu S, Pathania R, Oldfield AJ, Kumar D, Perera D, Yang JYH, James DE, Mann M, Jothi R. Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency. Cell Syst 2019; 8:427-445.e10. [PMID: 31078527 DOI: 10.1016/j.cels.2019.03.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/12/2019] [Accepted: 03/19/2019] [Indexed: 12/28/2022]
Abstract
Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem cell states. The two states that bookend the pluripotency continuum, naive and primed, are well characterized, but our understanding of the intermediate states and transitions between them remains incomplete. Here, we dissect the dynamics of pluripotent state transitions underlying pre- to post-implantation epiblast differentiation. Through comprehensive mapping of the proteome, phosphoproteome, transcriptome, and epigenome of embryonic stem cells transitioning from naive to primed pluripotency, we find that rapid, acute, and widespread changes to the phosphoproteome precede ordered changes to the epigenome, transcriptome, and proteome. Reconstruction of the kinase-substrate networks reveals signaling cascades, dynamics, and crosstalk. Distinct waves of global proteomic changes mark discrete phases of pluripotency, with cell-state-specific surface markers tracking pluripotent state transitions. Our data provide new insights into multi-layered control of the phased progression of pluripotency and a foundation for modeling mechanisms regulating pluripotent state transitions (www.stemcellatlas.org).
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Affiliation(s)
- Pengyi Yang
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA; Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.
| | - Sean J Humphrey
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Senthilkumar Cinghu
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Rajneesh Pathania
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Andrew J Oldfield
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Dhirendra Kumar
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Dinuka Perera
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Jean Y H Yang
- Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Raja Jothi
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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93
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Battle SL, Doni Jayavelu N, Azad RN, Hesson J, Ahmed FN, Overbey EG, Zoller JA, Mathieu J, Ruohola-Baker H, Ware CB, Hawkins RD. Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States. Stem Cell Reports 2019; 12:1129-1144. [PMID: 31056477 PMCID: PMC6524944 DOI: 10.1016/j.stemcr.2019.04.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 12/01/2022] Open
Abstract
During mammalian embryogenesis, changes in morphology and gene expression are concurrent with epigenomic reprogramming. Using human embryonic stem cells representing the preimplantation blastocyst (naive) and postimplantation epiblast (primed), our data in 2iL/I/F naive cells demonstrate that a substantial portion of known human enhancers are premarked by H3K4me1, providing an enhanced open chromatin state in naive pluripotency. The 2iL/I/F enhancer repertoire occupies 9% of the genome, three times that of primed cells, and can exist in broad chromatin domains over 50 kb. Enhancer chromatin states are largely poised. Seventy-seven percent of 2iL/I/F enhancers are decommissioned in a stepwise manner as cells become primed. While primed topologically associating domains are largely unaltered upon differentiation, naive 2iL/I/F domains expand across primed boundaries, affecting three-dimensional genome architecture. Differential topologically associating domain edges coincide with 2iL/I/F H3K4me1 enrichment. Our results suggest that naive-derived 2iL/I/F cells have a unique chromatin landscape, which may reflect early embryogenesis.
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Affiliation(s)
- Stephanie L Battle
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Naresh Doni Jayavelu
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Robert N Azad
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Jennifer Hesson
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA; Department of Comparative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Faria N Ahmed
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Eliah G Overbey
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Joseph A Zoller
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, USA
| | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, USA
| | - Carol B Ware
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, USA
| | - R David Hawkins
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA.
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94
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Bredenkamp N, Stirparo GG, Nichols J, Smith A, Guo G. The Cell-Surface Marker Sushi Containing Domain 2 Facilitates Establishment of Human Naive Pluripotent Stem Cells. Stem Cell Reports 2019; 12:1212-1222. [PMID: 31031191 PMCID: PMC6565611 DOI: 10.1016/j.stemcr.2019.03.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/31/2022] Open
Abstract
Recently naive human pluripotent stem cells (hPSCs) have been described that relate to an earlier stage of development than conventional hPSCs. Naive hPSCs remain challenging to generate and authenticate, however. Here we report that Sushi Containing Domain 2 (SUSD2) is a robust cell-surface marker of naive hPSCs in the embryo and in vitro. SUSD2 transcripts are enriched in the pre-implantation epiblast of human blastocysts and immunostaining shows localization of SUSD2 to KLF17-positive epiblast cells. SUSD2 mRNA is strongly expressed in naive hPSCs but is negligible in other hPSCs. SUSD2 immunostaining of live or fixed cells provides unambiguous discrimination of naive versus conventional hPSCs. SUSD2 staining or flow cytometry enable monitoring of naive hPSCs in maintenance culture, and their isolation and quantification during resetting of conventional hPSCs or somatic cell reprogramming. Thus SUSD2 is a powerful non-invasive tool for reliable identification and purification of the naive hPSC phenotype.
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Affiliation(s)
- Nicholas Bredenkamp
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | | | - Jennifer Nichols
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Austin Smith
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK; Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - Ge Guo
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK.
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95
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Pontis J, Planet E, Offner S, Turelli P, Duc J, Coudray A, Theunissen TW, Jaenisch R, Trono D. Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs. Cell Stem Cell 2019; 24:724-735.e5. [PMID: 31006620 PMCID: PMC6509360 DOI: 10.1016/j.stem.2019.03.012] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/04/2019] [Accepted: 03/12/2019] [Indexed: 11/17/2022]
Abstract
Expansion of transposable elements (TEs) coincides with evolutionary shifts in gene expression. TEs frequently harbor binding sites for transcriptional regulators, thus enabling coordinated genome-wide activation of species- and context-specific gene expression programs, but such regulation must be balanced against their genotoxic potential. Here, we show that Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) control the timely and pleiotropic activation of TE-derived transcriptional cis regulators during early embryogenesis. Evolutionarily recent SVA, HERVK, and HERVH TE subgroups contribute significantly to chromatin opening during human embryonic genome activation and are KLF-stimulated enhancers in naive human embryonic stem cells (hESCs). KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. Finally, the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific enhancers. Thus, by controlling the transcriptional impact of TEs during embryogenesis, KZFPs facilitate their genome-wide incorporation into transcriptional networks, thereby contributing to human genome regulation. KLFs foster EGA by activating enhancers embedded in young TEs (TEENhancers) TEENhancers confer a degree of species specificity to early genome activation TEENhancers stimulate the expression of KZFPs responsible for their repression These KZFPs in turn facilitate TEENhancers’ exaptation as tissue-specific regulators
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Affiliation(s)
- Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Thorold W Theunissen
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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96
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MKL1-actin pathway restricts chromatin accessibility and prevents mature pluripotency activation. Nat Commun 2019; 10:1695. [PMID: 30979898 PMCID: PMC6461646 DOI: 10.1038/s41467-019-09636-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 03/01/2019] [Indexed: 12/19/2022] Open
Abstract
Actin cytoskeleton is well-known for providing structural/mechanical support, but whether and how it regulates chromatin and cell fate reprogramming is far less clear. Here, we report that MKL1, the key transcriptional co-activator of many actin cytoskeletal genes, regulates genomic accessibility and cell fate reprogramming. The MKL1-actin pathway weakens during somatic cell reprogramming by pluripotency transcription factors. Cells that reprogram efficiently display low endogenous MKL1 and inhibition of actin polymerization promotes mature pluripotency activation. Sustained MKL1 expression at a level seen in typical fibroblasts yields excessive actin cytoskeleton, decreases nuclear volume and reduces global chromatin accessibility, stalling cells on their trajectory toward mature pluripotency. In addition, the MKL1-actin imposed block of pluripotency can be bypassed, at least partially, when the Sun2-containing linker of the nucleoskeleton and cytoskeleton (LINC) complex is inhibited. Thus, we unveil a previously unappreciated aspect of control on chromatin and cell fate reprogramming exerted by the MKL1-actin pathway. MKL1 is a key transcriptional co-activator of actin cytoskeleton genes. Here the authors show that MKL1 activation in somatic cells reduces chromatin accessibility and hinders full reprogramming to pluripotency. Reduction of MKL1, disruption of actin cytoskeleton and its links to the nucleus relieve this repression.
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97
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Sayago C, Martinez-Val A, Munoz J. Proteotyping pluripotency with mass spectrometry. Expert Rev Proteomics 2019; 16:391-400. [PMID: 30947573 DOI: 10.1080/14789450.2019.1604229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Pluripotency emerges transiently during embryogenesis in two main forms with different developmental potential, termed naïve and primed states. Importantly, these pluripotent states can be recapitulated in vitro under specific culture conditions, representing a unique model to study the regulatory principles of development and cellular plasticity. Areas covered: A complex network of signaling pathways that senses intrinsic and extrinsic cues controls the fine balance between self-renewal and differentiation. Much of our knowledge on this tight regulation originates from epigenetic and transcriptomic approaches. However, the presence of post-transcriptional and post-translational mechanisms demands a direct assessment of the proteome in its multiple facets. Mass spectrometry-based proteomics is now a mature technique and has started to deliver new insights in the stem cell field. Expert opinion: Here, we review our current understanding on the mechanisms that dictate the spectrum of pluripotency levels. We put special emphasis on the emerging proteomic studies that focused on the molecular properties behind the naïve and primed states. In addition, we hypothesize on the impact that future developments in proteomic technologies can have to improve our view of pluripotency.
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Affiliation(s)
- Cristina Sayago
- a Proteomics Unit , Spanish National Cancer Research Centre (CNIO) , Madrid , Spain.,b ISCIII-ProteoRed , Spain
| | - Ana Martinez-Val
- a Proteomics Unit , Spanish National Cancer Research Centre (CNIO) , Madrid , Spain.,b ISCIII-ProteoRed , Spain
| | - Javier Munoz
- a Proteomics Unit , Spanish National Cancer Research Centre (CNIO) , Madrid , Spain.,b ISCIII-ProteoRed , Spain
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98
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Xu H, Wang B, Ono M, Kagita A, Fujii K, Sasakawa N, Ueda T, Gee P, Nishikawa M, Nomura M, Kitaoka F, Takahashi T, Okita K, Yoshida Y, Kaneko S, Hotta A. Targeted Disruption of HLA Genes via CRISPR-Cas9 Generates iPSCs with Enhanced Immune Compatibility. Cell Stem Cell 2019; 24:566-578.e7. [PMID: 30853558 DOI: 10.1016/j.stem.2019.02.005] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 12/18/2018] [Accepted: 02/06/2019] [Indexed: 12/18/2022]
Abstract
Induced pluripotent stem cells (iPSCs) have strong potential in regenerative medicine applications; however, immune rejection caused by HLA mismatching is a concern. B2M gene knockout and HLA-homozygous iPSC stocks can address this issue, but the former approach may induce NK cell activity and fail to present antigens, and it is challenging to recruit rare donors for the latter method. Here, we show two genome-editing strategies for making immunocompatible donor iPSCs. First, we generated HLA pseudo-homozygous iPSCs with allele-specific editing of HLA heterozygous iPSCs. Second, we generated HLA-C-retained iPSCs by disrupting both HLA-A and -B alleles to suppress the NK cell response while maintaining antigen presentation. HLA-C-retained iPSCs could evade T cells and NK cells in vitro and in vivo. We estimated that 12 lines of HLA-C-retained iPSCs combined with HLA-class II knockout are immunologically compatible with >90% of the world's population, greatly facilitating iPSC-based regenerative medicine applications.
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Affiliation(s)
- Huaigeng Xu
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Bo Wang
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Miyuki Ono
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Akihiro Kagita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kaho Fujii
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Noriko Sasakawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Tatsuki Ueda
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Peter Gee
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Misato Nishikawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Masaki Nomura
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Fumiyo Kitaoka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomoko Takahashi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Keisuke Okita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shin Kaneko
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
| | - Akitsu Hotta
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
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99
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Mishra S, Kacin E, Stamatiadis P, Franck S, Van der Jeught M, Mertes H, Pennings G, De Sutter P, Sermon K, Heindryckx B, Geens M. The role of the reprogramming method and pluripotency state in gamete differentiation from patient-specific human pluripotent stem cells. Mol Hum Reprod 2019; 24:173-184. [PMID: 29471503 DOI: 10.1093/molehr/gay007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/10/2018] [Indexed: 12/16/2022] Open
Abstract
The derivation of gametes from patient-specific pluripotent stem cells may provide new perspectives for genetic parenthood for patients currently facing sterility. We use current data to assess the gamete differentiation potential of patient-specific pluripotent stem cells and to determine which reprogramming strategy holds the greatest promise for future clinical applications. First, we compare the two best established somatic cell reprogramming strategies: the production of induced pluripotent stem cells (iPSC) and somatic cell nuclear transfer followed by embryonic stem cell derivation (SCNT-ESC). Recent reports have indicated that these stem cells, though displaying a similar pluripotency potential, show important differences at the epigenomic level, which may have repercussions on their applicability. By comparing data on the genetic and epigenetic stability of these cell types during derivation and in-vitro culture, we assess the reprogramming efficiency of both technologies and possible effects on the subsequent differentiation potential of these cells. Moreover, we discuss possible implications of mitochondrial heteroplasmy. We also address the ethical aspects of both cell types, as well as the safety considerations associated with clinical applications using these cells, e.g. the known genomic instability of human PSCs during long-term culture. Secondly, we discuss the role of the stem cell pluripotency state in germ cell differentiation. In mice, success in germ cell development from pluripotent stem cells could only be achieved when starting from a naive state of pluripotency. It remains to be investigated if the naive state is also crucial for germ cell differentiation in human cells and to what extent human naive pluripotency resembles the naive state in mouse.
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Affiliation(s)
- S Mishra
- Ghent-Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - E Kacin
- Research Group, Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Brussels, Belgium
| | - P Stamatiadis
- Ghent-Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - S Franck
- Research Group, Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Brussels, Belgium
| | - M Van der Jeught
- Ghent-Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - H Mertes
- Bioethics Institute Ghent, Department of Philosophy and Moral Sciences, Blandijnberg 2, 9000 Ghent, Belgium
| | - G Pennings
- Bioethics Institute Ghent, Department of Philosophy and Moral Sciences, Blandijnberg 2, 9000 Ghent, Belgium
| | - P De Sutter
- Ghent-Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - K Sermon
- Research Group, Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Brussels, Belgium
| | - B Heindryckx
- Ghent-Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - M Geens
- Research Group, Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Brussels, Belgium
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100
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Karagiannis P, Takahashi K, Saito M, Yoshida Y, Okita K, Watanabe A, Inoue H, Yamashita JK, Todani M, Nakagawa M, Osawa M, Yashiro Y, Yamanaka S, Osafune K. Induced Pluripotent Stem Cells and Their Use in Human Models of Disease and Development. Physiol Rev 2019; 99:79-114. [PMID: 30328784 DOI: 10.1152/physrev.00039.2017] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The discovery of somatic cell nuclear transfer proved that somatic cells can carry the same genetic code as the zygote, and that activating parts of this code are sufficient to reprogram the cell to an early developmental state. The discovery of induced pluripotent stem cells (iPSCs) nearly half a century later provided a molecular mechanism for the reprogramming. The initial creation of iPSCs was accomplished by the ectopic expression of four specific genes (OCT4, KLF4, SOX2, and c-Myc; OSKM). iPSCs have since been acquired from a wide range of cell types and a wide range of species, suggesting a universal molecular mechanism. Furthermore, cells have been reprogrammed to iPSCs using a myriad of methods, although OSKM remains the gold standard. The sources for iPSCs are abundant compared with those for other pluripotent stem cells; thus the use of iPSCs to model the development of tissues, organs, and other systems of the body is increasing. iPSCs also, through the reprogramming of patient samples, are being used to model diseases. Moreover, in the 10 years since the first report, human iPSCs are already the basis for new cell therapies and drug discovery that have reached clinical application. In this review, we examine the generation of iPSCs and their application to disease and development.
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Affiliation(s)
- Peter Karagiannis
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Kazutoshi Takahashi
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Megumu Saito
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Keisuke Okita
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Akira Watanabe
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Haruhisa Inoue
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Jun K Yamashita
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Masaya Todani
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Masato Nakagawa
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Mitsujiro Osawa
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Yoshimi Yashiro
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Kenji Osafune
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
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