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Onfray C, Chevolleau S, Moinard E, Girard O, Mahadik K, Allsop R, Georgolopoulos G, Lavigne R, Renoult O, Aksoy I, Lemaitre E, Hulin P, Ouimette JF, Fréour T, Pecqueur C, Pineau C, Pasque V, Rougeulle C, David L. Unraveling hallmark suitability for staging pre- and post-implantation stem cell models. Cell Rep 2024; 43:114232. [PMID: 38761378 DOI: 10.1016/j.celrep.2024.114232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 02/02/2024] [Accepted: 04/26/2024] [Indexed: 05/20/2024] Open
Abstract
The advent of novel 2D and 3D models for human development, including trophoblast stem cells and blastoids, has expanded opportunities for investigating early developmental events, gradually illuminating the enigmatic realm of human development. While these innovations have ushered in new prospects, it has become essential to establish well-defined benchmarks for the cell sources of these models. We aimed to propose a comprehensive characterization of pluripotent and trophoblastic stem cell models by employing a combination of transcriptomic, proteomic, epigenetic, and metabolic approaches. Our findings reveal that extended pluripotent stem cells share many characteristics with primed pluripotent stem cells, with the exception of metabolic activity. Furthermore, our research demonstrates that DNA hypomethylation and high metabolic activity define trophoblast stem cells. These results underscore the necessity of considering multiple hallmarks of pluripotency rather than relying on a single criterion. Multiplying hallmarks alleviate stage-matching bias.
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Affiliation(s)
- Constance Onfray
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Simon Chevolleau
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Eva Moinard
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Océane Girard
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Kasturi Mahadik
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, 75013 Paris, France
| | - Ryan Allsop
- KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Institute for Single Cell Omics and Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Grigorios Georgolopoulos
- KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Institute for Single Cell Omics and Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Régis Lavigne
- University Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 35000 Rennes, France; University Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, 35000 Rennes, France
| | - Ophélie Renoult
- Nantes Université, CNRS, Inserm, CRCI2NA, 44000 Nantes, France
| | - Irene Aksoy
- University Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Elsa Lemaitre
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, SFR Bonamy, 44000 Nantes, France
| | - Philippe Hulin
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, SFR Bonamy, 44000 Nantes, France
| | | | - Thomas Fréour
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France; Department of Obstetrics, Gynecology and Reproductive Medicine, Dexeus University Hospital, 08028 Barcelona, Spain; CHU Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France
| | - Claire Pecqueur
- Nantes Université, CNRS, Inserm, CRCI2NA, 44000 Nantes, France
| | - Charles Pineau
- University Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 35000 Rennes, France; University Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, 35000 Rennes, France
| | - Vincent Pasque
- KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Institute for Single Cell Omics and Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Claire Rougeulle
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, 75013 Paris, France
| | - Laurent David
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France; Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, SFR Bonamy, 44000 Nantes, France.
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2
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Karakis V, Britt JW, Jabeen M, Miguel AS, Rao BM. Derivation of human trophoblast stem cells from placentas at birth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592064. [PMID: 38746283 PMCID: PMC11092656 DOI: 10.1101/2024.05.01.592064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Human trophoblast stem cells (hTSCs) have emerged as a powerful tool for modeling the placental cytotrophoblast (CTB) in vitro. hTSCs were originally derived from CTBs of the first trimester placenta or blastocyst-stage embryos in trophoblast stem cell medium (TSCM) that contains epidermal growth factor (EGF), the glycogen synthase kinase-beta (GSK3β) inhibitor CHIR99021, the transforming growth factor-beta (TGFβ) inhibitors A83-01 and SB431542, valproic acid (VPA), and the Rho-associated protein kinase (ROCK) inhibitor Y-27632. Here we show that hTSCs can be derived from CTBs isolated from the term placenta, using TSCM supplemented with a low concentration of mitochondrial pyruvate uptake inhibitor UK5099 and lipid-rich albumin (TUA medium). Notably, hTSCs could not be derived from term CTBs using TSCM alone, or in the absence of either UK5099 or lipid-rich albumin. Strikingly, hTSCs cultured in TUA medium for a few passages could be transitioned into TSCM and cultured thereafter in TSCM. hTSCs from term CTBs cultured in TUA medium as well as those transitioned into and cultured in TSCM thereafter could be differentiated to the extravillous trophoblast and syncytiotrophoblast lineages and exhibited high transcriptome similarity with hTSCs derived from first trimester CTBs. We anticipate that these results will enable facile derivation of hTSCs from normal and pathological placentas at birth with diverse genetic backgrounds and facilitate in vitro mechanistic studies in trophoblast biology.
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Wang J, Zhang Y, Gao J, Feng G, Liu C, Li X, Li P, Liu Z, Lu F, Wang L, Li W, Zhou Q, Liu Y. Alternative splicing of CARM1 regulated by LincGET-guided paraspeckles biases the first cell fate in mammalian early embryos. Nat Struct Mol Biol 2024:10.1038/s41594-024-01292-9. [PMID: 38658621 DOI: 10.1038/s41594-024-01292-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
The heterogeneity of CARM1 controls first cell fate bias during early mouse development. However, how this heterogeneity is established is unknown. Here, we show that Carm1 mRNA is of a variety of specific exon-skipping splicing (ESS) isoforms in mouse two-cell to four-cell embryos that contribute to CARM1 heterogeneity. Disruption of paraspeckles promotes the ESS of Carm1 precursor mRNAs (pre-mRNAs). LincGET, but not Neat1, is required for paraspeckle assembly and inhibits the ESS of Carm1 pre-mRNAs in mouse two-cell to four-cell embryos. We further find that LincGET recruits paraspeckles to the Carm1 gene locus through HNRNPU. Interestingly, PCBP1 binds the Carm1 pre-mRNAs and promotes its ESS in the absence of LincGET. Finally, we find that the ESS seen in mouse two-cell to four-cell embryos decreases CARM1 protein levels and leads to trophectoderm fate bias. Our findings demonstrate that alternative splicing of CARM1 has an important role in first cell fate determination.
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Affiliation(s)
- Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, China.
| | - Yiwei Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jiaze Gao
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xueke Li
- College of Life Science, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Pengcheng Li
- College of Life Science, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Yusheng Liu
- College of Life Science, Northeast Forestry University, Harbin, China.
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Azagury M, Buganim Y. Unlocking trophectoderm mysteries: In vivo and in vitro perspectives on human and mouse trophoblast fate induction. Dev Cell 2024; 59:941-960. [PMID: 38653193 DOI: 10.1016/j.devcel.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/10/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
In recent years, the pursuit of inducing the trophoblast stem cell (TSC) state has gained prominence as a compelling research objective, illuminating the establishment of the trophoblast lineage and unlocking insights into early embryogenesis. In this review, we examine how advancements in diverse technologies, including in vivo time course transcriptomics, cellular reprogramming to TSC state, chemical induction of totipotent stem-cell-like state, and stem-cell-based embryo-like structures, have enriched our insights into the intricate molecular mechanisms and signaling pathways that define the mouse and human trophectoderm/TSC states. We delve into disparities between mouse and human trophectoderm/TSC fate establishment, with a special emphasis on the intriguing role of pluripotency in this context. Additionally, we re-evaluate recent findings concerning the potential of totipotent-stem-like cells and embryo-like structures to fully manifest the trophectoderm/trophoblast lineage's capabilities. Lastly, we briefly discuss the potential applications of induced TSCs in pregnancy-related disease modeling.
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Affiliation(s)
- Meir Azagury
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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5
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Tan JP, Liu X, Polo JM. Reprogramming fibroblast into human iBlastoids. Nat Protoc 2024:10.1038/s41596-024-00984-2. [PMID: 38632379 DOI: 10.1038/s41596-024-00984-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 02/12/2024] [Indexed: 04/19/2024]
Abstract
The study of early human embryogenesis has relied on the use of blastocysts donated to research or simple stem cell culture systems such as pluripotent and trophoblast stem cells, which have been seminal in shedding light on many key developmental processes. However, simple culture systems lack the necessary complexity to adequately model the spatiotemporal, cellular and molecular dynamics occurring during the early phases of embryonic development. As such, an in vitro model of the human blastocyst is advantageous in many aspects to decipher human embryogenesis. Here we describe a step-by-step protocol for the generation of induced blastoids (iBlastoids), an in vitro integrated model of the human blastocyst derived via somatic reprogramming. This protocol details the workflow for reprogramming of human dermal fibroblasts and subsequent generation of iBlastoids using the reprogramming intermediates, which together takes ~27 days (21 days for reprogramming and 6 days for iBlastoid generation). We also discuss several characterization/functional assays that can be used on the iBlastoids. We believe that a person trained in cell culture with ~1 year of experience with human somatic cell and reprogramming/cell differentiation assays would be able to perform this protocol. In short, the iBlastoids present an alternative tool as a model to the blastocyst to facilitate the scientific community in the exploration of early human development.
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Affiliation(s)
- Jia Ping Tan
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Xiaodong Liu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Research Center for Industries of the Future, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
- The South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
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6
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De Los Angeles A, Hug CB, Gladyshev VN, Church GM, Velychko S. Sendai virus persistence questions the transient naive reprogramming method for iPSC generation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583804. [PMID: 38559172 PMCID: PMC10979911 DOI: 10.1101/2024.03.07.583804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Since the revolutionary discovery of induced pluripotent stem cells (iPSCs) by Shinya Yamanaka, the comparison between iPSCs and embryonic stem cells (ESCs) has revealed significant differences in their epigenetic states and developmental potential. A recent compelling study published in Nature by Buckberry et al.1 demonstrated that a transient-naive-treatment (TNT) could facilitate epigenetic reprogramming and improve the developmental potential of human iPSCs (hiPSCs). However, the study characterized bulk hiPSCs instead of isolating clonal lines and overlooked the persistent expression of Sendai virus carrying exogenous Yamanaka factors. Our analyses revealed that Sendai genes were expressed in most control PSC samples, including hESCs, which were not intentionally infected. The highest levels of Sendai expression were detected in samples continuously treated with naive media, where it led to overexpression of exogenous MYC, SOX2, and KLF4, altering both the expression levels and ratios of reprogramming factors. Our findings call for further research to verify the effectiveness of the TNT method in the context of delivery methods that ensure prompt elimination of exogenous factors, leading to the generation of bona fide transgene-independent iPSCs.
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Affiliation(s)
| | - Clemens B. Hug
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute, Harvard University, Boston, MA, USA
| | - Sergiy Velychko
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute, Harvard University, Boston, MA, USA
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Huyghe A, Trajkova A, Lavial F. Cellular plasticity in reprogramming, rejuvenation and tumorigenesis: a pioneer TF perspective. Trends Cell Biol 2024; 34:255-267. [PMID: 37648593 DOI: 10.1016/j.tcb.2023.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
The multistep process of in vivo reprogramming, mediated by the transcription factors (TFs) Oct4, Sox2, Klf4, and c-Myc (OSKM), holds great promise for the development of rejuvenating and regenerative strategies. However, most of the approaches developed so far are accompanied by a persistent risk of tumorigenicity. Here, we review the groundbreaking effects of in vivo reprogramming with a particular focus on rejuvenation and regeneration. We discuss how the activity of pioneer TFs generates cellular plasticity that may be critical for inducing not only reprogramming and regeneration, but also cancer initiation. Finally, we highlight how a better understanding of the uncoupled control of cellular identity, plasticity, and aging during reprogramming might pave the way to the development of rejuvenating/regenerating strategies in a nontumorigenic manner.
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Affiliation(s)
- Aurélia Huyghe
- Cellular Reprogramming, Stem Cells and Oncogenesis Laboratory, Equipe Labellisée la Ligue Contre le Cancer, Labex Dev2Can - Univeristy of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Aneta Trajkova
- Cellular Reprogramming, Stem Cells and Oncogenesis Laboratory, Equipe Labellisée la Ligue Contre le Cancer, Labex Dev2Can - Univeristy of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Fabrice Lavial
- Cellular Reprogramming, Stem Cells and Oncogenesis Laboratory, Equipe Labellisée la Ligue Contre le Cancer, Labex Dev2Can - Univeristy of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France.
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8
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Hori T, Okae H, Shibata S, Kobayashi N, Kobayashi EH, Oike A, Sekiya A, Arima T, Kaji H. Trophoblast stem cell-based organoid models of the human placental barrier. Nat Commun 2024; 15:962. [PMID: 38332125 PMCID: PMC10853531 DOI: 10.1038/s41467-024-45279-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Human placental villi have essential roles in producing hormones, mediating nutrient and waste exchange, and protecting the fetus from exposure to xenobiotics. Human trophoblast organoids that recapitulate the structure of villi could provide an important in vitro tool to understand placental development and the transplacental passage of xenobiotics. However, such organoids do not currently exist. Here we describe the generation of trophoblast organoids using human trophoblast stem (TS) cells. Following treatment with three kinds of culture medium, TS cells form spherical organoids with a single outer layer of syncytiotrophoblast (ST) cells that display a barrier function. Furthermore, we develop a column-type ST barrier model based on the culture condition of the trophoblast organoids. The bottom membrane of the column is almost entirely covered with syndecan 1-positive ST cells. The barrier integrity and maturation levels of the model are confirmed by measuring transepithelial/transendothelial electrical resistance (TEER) and the amount of human chorionic gonadotropin. Further analysis reveals that the model can be used to derive the apparent permeability coefficients of model compounds. In addition to providing a suite of tools for the study of placental development, our trophoblast models allow the evaluation of compound transfer and toxicity, which will facilitate drug development.
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Affiliation(s)
- Takeshi Hori
- Department of Diagnostic and Therapeutic Systems Engineering, Institute of Biomaterials and Bioengineering (IBB), Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575, Japan
- Department of Trophoblast Research, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Shun Shibata
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575, Japan
| | - Norio Kobayashi
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575, Japan
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eri H Kobayashi
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575, Japan
| | - Akira Oike
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575, Japan
- Department of Trophoblast Research, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Asato Sekiya
- Department of Trophoblast Research, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575, Japan
| | - Hirokazu Kaji
- Department of Diagnostic and Therapeutic Systems Engineering, Institute of Biomaterials and Bioengineering (IBB), Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan.
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9
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Tietze E, Barbosa AR, Araujo B, Euclydes V, Spiegelberg B, Cho HJ, Lee YK, Wang Y, McCord A, Lorenzetti A, Feltrin A, van de Leemput J, Di Carlo P, Ursini G, Benjamin KJ, Brentani H, Kleinman JE, Hyde TM, Weinberger DR, McKay R, Shin JH, Sawada T, Paquola ACM, Erwin JA. Human archetypal pluripotent stem cells differentiate into trophoblast stem cells via endogenous BMP5/7 induction without transitioning through naive state. Sci Rep 2024; 14:3291. [PMID: 38332235 PMCID: PMC10853519 DOI: 10.1038/s41598-024-53381-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
Primary human trophoblast stem cells (TSCs) and TSCs derived from human pluripotent stem cells (hPSCs) can potentially model placental processes in vitro. Yet, the pluripotent states and factors involved in the differentiation of hPSCs to TSCs remain poorly understood. In this study, we demonstrate that the primed pluripotent state can generate TSCs by activating pathways such as Epidermal Growth Factor (EGF) and Wingless-related integration site (WNT), and by suppressing tumor growth factor beta (TGFβ), histone deacetylases (HDAC), and Rho-associated protein kinase (ROCK) signaling pathways, all without the addition of exogenous Bone morphogenetic protein 4 (BMP4)-a condition we refer to as the TS condition. We characterized this process using temporal single-cell RNA sequencing to compare TS conditions with differentiation protocols involving BMP4 activation alone or BMP4 activation in conjunction with WNT inhibition. The TS condition consistently produced a stable, proliferative cell type that closely mimics first-trimester placental cytotrophoblasts, marked by the activation of endogenous retroviral genes and the absence of amnion expression. This was observed across multiple cell lines, including various primed induced pluripotent stem cell (iPSC) and embryonic stem cell (ESC) lines. Primed-derived TSCs can proliferate for over 30 passages and further specify into multinucleated syncytiotrophoblasts and extravillous trophoblast cells. Our research establishes that the differentiation of primed hPSCs to TSC under TS conditions triggers the induction of TMSB4X, BMP5/7, GATA3, and TFAP2A without progressing through a naive state. These findings propose that the primed hPSC state is part of a continuum of potency with the capacity to differentiate into TSCs through multiple routes.
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Affiliation(s)
- Ethan Tietze
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Andre Rocha Barbosa
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Inter-Institutional Graduate Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil
| | - Bruno Araujo
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Veronica Euclydes
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry, University of Sao Paulo, Medical School, São Paulo, Brazil
| | - Bailey Spiegelberg
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hyeon Jin Cho
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Yong Kyu Lee
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Yanhong Wang
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | | | | | - Arthur Feltrin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Center for Mathematics, Computation and Cognition, Federal University of ABC, Santo André, SP, Brazil
| | - Joyce van de Leemput
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Center for Precision Disease Modeling and Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Pasquale Di Carlo
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Basic Medical Science, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Gianluca Ursini
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kynon J Benjamin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Helena Brentani
- Inter-Institutional Graduate Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil
- Department of Psychiatry, University of Sao Paulo, Medical School, São Paulo, Brazil
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ronald McKay
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tomoyo Sawada
- Lieber Institute for Brain Development, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Apua C M Paquola
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jennifer A Erwin
- Lieber Institute for Brain Development, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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10
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Liu X, Polo JM. Human blastoid as an in vitro model of human blastocysts. Curr Opin Genet Dev 2024; 84:102135. [PMID: 38052115 DOI: 10.1016/j.gde.2023.102135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/23/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023]
Abstract
Human development is a highly coordinated process, with any abnormalities during the early embryonic stages that can often have detrimental consequences. The complexity and nuances of human development underpin its significance in embryo research. However, this research is often hindered by limited availability and ethical considerations associated with the use of donated blastocysts from in vitro fertilization (IVF) surplus. Human blastoids offer promising alternatives as they can be easily generated and manipulated in the laboratory while preserving key characteristics of human blastocysts. In this way, they hold the potential to serve as a scalable and ethically permissible resource in embryology research. By utilizing such human embryo models, we can establish a transformative platform that complements the study with IVF embryos, ultimately enhancing our understanding of human embryogenesis.
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Affiliation(s)
- Xiaodong Liu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Research Center for Industries of the Future, Westlake University, Hangzhou, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Jose M Polo
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, South Australia, Australia; The South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, South Australia, Australia; Department of Anatomy and Developmental Biology, Monash University, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Victoria, Australia.
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11
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Yang Y, Jia W, Luo Z, Li Y, Liu H, Fu L, Li J, Jiang Y, Lai J, Li H, Saeed BJ, Zou Y, Lv Y, Wu L, Zhou T, Shan Y, Liu C, Lai Y, Liu L, Hutchins AP, Esteban MA, Mazid MA, Li W. VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification. Nat Commun 2024; 15:583. [PMID: 38233381 PMCID: PMC10794710 DOI: 10.1038/s41467-024-44780-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
In contrast to rodents, the mechanisms underlying human trophectoderm and early placenta specification are understudied due to ethical barriers and the scarcity of embryos. Recent reports have shown that human pluripotent stem cells (PSCs) can differentiate into trophectoderm (TE)-like cells (TELCs) and trophoblast stem cells (TSCs), offering a valuable in vitro model to study early placenta specification. Here, we demonstrate that the VGLL1 (vestigial-like family member 1), which is highly expressed during human and non-human primate TE specification in vivo but is negligibly expressed in mouse, is a critical regulator of cell fate determination and self-renewal in human TELCs and TSCs derived from naïve PSCs. Mechanistically, VGLL1 partners with the transcription factor TEAD4 (TEA domain transcription factor 4) to regulate chromatin accessibility at target gene loci through histone acetylation and acts in cooperation with GATA3 and TFAP2C. Our work is relevant to understand primate early embryogenesis and how it differs from other mammalian species.
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Affiliation(s)
- Yueli Yang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wenqi Jia
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiwei Luo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Yunpan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Lixin Fu
- University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Shenzhen, China
| | - Jinxiu Li
- University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Shenzhen, China
| | - Yu Jiang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Junjian Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
- BGI Research, Shenzhen, China
| | - Haiwei Li
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Babangida Jabir Saeed
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Yi Zou
- BGI Research, Shenzhen, China
| | - Yuan Lv
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
- BGI Research, Shenzhen, China
| | - Liang Wu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Ting Zhou
- Stem Cell Research Facility, Sloan Kettering Institute, New York, NY, USA
| | - Yongli Shan
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | | | - Yiwei Lai
- BGI Research, Shenzhen, China
- BGI Research, Hangzhou, China
| | - Longqi Liu
- BGI Research, Shenzhen, China
- BGI Research, Hangzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Miguel A Esteban
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China.
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China.
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.
- BGI Research, Shenzhen, China.
- BGI Research, Hangzhou, China.
| | - Md Abdul Mazid
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China.
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.
| | - Wenjuan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China.
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.
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12
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Sinenko SA, Tomilin AN. Metabolic control of induced pluripotency. Front Cell Dev Biol 2024; 11:1328522. [PMID: 38274274 PMCID: PMC10808704 DOI: 10.3389/fcell.2023.1328522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Pluripotent stem cells of the mammalian epiblast and their cultured counterparts-embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs)-have the capacity to differentiate in all cell types of adult organisms. An artificial process of reactivation of the pluripotency program in terminally differentiated cells was established in 2006, which allowed for the generation of induced pluripotent stem cells (iPSCs). This iPSC technology has become an invaluable tool in investigating the molecular mechanisms of human diseases and therapeutic drug development, and it also holds tremendous promise for iPSC applications in regenerative medicine. Since the process of induced reprogramming of differentiated cells to a pluripotent state was discovered, many questions about the molecular mechanisms involved in this process have been clarified. Studies conducted over the past 2 decades have established that metabolic pathways and retrograde mitochondrial signals are involved in the regulation of various aspects of stem cell biology, including differentiation, pluripotency acquisition, and maintenance. During the reprogramming process, cells undergo major transformations, progressing through three distinct stages that are regulated by different signaling pathways, transcription factor networks, and inputs from metabolic pathways. Among the main metabolic features of this process, representing a switch from the dominance of oxidative phosphorylation to aerobic glycolysis and anabolic processes, are many critical stage-specific metabolic signals that control the path of differentiated cells toward a pluripotent state. In this review, we discuss the achievements in the current understanding of the molecular mechanisms of processes controlled by metabolic pathways, and vice versa, during the reprogramming process.
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Affiliation(s)
- Sergey A. Sinenko
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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13
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Long C, Li H, Liang P, Chao L, Hong Y, Zhang J, Xi Q, Zuo Y. Deciphering the decisive factors driving fate bifurcations in somatic cell reprogramming. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102044. [PMID: 37869261 PMCID: PMC10585637 DOI: 10.1016/j.omtn.2023.102044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/28/2023] [Indexed: 10/24/2023]
Abstract
Single-cell studies have demonstrated that somatic cell reprogramming is a continuous process of cell fates transition. Only partial reprogramming intermediates can overcome the molecular bottlenecks to acquire pluripotency. To decipher the underlying decisive factors driving cell fate, we identified induced pluripotent stem cells or stromal-like cells (iPSCs/SLCs) and iPSCs or trophoblast-like cells (iPSCs/TLCs) fate bifurcations by reconstructing cellular trajectory. The mesenchymal-epithelial transition and the activation of pluripotency networks are the main molecular series in successful reprogramming. Correspondingly, intermediates diverge into SLCs accompanied by the inhibition of cell cycle genes and the activation of extracellular matrix genes, whereas the TLCs fate is characterized by the up-regulation of placenta development genes. Combining putative gene regulatory networks, seven (Taf7, Ezh2, Klf2, etc.) and three key factors (Cdc5l, Klf4, and Nanog) were individually identified as drivers of the successful reprogramming by triggering downstream pluripotent networks during iPSCs/SLCs and iPSCs/TLCs fate bifurcation. Conversely, 11 factors (Cebpb, Sox4, Junb, etc.) and four factors (Gata2, Jund, Ctnnb1, etc.) drive SLCs fate and TLCs fate, respectively. Our study sheds new light on the understanding of decisive factors driving cell fate, which is helpful for improving reprogramming efficiency through manipulating cell fates to avoid alternative fates.
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Affiliation(s)
- Chunshen Long
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Hanshuang Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Pengfei Liang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Lemuge Chao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yan Hong
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Junping Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Qilemuge Xi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
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14
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Sadovsky E, Chu T, Barak O, Sadovsky Y, Ouyang Y. The impact of opioids on the transcriptional landscape of human villous trophoblasts. Placenta 2023; 143:54-61. [PMID: 37832183 PMCID: PMC10841529 DOI: 10.1016/j.placenta.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 09/15/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
INTRODUCTION Opioid use disorder (OUD) is implicated in major obstetrical diseases such as fetal growth restriction. Whether or not opioids directly impact placental trophoblast development and function remains unclear. We sought to examine the expression of opioid receptors (OPRs) in villous trophoblasts and the effect of opioids on placental transcriptomics. METHODS Trophoblast stem (TS) cells and primary human trophoblast (PHT) cells from healthy term placentas were used to assess OPR expression in conditions that enhance trophoblast stemness vs differentiation. Placental RNAseq was conducted using our retrospective cohorts of pregnant people with OUD vs controls, both without major obstetrical complications. RT-qPCR was used to determine the effect of fentanyl on the expression of putative opioid targets and stemness or differentiation-associated genes in TS and PHT cells. RESULTS Three main OPRs, including OPRM1, OPRD1, and OPRK1 were expressed in term PHT cells cultured in the stemness medium, whereas only OPRD1 and OPRK1 were expressed in TS cells. Interestingly, upon induction of differentiation, the expressed OPR mRNAs in TS or in PHT cells were downregulated. We found 286 differentially expressed long RNAs in placentas from the OUD participants vs controls. While three putative opioid targets differed their expression in stemness vs differentiation states of trophoblasts, fentanyl had no effect on their expression or the expression of major stemness or differentiation-relevant genes in TS and PHT cells. DISCUSSION Trophoblastic expression of OPRs and opioid RNA targets is impacted by cell differentiation, suggesting differential susceptibility of villous trophoblasts to the effect of opioids.
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Affiliation(s)
- Elena Sadovsky
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tianjiao Chu
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Oren Barak
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingshi Ouyang
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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15
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Nair S, Ameen M, Sundaram L, Pampari A, Schreiber J, Balsubramani A, Wang YX, Burns D, Blau HM, Karakikes I, Wang KC, Kundaje A. Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.04.560808. [PMID: 37873116 PMCID: PMC10592962 DOI: 10.1101/2023.10.04.560808] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ectopic expression of OCT4, SOX2, KLF4 and MYC (OSKM) transforms differentiated cells into induced pluripotent stem cells. To refine our mechanistic understanding of reprogramming, especially during the early stages, we profiled chromatin accessibility and gene expression at single-cell resolution across a densely sampled time course of human fibroblast reprogramming. Using neural networks that map DNA sequence to ATAC-seq profiles at base-resolution, we annotated cell-state-specific predictive transcription factor (TF) motif syntax in regulatory elements, inferred affinity- and concentration-dependent dynamics of Tn5-bias corrected TF footprints, linked peaks to putative target genes, and elucidated rewiring of TF-to-gene cis-regulatory networks. Our models reveal that early in reprogramming, OSK, at supraphysiological concentrations, rapidly open transient regulatory elements by occupying non-canonical low-affinity binding sites. As OSK concentration falls, the accessibility of these transient elements decays as a function of motif affinity. We find that these OSK-dependent transient elements sequester the somatic TF AP-1. This redistribution is strongly associated with the silencing of fibroblast-specific genes within individual nuclei. Together, our integrated single-cell resource and models reveal insights into the cis-regulatory code of reprogramming at unprecedented resolution, connect TF stoichiometry and motif syntax to diversification of cell fate trajectories, and provide new perspectives on the dynamics and role of transient regulatory elements in somatic silencing.
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Affiliation(s)
- Surag Nair
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Mohamed Ameen
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | | | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jacob Schreiber
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Yu Xin Wang
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - David Burns
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kevin C Wang
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
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16
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Li X, Li ZH, Wang YX, Liu TH. A comprehensive review of human trophoblast fusion models: recent developments and challenges. Cell Death Discov 2023; 9:372. [PMID: 37816723 PMCID: PMC10564767 DOI: 10.1038/s41420-023-01670-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/23/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
As an essential component of the maternal-fetal interface, the placental syncytiotrophoblast layer contributes to a successful pregnancy by secreting hormones necessary for pregnancy, transporting nutrients, mediating gas exchange, balancing immune tolerance, and resisting pathogen infection. Notably, the deficiency in mononuclear trophoblast cells fusing into multinucleated syncytiotrophoblast has been linked to adverse pregnancy outcomes, such as preeclampsia, fetal growth restriction, preterm birth, and stillbirth. Despite the availability of many models for the study of trophoblast fusion, there exists a notable disparity from the ideal model, limiting the deeper exploration into the placental development. Here, we reviewed the existing models employed for the investigation of human trophoblast fusion from several aspects, including the development history, latest progress, advantages, disadvantages, scope of application, and challenges. The literature searched covers the monolayer cell lines, primary human trophoblast, placental explants, human trophoblast stem cells, human pluripotent stem cells, three-dimensional cell spheres, organoids, and placenta-on-a-chip from 1938 to 2023. These diverse models have significantly enhanced our comprehension of placental development regulation and the underlying mechanisms of placental-related disorders. Through this review, our objective is to provide readers with a thorough understanding of the existing trophoblast fusion models, making it easier to select most suitable models to address specific experimental requirements or scientific inquiries. Establishment and application of the existing human placental trophoblast fusion models.
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Affiliation(s)
- Xia Li
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, 400016, Chongqing, China
- The Joint International Research Laboratory of Reproduction and Development, Ministry of Education, 400016, Chongqing, China
| | - Zhuo-Hang Li
- The Joint International Research Laboratory of Reproduction and Development, Ministry of Education, 400016, Chongqing, China
- Medical Laboratory Department, Traditional Chinese Medicine Hospital of Yaan, 625099, Sichuan, China
| | - Ying-Xiong Wang
- The Joint International Research Laboratory of Reproduction and Development, Ministry of Education, 400016, Chongqing, China.
| | - Tai-Hang Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, 400016, Chongqing, China.
- The Joint International Research Laboratory of Reproduction and Development, Ministry of Education, 400016, Chongqing, China.
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17
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Bernabé-Rubio M, Ali S, Bhosale PG, Goss G, Mobasseri SA, Tapia-Rojo R, Zhu T, Hiratsuka T, Battilocchi M, Tomás IM, Ganier C, Garcia-Manyes S, Watt FM. Myc-dependent dedifferentiation of Gata6 + epidermal cells resembles reversal of terminal differentiation. Nat Cell Biol 2023; 25:1426-1438. [PMID: 37735598 PMCID: PMC10567550 DOI: 10.1038/s41556-023-01234-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 08/16/2023] [Indexed: 09/23/2023]
Abstract
Dedifferentiation is the process by which terminally differentiated cells acquire the properties of stem cells. During mouse skin wound healing, the differentiated Gata6-lineage positive cells of the sebaceous duct are able to dedifferentiate. Here we have integrated lineage tracing and single-cell mRNA sequencing to uncover the underlying mechanism. Gata6-lineage positive and negative epidermal stem cells in wounds are transcriptionally indistinguishable. Furthermore, in contrast to reprogramming of induced pluripotent stem cells, the same genes are expressed in the epidermal dedifferentiation and differentiation trajectories, indicating that dedifferentiation does not involve adoption of a new cell state. We demonstrate that dedifferentiation is not only induced by wounding, but also by retinoic acid treatment or mechanical expansion of the epidermis. In all three cases, dedifferentiation is dependent on the master transcription factor c-Myc. Mechanotransduction and actin-cytoskeleton remodelling are key features of dedifferentiation. Our study elucidates the molecular basis of epidermal dedifferentiation, which may be generally applicable to adult tissues.
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Affiliation(s)
- Miguel Bernabé-Rubio
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Shahnawaz Ali
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Priyanka G Bhosale
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Georgina Goss
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | | | - Rafael Tapia-Rojo
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
| | - Tong Zhu
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
| | - Toru Hiratsuka
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
- Department of Oncogenesis and Growth Regulation, Research Center, Osaka International Cancer Institute, Chuoku, Japan
| | - Matteo Battilocchi
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Inês M Tomás
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Clarisse Ganier
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King's College London, London, UK
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
| | - Fiona M Watt
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK.
- Directors' Unit, EMBL Heidelberg, Heidelberg, Germany.
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18
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Weatherbee BAT, Gantner CW, Iwamoto-Stohl LK, Daza RM, Hamazaki N, Shendure J, Zernicka-Goetz M. Pluripotent stem cell-derived model of the post-implantation human embryo. Nature 2023; 622:584-593. [PMID: 37369347 PMCID: PMC10584688 DOI: 10.1038/s41586-023-06368-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
The human embryo undergoes morphogenetic transformations following implantation into the uterus, but our knowledge of this crucial stage is limited by the inability to observe the embryo in vivo. Models of the embryo derived from stem cells are important tools for interrogating developmental events and tissue-tissue crosstalk during these stages1. Here we establish a model of the human post-implantation embryo, a human embryoid, comprising embryonic and extraembryonic tissues. We combine two types of extraembryonic-like cell generated by overexpression of transcription factors with wild-type embryonic stem cells and promote their self-organization into structures that mimic several aspects of the post-implantation human embryo. These self-organized aggregates contain a pluripotent epiblast-like domain surrounded by extraembryonic-like tissues. Our functional studies demonstrate that the epiblast-like domain robustly differentiates into amnion, extraembryonic mesenchyme and primordial germ cell-like cells in response to bone morphogenetic protein cues. In addition, we identify an inhibitory role for SOX17 in the specification of anterior hypoblast-like cells2. Modulation of the subpopulations in the hypoblast-like compartment demonstrates that extraembryonic-like cells influence epiblast-like domain differentiation, highlighting functional tissue-tissue crosstalk. In conclusion, we present a modular, tractable, integrated3 model of the human embryo that will enable us to probe key questions of human post-implantation development, a critical window during which substantial numbers of pregnancies fail.
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Affiliation(s)
- Bailey A T Weatherbee
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Carlos W Gantner
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Lisa K Iwamoto-Stohl
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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19
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Morey R, Bui T, Fisch KM, Horii M. Modeling placental development and disease using human pluripotent stem cells. Placenta 2023; 141:18-25. [PMID: 36333266 PMCID: PMC10148925 DOI: 10.1016/j.placenta.2022.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/03/2022] [Accepted: 10/18/2022] [Indexed: 11/08/2022]
Abstract
Our current knowledge of the cellular and molecular mechanisms of placental epithelial cells, trophoblast, primarily came from the use of mouse trophoblast stem cells and tumor-derived or immortalized human trophoblast cell lines. This was mainly due to the difficulties in maintaining primary trophoblast in culture and establishing human trophoblast stem cell (hTSC) lines. However, in-depth characterization of these cellular models and in vivo human trophoblast have revealed significant discrepancies. For the past two decades, multiple groups have shown that human pluripotent stem cells (hPSCs) can be differentiated into trophoblast, and thus could be used as a model for normal and disease trophoblast differentiation. During this time, trophoblast differentiation protocols have evolved, enabling researchers to study cellular characteristics at trophectoderm (TE), trophoblast stem cells (TSC), syncytiotrophoblast (STB), and extravillous trophoblast (EVT) stages. Recently, several groups reported methods to derive hTSC from pre-implantation blastocyst or early gestation placenta, and trophoblast organoids from early gestation placenta, drastically changing the landscape of trophoblast research. These culture conditions have been rapidly applied to generate hPSC-derived TSC and trophoblast organoids. As a result of these technological advancements, the field's capacity to better understand trophoblast differentiation and their involvement in pregnancy related disease has greatly expanded. Here, we present in vitro models of human trophoblast differentiation, describing both primary and hPSC-derived TSC, maintained as monolayers and 3-dimensional trophoblast organoids, as a tool to study early placental development and disease in multiple settings.
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Affiliation(s)
- Robert Morey
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA; Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tony Bui
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA; Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mariko Horii
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA; Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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20
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Wang J, Xie W, Li N, Li W, Zhang Z, Fan N, Ouyang Z, Zhao Y, Lai C, Li H, Chen M, Quan L, Li Y, Jiang Y, Jia W, Fu L, Mazid MA, Zhu Y, Maxwell PH, Pan G, Esteban MA, Dai Z, Lai L. Generation of a humanized mesonephros in pigs from induced pluripotent stem cells via embryo complementation. Cell Stem Cell 2023; 30:1235-1245.e6. [PMID: 37683604 DOI: 10.1016/j.stem.2023.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/12/2023] [Accepted: 08/07/2023] [Indexed: 09/10/2023]
Abstract
Heterologous organ transplantation is an effective way of replacing organ function but is limited by severe organ shortage. Although generating human organs in other large mammals through embryo complementation would be a groundbreaking solution, it faces many challenges, especially the poor integration of human cells into the recipient tissues. To produce human cells with superior intra-niche competitiveness, we combined optimized pluripotent stem cell culture conditions with the inducible overexpression of two pro-survival genes (MYCN and BCL2). The resulting cells had substantially enhanced viability in the xeno-environment of interspecies chimeric blastocyst and successfully formed organized human-pig chimeric middle-stage kidney (mesonephros) structures up to embryonic day 28 inside nephric-defective pig embryos lacking SIX1 and SALL1. Our findings demonstrate proof of principle of the possibility of generating a humanized primordial organ in organogenesis-disabled pigs, opening an exciting avenue for regenerative medicine and an artificial window for studying human kidney development.
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Affiliation(s)
- Jiaowei Wang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100039, China; Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
| | - Wenguang Xie
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
| | - Nan Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Wenjuan Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Zhishuai Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Nana Fan
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
| | - Zhen Ouyang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Yu Zhao
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Chengdan Lai
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Hao Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Mengqi Chen
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Longquan Quan
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
| | - Yunpan Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yu Jiang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130012, China
| | - Wenqi Jia
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100039, China; Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lixin Fu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Md Abdul Mazid
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yanling Zhu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Patrick H Maxwell
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 0ST, UK
| | - Guangjin Pan
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100039, China.
| | - Miguel A Esteban
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130012, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100039, China.
| | - Zhen Dai
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.
| | - Liangxue Lai
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen 529020, China; Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130012, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100039, China; Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences, Guangzhou 510530, China.
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21
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Oh SY, Na SB, Kang YK, Do JT. In Vitro Embryogenesis and Gastrulation Using Stem Cells in Mice and Humans. Int J Mol Sci 2023; 24:13655. [PMID: 37686459 PMCID: PMC10563085 DOI: 10.3390/ijms241713655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
During early mammalian embryonic development, fertilized one-cell embryos develop into pre-implantation blastocysts and subsequently establish three germ layers through gastrulation during post-implantation development. In recent years, stem cells have emerged as a powerful tool to study embryogenesis and gastrulation without the need for eggs, allowing for the generation of embryo-like structures known as synthetic embryos or embryoids. These in vitro models closely resemble early embryos in terms of morphology and gene expression and provide a faithful recapitulation of early pre- and post-implantation embryonic development. Synthetic embryos can be generated through a combinatorial culture of three blastocyst-derived stem cell types, such as embryonic stem cells, trophoblast stem cells, and extraembryonic endoderm cells, or totipotent-like stem cells alone. This review provides an overview of the progress and various approaches in studying in vitro embryogenesis and gastrulation in mice and humans using stem cells. Furthermore, recent findings and breakthroughs in synthetic embryos and gastruloids are outlined. Despite ethical considerations, synthetic embryo models hold promise for understanding mammalian (including humans) embryonic development and have potential implications for regenerative medicine and developmental research.
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Affiliation(s)
| | | | | | - Jeong Tae Do
- Department of Stem Cell Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul 05029, Republic of Korea; (S.Y.O.); (S.B.N.); (Y.K.K.)
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22
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Varberg KM, Dominguez EM, Koseva B, Varberg JM, McNally RP, Moreno-Irusta A, Wesley ER, Iqbal K, Cheung WA, Schwendinger-Schreck C, Smail C, Okae H, Arima T, Lydic M, Holoch K, Marsh C, Soares MJ, Grundberg E. Extravillous trophoblast cell lineage development is associated with active remodeling of the chromatin landscape. Nat Commun 2023; 14:4826. [PMID: 37563143 PMCID: PMC10415281 DOI: 10.1038/s41467-023-40424-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
The extravillous trophoblast cell lineage is a key feature of placentation and successful pregnancy. Knowledge of transcriptional regulation driving extravillous trophoblast cell development is limited. Here, we map the transcriptome and epigenome landscape as well as chromatin interactions of human trophoblast stem cells and their transition into extravillous trophoblast cells. We show that integrating chromatin accessibility, long-range chromatin interactions, transcriptomic, and transcription factor binding motif enrichment enables identification of transcription factors and regulatory mechanisms critical for extravillous trophoblast cell development. We elucidate functional roles for TFAP2C, SNAI1, and EPAS1 in the regulation of extravillous trophoblast cell development. EPAS1 is identified as an upstream regulator of key extravillous trophoblast cell transcription factors, including ASCL2 and SNAI1 and together with its target genes, is linked to pregnancy loss and birth weight. Collectively, we reveal activation of a dynamic regulatory network and provide a framework for understanding extravillous trophoblast cell specification in trophoblast cell lineage development and human placentation.
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Affiliation(s)
- Kaela M Varberg
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Esteban M Dominguez
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Boryana Koseva
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Joseph M Varberg
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Ross P McNally
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Ayelen Moreno-Irusta
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Emily R Wesley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Carl Schwendinger-Schreck
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Craig Smail
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
- Department of Trophoblast Research, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Michael Lydic
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Kristin Holoch
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Courtney Marsh
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Michael J Soares
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Center for Perinatal Research, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
| | - Elin Grundberg
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
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23
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Yoshihara M, Kere J. Transcriptomic differences between human 8-cell-like cells reprogrammed with different methods. Stem Cell Reports 2023; 18:1621-1628. [PMID: 37478859 PMCID: PMC10444576 DOI: 10.1016/j.stemcr.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023] Open
Abstract
Embryonic genome activation (EGA) is a critical step in embryonic development. However, while EGA has been studied in mice using mouse 2-cell-like cells, human EGA remains incompletely elucidated due to the lack of an in vitro cell model recapitulating the early blastomere stage in humans. Recently, five groups independently reported human 8-cell-like cells (8CLCs, also called induced blastomere-like cells) developed from pluripotent stem cells and used single-cell RNA sequencing (scRNA-seq) to specify their cellular identities. Here we summarize the methods developed to produce the 8CLCs and compare their transcriptomic profiles by integrating them with the scRNA-seq datasets of human embryos. These observations will allow comparison and validation of the models, stimulate further in-depth research to characterize the genes involved in human EGA and pre-implantation development, and facilitate studies on human embryogenesis.
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Affiliation(s)
- Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Institute for Advanced Academic Research, Chiba University, Chiba, Japan; Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Folkhälsan Research Center, Helsinki, Finland; Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland.
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24
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Abel A, Sozen B. Shifting early embryology paradigms: Applications of stem cell-based embryo models in bioengineering. Curr Opin Genet Dev 2023; 81:102069. [PMID: 37392541 PMCID: PMC10530566 DOI: 10.1016/j.gde.2023.102069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/16/2023] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
Technologies to reproduce specific aspects of early mammalian embryogenesis in vitro using stem cells have skyrocketed over the last several years. With these advances, we have gained new perspectives on how embryonic and extraembryonic cells self-organize to form the embryo. These reductionist approaches hold promise for the future implementation of precise environmental and genetic controls to understand variables affecting embryo development. Our review discusses recent progress in cellular models of early mammalian embryo development and bioengineering advancements that can be leveraged to study the embryo-maternal interface. We summarize current gaps in the field, emphasizing the importance of understanding how intercellular interactions at this interface contribute to reproductive and developmental health.
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Affiliation(s)
- Ashley Abel
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06520, USA. https://twitter.com/@caitrionacunn
| | - Berna Sozen
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, Yale University, New Haven, CT 06520, USA.
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25
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DiRusso JA, Clark AT. Transposable elements in early human embryo development and embryo models. Curr Opin Genet Dev 2023; 81:102086. [PMID: 37441874 PMCID: PMC10917458 DOI: 10.1016/j.gde.2023.102086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
Abstract
Transposable elements (TEs), long discounted as 'selfish genomic elements,' are increasingly appreciated as the drivers of genomic evolution, genome organization, and gene regulation. TEs are particularly important in early embryo development, where advances in stem cell technologies, in tandem with improved computational and next-generation sequencing approaches, have provided an unprecedented opportunity to study the contribution of TEs to early mammalian development. Here, we summarize advances in our understanding of TEs in early human development and expand on how new stem cell-based embryo models can be leveraged to augment this understanding.
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Affiliation(s)
- Jonathan A DiRusso
- Department of Molecular, Cell and Developmental Biology, University of California, 90095 Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, 90095 Los Angeles, CA, USA.; Molecular Biology Institute, University of California, 90095 Los Angeles, CA, USA; Center for Reproductive Science, Health and Education, University of California, 90095 Los Angeles, CA, USA
| | - Amander T Clark
- Department of Molecular, Cell and Developmental Biology, University of California, 90095 Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, 90095 Los Angeles, CA, USA.; Molecular Biology Institute, University of California, 90095 Los Angeles, CA, USA; Center for Reproductive Science, Health and Education, University of California, 90095 Los Angeles, CA, USA.
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26
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Naama M, Buganim Y. Human trophoblast stem cell-state acquisition from pluripotent stem cells and somatic cells. Curr Opin Genet Dev 2023; 81:102084. [PMID: 37451165 DOI: 10.1016/j.gde.2023.102084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/10/2023] [Accepted: 06/11/2023] [Indexed: 07/18/2023]
Abstract
For an extended period of time, research on human embryo implantation and early placentation was hindered by ethical limitation and lack of appropriate in vitro models. Recently, an explosion of new research has significantly expanded our knowledge of early human trophoblast development and facilitated the derivation and culture of self-renewing human trophoblast stem cells (hTSCs). Multiple approaches have been undertaken in efforts to derive and understand hTSCs, including from blastocysts, early trophoblast tissue, and, more recently, from human pluripotent stem cells (hPSCs) and somatic cells. In this concise review, we summarize recent advances in derivation of hTSCs, with a focus on derivation from naive and primed hPSCs, as well as via reprogramming of somatic cells into induced hTSCs. Each of these methods harbors distinct advantages and setbacks, which are discussed. Finally, we briefly explore the possibility of the existence of trophectoderm-like hTSCs corresponding to earlier, preimplantation trophoblast cells.
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Affiliation(s)
- Moriyah Naama
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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27
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Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, de Mendoza A, Pflueger J, Frazer T, Vargas-Landín DB, Paynter JM, Smits N, Liu N, Ouyang JF, Rossello FJ, Chy HS, Rackham OJL, Laslett AL, Breen J, Faulkner GJ, Nefzger CM, Polo JM, Lister R. Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature 2023; 620:863-872. [PMID: 37587336 PMCID: PMC10447250 DOI: 10.1038/s41586-023-06424-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function1-8. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. We found that reprogramming-induced epigenetic aberrations emerge midway through primed reprogramming, whereas DNA demethylation begins early in naive reprogramming. Using this knowledge, we developed a transient-naive-treatment (TNT) reprogramming strategy that emulates the embryonic epigenetic reset. We show that the epigenetic memory in hiPS cells is concentrated in cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1 and aberrant CpH methylation. TNT reprogramming reconfigures these domains to a hES cell-like state and does not disrupt genomic imprinting. Using an isogenic system, we demonstrate that TNT reprogramming can correct the transposable element overexpression and differential gene expression seen in conventional hiPS cells, and that TNT-reprogrammed hiPS and hES cells show similar differentiation efficiencies. Moreover, TNT reprogramming enhances the differentiation of hiPS cells derived from multiple cell types. Thus, TNT reprogramming corrects epigenetic memory and aberrations, producing hiPS cells that are molecularly and functionally more similar to hES cells than conventional hiPS cells. We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications and providing a novel system for studying epigenetic memory.
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Affiliation(s)
- Sam Buckberry
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Telethon Kids Institute, Perth, Western Australia, Australia
- John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Xiaodong Liu
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- School of Life Sciences, Westlake University, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Westlake Institute for Advanced Study, Hangzhou, China
| | - Daniel Poppe
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jia Ping Tan
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Guizhi Sun
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Trung Viet Nguyen
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Alex de Mendoza
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Thomas Frazer
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Dulce B Vargas-Landín
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jacob M Paynter
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Nathan Smits
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Ning Liu
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Fernando J Rossello
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Hun S Chy
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Victoria, Australia
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Andrew L Laslett
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Victoria, Australia
| | - James Breen
- John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia.
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia.
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
- The South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia.
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
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28
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Chen J, Neil JA, Tan JP, Rudraraju R, Mohenska M, Sun YBY, Walters E, Bediaga NG, Sun G, Zhou Y, Li Y, Drew D, Pymm P, Tham WH, Wang Y, Rossello FJ, Nie G, Liu X, Subbarao K, Polo JM. A placental model of SARS-CoV-2 infection reveals ACE2-dependent susceptibility and differentiation impairment in syncytiotrophoblasts. Nat Cell Biol 2023; 25:1223-1234. [PMID: 37443288 PMCID: PMC10415184 DOI: 10.1038/s41556-023-01182-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/02/2023] [Indexed: 07/15/2023]
Abstract
SARS-CoV-2 infection causes COVID-19. Several clinical reports have linked COVID-19 during pregnancy to negative birth outcomes and placentitis. However, the pathophysiological mechanisms underpinning SARS-CoV-2 infection during placentation and early pregnancy are not clear. Here, to shed light on this, we used induced trophoblast stem cells to generate an in vitro early placenta infection model. We identified that syncytiotrophoblasts could be infected through angiotensin-converting enzyme 2 (ACE2). Using a co-culture model of vertical transmission, we confirmed the ability of the virus to infect syncytiotrophoblasts through a previous endometrial cell infection. We further demonstrated transcriptional changes in infected syncytiotrophoblasts that led to impairment of cellular processes, reduced secretion of HCG hormone and morphological changes vital for syncytiotrophoblast function. Furthermore, different antibody strategies and antiviral drugs restore these impairments. In summary, we have established a scalable and tractable platform to study early placental cell types and highlighted its use in studying strategies to protect the placenta.
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Affiliation(s)
- J Chen
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - J A Neil
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - J P Tan
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - R Rudraraju
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - M Mohenska
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Y B Y Sun
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - E Walters
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- Adelaide Centre for Epigenetics, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - N G Bediaga
- Adelaide Centre for Epigenetics, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - G Sun
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Y Zhou
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Y Li
- Implantation and Pregnancy Research Laboratory, School of Health and Biomedical Sciences, RMIT University, Melbourne, Victoria, Australia
| | - D Drew
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - P Pymm
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - W H Tham
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Y Wang
- Implantation and Pregnancy Research Laboratory, School of Health and Biomedical Sciences, RMIT University, Melbourne, Victoria, Australia
| | - F J Rossello
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - G Nie
- Implantation and Pregnancy Research Laboratory, School of Health and Biomedical Sciences, RMIT University, Melbourne, Victoria, Australia
| | - X Liu
- School of Life Sciences, Westlake University, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Westlake Institute for Advanced Study, Hangzhou, China
| | - K Subbarao
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia.
| | - J M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.
- Adelaide Centre for Epigenetics, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
- South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
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29
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Park SY, Ter-Saakyan S, Faraci G, Lee HY. Immune cell identifier and classifier (ImmunIC) for single cell transcriptomic readouts. Sci Rep 2023; 13:12093. [PMID: 37495649 PMCID: PMC10372073 DOI: 10.1038/s41598-023-39282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/22/2023] [Indexed: 07/28/2023] Open
Abstract
Single cell RNA sequencing has a central role in immune profiling, identifying specific immune cells as disease markers and suggesting therapeutic target genes of immune cells. Immune cell-type annotation from single cell transcriptomics is in high demand for dissecting complex immune signatures from multicellular blood and organ samples. However, accurate cell type assignment from single-cell RNA sequencing data alone is complicated by a high level of gene expression heterogeneity. Many computational methods have been developed to respond to this challenge, but immune cell annotation accuracy is not highly desirable. We present ImmunIC, a simple and robust tool for immune cell identification and classification by combining marker genes with a machine learning method. With over two million immune cells and half-million non-immune cells from 66 single cell RNA sequencing studies, ImmunIC shows 98% accuracy in the identification of immune cells. ImmunIC outperforms existing immune cell classifiers, categorizing into ten immune cell types with 92% accuracy. We determine peripheral blood mononuclear cell compositions of severe COVID-19 cases and healthy controls using previously published single cell transcriptomic data, permitting the identification of immune cell-type specific differential pathways. Our publicly available tool can maximize the utility of single cell RNA profiling by functioning as a stand-alone bioinformatic cell sorter, advancing cell-type specific immune profiling for the discovery of disease-specific immune signatures and therapeutic targets.
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Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Sonia Ter-Saakyan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Gina Faraci
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA.
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30
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Wang G, Wang Y, Lyu Y, He H, Liuyang S, Wang J, Sun S, Cheng L, Fu Y, Zhu J, Zhong X, Yang Z, Chen Q, Li C, Guan J, Deng H. Chemical-induced epigenome resetting for regeneration program activation in human cells. Cell Rep 2023; 42:112547. [PMID: 37224020 DOI: 10.1016/j.celrep.2023.112547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/30/2023] [Accepted: 05/04/2023] [Indexed: 05/26/2023] Open
Abstract
Human somatic cells can be reprogrammed to pluripotent stem cells by small molecules through an intermediate stage with a regeneration signature, but how this regeneration state is induced remains largely unknown. Here, through integrated single-cell analysis of transcriptome, we demonstrate that the pathway of human chemical reprogramming with regeneration state is distinct from that of transcription-factor-mediated reprogramming. Time-course construction of chromatin landscapes unveils hierarchical histone modification remodeling underlying the regeneration program, which involved sequential enhancer recommissioning and mirrored the reversal process of regeneration potential lost in organisms as they mature. In addition, LEF1 is identified as a key upstream regulator for regeneration gene program activation. Furthermore, we reveal that regeneration program activation requires sequential enhancer silencing of somatic and proinflammatory programs. Altogether, chemical reprogramming resets the epigenome through reversal of the loss of natural regeneration, representing a distinct concept for cellular reprogramming and advancing the development of regenerative therapeutic strategies.
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Affiliation(s)
- Guan Wang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yanglu Wang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Academy for Advanced Interdisciplinary Studies, The Center for Biomed-X Research, Peking University, Beijing, China
| | - Yulin Lyu
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Huanjing He
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shijia Liuyang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jinlin Wang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shicheng Sun
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Lin Cheng
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yao Fu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jialiang Zhu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xinxing Zhong
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Zhihan Yang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Qijing Chen
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Cheng Li
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.
| | - Jingyang Guan
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China.
| | - Hongkui Deng
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences and MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
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31
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Li Q. scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics. Genome Biol 2023; 24:149. [PMID: 37353848 DOI: 10.1186/s13059-023-02988-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 06/13/2023] [Indexed: 06/25/2023] Open
Abstract
Despite the continued efforts, a batch-insensitive tool that can both infer and predict the developmental dynamics using single-cell genomics is lacking. Here, I present scTour, a novel deep learning architecture to perform robust inference and accurate prediction of cellular dynamics with minimal influence from batch effects. For inference, scTour simultaneously estimates the developmental pseudotime, delineates the vector field, and maps the transcriptomic latent space under a single, integrated framework. For prediction, scTour precisely reconstructs the underlying dynamics of unseen cellular states or a new independent dataset. scTour's functionalities are demonstrated in a variety of biological processes from 19 datasets.
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Affiliation(s)
- Qian Li
- Department of Pathology, University of Cambridge, Cambridge, UK.
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32
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Naama M, Rahamim M, Zayat V, Sebban S, Radwan A, Orzech D, Lasry R, Ifrah A, Jaber M, Sabag O, Yassen H, Khatib A, Epsztejn-Litman S, Novoselsky-Persky M, Makedonski K, Deri N, Goldman-Wohl D, Cedar H, Yagel S, Eiges R, Buganim Y. Pluripotency-independent induction of human trophoblast stem cells from fibroblasts. Nat Commun 2023; 14:3359. [PMID: 37291192 PMCID: PMC10250329 DOI: 10.1038/s41467-023-39104-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Human trophoblast stem cells (hTSCs) can be derived from embryonic stem cells (hESCs) or be induced from somatic cells by OCT4, SOX2, KLF4 and MYC (OSKM). Here we explore whether the hTSC state can be induced independently of pluripotency, and what are the mechanisms underlying its acquisition. We identify GATA3, OCT4, KLF4 and MYC (GOKM) as a combination of factors that can generate functional hiTSCs from fibroblasts. Transcriptomic analysis of stable GOKM- and OSKM-hiTSCs reveals 94 hTSC-specific genes that are aberrant specifically in OSKM-derived hiTSCs. Through time-course-RNA-seq analysis, H3K4me2 deposition and chromatin accessibility, we demonstrate that GOKM exert greater chromatin opening activity than OSKM. While GOKM primarily target hTSC-specific loci, OSKM mainly induce the hTSC state via targeting hESC and hTSC shared loci. Finally, we show that GOKM efficiently generate hiTSCs from fibroblasts that harbor knockout for pluripotency genes, further emphasizing that pluripotency is dispensable for hTSC state acquisition.
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Affiliation(s)
- Moriyah Naama
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Moran Rahamim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Valery Zayat
- Department of Stem Cell Bioengineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Shulamit Sebban
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Ahmed Radwan
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Dana Orzech
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Rachel Lasry
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Annael Ifrah
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Mohammad Jaber
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Ofra Sabag
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Hazar Yassen
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Areej Khatib
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Silvina Epsztejn-Litman
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, 91031, Jerusalem, Israel
- The Hebrew University School of Medicine, 91120, Jerusalem, Israel
| | - Michal Novoselsky-Persky
- The Magda and Richard Hoffman Laboratory of Human Placental Research, Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Kirill Makedonski
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Noy Deri
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Debra Goldman-Wohl
- The Magda and Richard Hoffman Laboratory of Human Placental Research, Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Simcha Yagel
- The Magda and Richard Hoffman Laboratory of Human Placental Research, Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Rachel Eiges
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, 91031, Jerusalem, Israel
- The Hebrew University School of Medicine, 91120, Jerusalem, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel.
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Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT. Transfer learning enables predictions in network biology. Nature 2023; 618:616-624. [PMID: 37258680 PMCID: PMC10949956 DOI: 10.1038/s41586-023-06139-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/27/2023] [Indexed: 06/02/2023]
Abstract
Mapping gene networks requires large amounts of transcriptomic data to learn the connections between genes, which impedes discoveries in settings with limited data, including rare diseases and diseases affecting clinically inaccessible tissues. Recently, transfer learning has revolutionized fields such as natural language understanding1,2 and computer vision3 by leveraging deep learning models pretrained on large-scale general datasets that can then be fine-tuned towards a vast array of downstream tasks with limited task-specific data. Here, we developed a context-aware, attention-based deep learning model, Geneformer, pretrained on a large-scale corpus of about 30 million single-cell transcriptomes to enable context-specific predictions in settings with limited data in network biology. During pretraining, Geneformer gained a fundamental understanding of network dynamics, encoding network hierarchy in the attention weights of the model in a completely self-supervised manner. Fine-tuning towards a diverse panel of downstream tasks relevant to chromatin and network dynamics using limited task-specific data demonstrated that Geneformer consistently boosted predictive accuracy. Applied to disease modelling with limited patient data, Geneformer identified candidate therapeutic targets for cardiomyopathy. Overall, Geneformer represents a pretrained deep learning model from which fine-tuning towards a broad range of downstream applications can be pursued to accelerate discovery of key network regulators and candidate therapeutic targets.
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Affiliation(s)
- Christina V Theodoris
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School Genetics Training Program, Boston, USA.
| | - Ling Xiao
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Anant Chopra
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
| | - Mark D Chaffin
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zeina R Al Sayed
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew C Hill
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Helene Mantineo
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
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Zhang M, Reis AH, Simunovic M. Human embryoids: A new strategy of recreating the first steps of embryonic development in vitro. Semin Cell Dev Biol 2023; 141:14-22. [PMID: 35871155 DOI: 10.1016/j.semcdb.2022.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/05/2022] [Accepted: 07/04/2022] [Indexed: 01/24/2023]
Abstract
Molecular mechanisms surrounding early human embryonic events such as blastocyst formation, implantation, and the specification of the body axes are some of the most attractive research questions of developmental biology today. A knowledge on the detailed signaling landscape underlying these critical events in the human could impact the way we treat early pregnancy disorders and infertility, and considerably advance our abilities to make precise human tissues in a lab. However, owing to ethical, technical, and policy restrictions, research on early human embryo development historically stalled behind animal models. The rapid progress in 3D culture of human embryonic stem cells over the past years created an opportunity to overcome this critical challenge. We review recently developed strategies of making 3D models of the human embryo built from embryonic stem cells, which we refer to as embryoids. We focus on models aimed at reconstituting the 3D epithelial characteristics of the early human embryo, namely the intra/extraembryonic signaling crosstalk, tissue polarity, and embryonic cavities. We identify distinct classes of embryoids based on whether they explicitly include extraembryonic tissues and we argue for the merit of compromising on certain aspects of embryo mimicry in balancing the experimental feasibility with ethical considerations. Human embryoids open gates toward a new field of synthetic human embryology, allowing to study the long inaccessible stages of early human development at unprecedented detail.
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Affiliation(s)
- Miaoci Zhang
- Department of Chemical Engineering, Fu Foundation School of Engineering and Applied Sciences, Columbia University, New York 10027, USA; Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York 10032, USA
| | - Alice H Reis
- Department of Chemical Engineering, Fu Foundation School of Engineering and Applied Sciences, Columbia University, New York 10027, USA; Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York 10032, USA
| | - Mijo Simunovic
- Department of Chemical Engineering, Fu Foundation School of Engineering and Applied Sciences, Columbia University, New York 10027, USA; Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York 10032, USA; Department of Genetics and Development, Columbia Irving Medical Center, New York 10032, USA.
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35
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Gong W, Dsouza N, Garry DJ. SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors. Genome Biol 2023; 24:125. [PMID: 37218013 DOI: 10.1186/s13059-023-02954-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently, no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variational autoencoder model to learn the latent representation of ATAC-seq V-plots and outperforms MACS2 and NucleoATAC on six separate tasks. Applying SeATAC to several pioneer factor-induced differentiation or reprogramming ATAC-seq datasets suggests that induction of these factors not only relaxes the closed chromatin but also decreases chromatin accessibility of 20% to 30% of their target sites. SeATAC is a novel tool to accurately reveal genomic regions with differential chromatin accessibility from ATAC-seq data.
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Affiliation(s)
- Wuming Gong
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.
- Lillehei Heart Institute, University of Minnesota, 2231 6Th St SE, Minneapolis, MN, 55455, USA.
| | - Nikita Dsouza
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Daniel J Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.
- Lillehei Heart Institute, University of Minnesota, 2231 6Th St SE, Minneapolis, MN, 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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Panariello F, Gagliano O, Luni C, Grimaldi A, Angiolillo S, Qin W, Manfredi A, Annunziata P, Slovin S, Vaccaro L, Riccardo S, Bouche V, Dionisi M, Salvi M, Martewicz S, Hu M, Cui M, Stuart H, Laterza C, Baruzzo G, Schiebinger G, Di Camillo B, Cacchiarelli D, Elvassore N. Cellular population dynamics shape the route to human pluripotency. Nat Commun 2023; 14:2829. [PMID: 37198156 DOI: 10.1038/s41467-023-37270-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/09/2023] [Indexed: 05/19/2023] Open
Abstract
Human cellular reprogramming to induced pluripotency is still an inefficient process, which has hindered studying the role of critical intermediate stages. Here we take advantage of high efficiency reprogramming in microfluidics and temporal multi-omics to identify and resolve distinct sub-populations and their interactions. We perform secretome analysis and single-cell transcriptomics to show functional extrinsic pathways of protein communication between reprogramming sub-populations and the re-shaping of a permissive extracellular environment. We pinpoint the HGF/MET/STAT3 axis as a potent enhancer of reprogramming, which acts via HGF accumulation within the confined system of microfluidics, and in conventional dishes needs to be supplied exogenously to enhance efficiency. Our data suggest that human cellular reprogramming is a transcription factor-driven process that it is deeply dependent on extracellular context and cell population determinants.
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Affiliation(s)
- Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Onelia Gagliano
- Department of Industrial Engineering, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Stem Cell and Regenerative Medicine Section, GOS Institute of Child Health, University College London, London, UK
| | - Camilla Luni
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, Bologna, Italy
| | - Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Silvia Angiolillo
- Department of Industrial Engineering, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Wei Qin
- Department of Industrial Engineering, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
| | - Anna Manfredi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- NEGEDIA (Next Generation Diagnostic srl), Pozzuoli, Italy
| | - Patrizia Annunziata
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- NEGEDIA (Next Generation Diagnostic srl), Pozzuoli, Italy
| | - Shaked Slovin
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Lorenzo Vaccaro
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Sara Riccardo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- NEGEDIA (Next Generation Diagnostic srl), Pozzuoli, Italy
| | - Valentina Bouche
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Manuela Dionisi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Marcello Salvi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Sebastian Martewicz
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
| | - Manli Hu
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
| | - Meihua Cui
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
| | - Hannah Stuart
- Department of Industrial Engineering, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Cecilia Laterza
- Department of Industrial Engineering, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Giacomo Baruzzo
- Department of Information Engineering, University of Padova, Padova, Italy
| | | | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padova, Italy
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
- CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy.
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples "Federico II", Naples, Italy.
| | - Nicola Elvassore
- Department of Industrial Engineering, University of Padova, Padova, Italy.
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy.
- Stem Cell and Regenerative Medicine Section, GOS Institute of Child Health, University College London, London, UK.
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China.
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37
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Li X, Gibson G, Qiu P. Gene representation in scRNA-seq is correlated with common motifs at the 3' end of transcripts. FRONTIERS IN BIOINFORMATICS 2023; 3:1120290. [PMID: 37255988 PMCID: PMC10226423 DOI: 10.3389/fbinf.2023.1120290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/02/2023] [Indexed: 06/01/2023] Open
Abstract
One important characteristic of single-cell RNA sequencing (scRNA-seq) data is its high sparsity, where the gene-cell count data matrix contains high proportion of zeros. The sparsity has motivated widespread discussions on dropouts and missing data, as well as imputation algorithms of scRNA-seq analysis. Here, we aim to investigate whether there exist genes that are more prone to be under-detected in scRNA-seq, and if yes, what commonalities those genes may share. From public data sources, we gathered paired bulk RNA-seq and scRNA-seq data from 53 human samples, which were generated in diverse biological contexts. We derived pseudo-bulk gene expression by averaging the scRNA-seq data across cells. Comparisons of the paired bulk and pseudo-bulk gene expression profiles revealed that there indeed exists a collection of genes that are frequently under-detected in scRNA-seq compared to bulk RNA-seq. This result was robust to randomization when unpaired bulk and pseudo-bulk gene expression profiles were compared. We performed motif search to the last 350 bp of the identified genes, and observed an enrichment of poly(T) motif. The poly(T) motif toward the tails of those genes may be able to form hairpin structures with the poly(A) tails of their mRNA transcripts, making it difficult for their mRNA transcripts to be captured during scRNA-seq library preparation, which is a mechanistic conjecture of why certain genes may be more prone to be under-detected in scRNA-seq.
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Affiliation(s)
- Xinling Li
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Greg Gibson
- School of Biological Sciences, and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Peng Qiu
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
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38
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Wesevich VG, Arkfeld C, Seifer DB. In Vitro Gametogenesis in Oncofertility: A Review of Its Potential Use and Present-Day Challenges in Moving toward Fertility Preservation and Restoration. J Clin Med 2023; 12:3305. [PMID: 37176745 PMCID: PMC10179531 DOI: 10.3390/jcm12093305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/12/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Current fertility preservation options are limited for cancer survivor patients who wish to have their own biological children. Human in vitro gametogenesis (IVG) has the hypothetical ability to offer a unique solution to individuals receiving treatment for cancer which subsequently shortens their reproductive lifespan. Through a simple skin punch biopsy, a patient's fertility could be restored via reprogramming of dermal fibroblast cells to induced pluripotent stem cells, then from primordial germ cell-like cells into viable oocytes and spermatocytes which could be used for embryogenesis. Induced pluripotent stem cells could also be used to form in vitro environments, similar to the ovary or testes, necessary for the maturation of oogonia. This would allow for the entire creation of embryos outside the body, ex vivo. While this area in stem cell biology research offers the potential to revolutionize reproduction as we know it, there are many critical barriers, both scientific and ethical, that need to be overcome to one day see this technology utilized clinically.
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Affiliation(s)
- Victoria G Wesevich
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510, USA
| | - Christopher Arkfeld
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale New Haven Hospital, New Haven, CT 06510, USA
| | - David B Seifer
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510, USA
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Zhou J, Hu J, Wang Y, Gao S. Induction and application of human naive pluripotency. Cell Rep 2023; 42:112379. [PMID: 37043354 DOI: 10.1016/j.celrep.2023.112379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 12/18/2022] [Accepted: 03/26/2023] [Indexed: 04/13/2023] Open
Abstract
Over the past few decades, many attempts have been made to capture different states of pluripotency in vitro. Naive and primed pluripotent stem cells, corresponding to the pluripotency states of pre- and post-implantation epiblasts, respectively, have been well characterized in mice and can be interconverted in vitro. Here, we summarize the recently reported strategies to generate human naive pluripotent stem cells in vitro. We discuss their applications in studies of regulatory mechanisms involved in early developmental processes, including identification of molecular features, X chromosome inactivation modeling, transposable elements regulation, metabolic characteristics, and cell fate regulation, as well as potential for extraembryonic differentiation and blastoid construction for embryogenesis modeling. We further discuss the naive pluripotency-related research, including 8C-like cell establishment and disease modeling. We also highlight limitations of current naive pluripotency studies, such as imperfect culture conditions and inadequate responsiveness to differentiation signals.
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Affiliation(s)
- Jianfeng Zhou
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Jindian Hu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yixuan Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Shaorong Gao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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40
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He L, Liu Q, Cheng J, Cao M, Zhang S, Wan X, Li J, Tu H. SIRT4 in ageing. Biogerontology 2023; 24:347-362. [PMID: 37067687 DOI: 10.1007/s10522-023-10022-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 01/31/2023] [Indexed: 04/18/2023]
Abstract
Ageing is a phenomenon in which cells, tissues and organs undergo systemic pathological changes as individuals age, leading to the occurrence of ageing-related diseases and the end of life. It is associated with many phenotypes known as ageing characteristics, such as genomic instability, nutritional imbalance, mitochondrial dysfunction, cell senescence, stem cell depletion, and an altered microenvironment. The sirtuin family (SIRT), known as longevity proteins, is thought to delay ageing and prolong life, and mammals, including humans, have seven family members (SIRT1-7). SIRT4 has been studied less among the sirtuin family thus far, but it has been reported that it has important physiological functions in organisms, such as promoting DNA damage repair, participating in the energy metabolism of three substances, inhibiting inflammatory reactions and apoptosis, and regulating mitochondrial function. Recently, some studies have demonstrated the involvement of SIRT4 in age-related processes, but knowledge in this field is still scarce. Therefore, this review aims to analyse the relationship between SIRT4 and ageing characteristics as well as some age-related diseases (e.g., cardiovascular diseases, metabolic diseases, neurodegenerative diseases and cancer).
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Affiliation(s)
- Ling He
- The Department of Geratology, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Qingcheng Liu
- The Department of Geratology, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Jielong Cheng
- The Department of Geratology, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Mei Cao
- The Department of Geratology, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Shuaimei Zhang
- The Department of Geratology, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Xiaolin Wan
- The Department of Geratology, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Jian Li
- The Key Laboratory of Hematology of Jiangxi Province, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, China.
| | - Huaijun Tu
- The Department of Geratology, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330006, Jiangxi, China.
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Luo L, Yao L, Xie Y, Chen E, Ding Y, Ge L. miR-526b-5p/c-Myc/Foxp1 participates in recurrent spontaneous abortion by regulating the proliferation, migration, and invasion of trophoblasts. J Assist Reprod Genet 2023:10.1007/s10815-023-02793-0. [PMID: 37052757 DOI: 10.1007/s10815-023-02793-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023] Open
Abstract
PURPOSE As a member of the C19MC family, miR-526b-5p is mainly expressed in the placental tissue and is a well-known tumor suppressor microRNA. However, its effect on the function of trophoblasts and its role in the development of recurrent spontaneous abortion (RSA) remains unclear. METHODS Transcriptome sequencing, quantitative real-time polymerase chain reaction (RT-qPCR), Western blot, 5-ethynyl-2'-deoxyuridine (Edu) proliferation analysis, cell counting kit-8 (CCK8) assay, Transwell assays, and wound healing were used to detect the proliferation, migration, and invasion capacity of trophoblasts. Target genes of miR-526b-5p were obtained by the dual luciferase reporter system. The promoter-reporter system and ChIP-qPCR were used to prove that c-Myc positively regulated the expression of Foxp1 RESULTS: The miR-526b-5p levels were significantly higher in patients with RSA than in controls. High expression of miR-526b-5p inhibited the proliferation, migration, and invasion of trophoblast cell line. By contrast, low expression of miR-526b-5p promoted the proliferation and migration of trophoblast cell line. Target genes of miR-526b-5p were c-Myc and Foxp1. c-Myc positively regulated the expression of Foxp1 by binding to the Foxp1 promoter location -146/-135. Finally, miR-526b-5p impeded the proliferation, migration, and invasion of trophoblasts by negatively regulating c-Myc by rescue experiments. CONCLUSION Thus, miR-526b-5p affected the proliferation, migration, and invasion of trophoblasts by targeting c-Myc and Foxp1. Low expression of c-Myc further deactivated the positive transcriptional regulation of c-Myc on Foxp1, which may be the mechanism of RSA. This study provides potential therapeutic targets and clues for the diagnosis and treatment of RSA.
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Affiliation(s)
- Li Luo
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, No. 1 Yixueyuan Rd, Chongqing, 400016, China
- , Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, No. 120, Longshan Rd, Chongqing, 401147, China
| | - Lu Yao
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, No. 1 Yixueyuan Rd, Chongqing, 400016, China
- , Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, No. 120, Longshan Rd, Chongqing, 401147, China
| | - Youlong Xie
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, No. 1 Yixueyuan Rd, Chongqing, 400016, China
| | - Enxiang Chen
- Department of Genetics, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yubin Ding
- , Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, No. 120, Longshan Rd, Chongqing, 401147, China
| | - Luxing Ge
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, No. 1 Yixueyuan Rd, Chongqing, 400016, China.
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42
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Dučić T, Sanchez-Mata A, Castillo-Sanchez J, Algarra M, Gonzalez-Munoz E. Monitoring oocyte-based human pluripotency acquisition using synchrotron-based FTIR microspectroscopy reveals specific biomolecular trajectories. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 297:122713. [PMID: 37084681 DOI: 10.1016/j.saa.2023.122713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/09/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
The reprogramming of human somatic cells to induced pluripotent cells (iPSCs) has become a milestone and a paradigm shift in the field of regenerative medicine and human disease modeling including drug testing and genome editing. However, the molecular processes occurring during reprogramming and affecting the pluripotent state acquired remain largely unknown. Of interest, different pluripotent states have been described depending on the reprogramming factors used and the oocyte has emerged as a valuable source of information for candidate factors. The present study investigates the molecular changes occurring in somatic cells during reprogramming with either canonical (OSK) or oocyte-based (AOX15) combinations using synchrotron-radiation Fourier transform infrared (SR FTIR) spectroscopy. The data acquired by SR FTIR indicates different representation and conformation of biological relevant macromolecules (lipids, nucleic acids, carbohydrates and proteins) depending on the reprogramming combination used and at different stages during the reprogramming process. Association analysis based on cells spectra suggest that pluripotency acquisition trajectories converge at late intermediate stages while they diverge at early stages. Our results suggest that OSK and AOX15 reprogramming operates through differential mechanisms affecting nucleic acids reorganization and day 10 comes out as a candidate hinge point to further study the molecular pathways involved in the reprogramming process. This study indicates that SR FTIR approach contribute unpaired information to distinguish pluripotent states and to decipher pluripotency acquisition roadmaps and landmarks that will enable advanced biomedical applications of iPSCs.
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Affiliation(s)
- Tanja Dučić
- ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain.
| | - Alicia Sanchez-Mata
- Biomedical Research Institute and Nanomedicine Platform (IBIMA-BIONAND), C/ Severo Ochoa, 35, Malaga, Spain; Department of Cell Biology, Genetics and Physiology, University of Málaga, 29071 Málaga, Spain
| | - Jesus Castillo-Sanchez
- Biomedical Research Institute and Nanomedicine Platform (IBIMA-BIONAND), C/ Severo Ochoa, 35, Malaga, Spain; Department of Cell Biology, Genetics and Physiology, University of Málaga, 29071 Málaga, Spain
| | - Manuel Algarra
- INAMAT(2) Institute for Advanced Materials and Mathematics, Department of Sciences, Public University of Navarre, Campus de Arrosadia, 31006 Pamplona, Spain
| | - Elena Gonzalez-Munoz
- Biomedical Research Institute and Nanomedicine Platform (IBIMA-BIONAND), C/ Severo Ochoa, 35, Malaga, Spain; Department of Cell Biology, Genetics and Physiology, University of Málaga, 29071 Málaga, Spain.
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43
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Zorzan I, Betto RM, Rossignoli G, Arboit M, Drusin A, Corridori C, Martini P, Martello G. Chemical conversion of human conventional PSCs to TSCs following transient naive gene activation. EMBO Rep 2023; 24:e55235. [PMID: 36847616 PMCID: PMC10074076 DOI: 10.15252/embr.202255235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 03/01/2023] Open
Abstract
In human embryos, naive pluripotent cells of the inner cell mass (ICM) generate epiblast, primitive endoderm and trophectoderm (TE) lineages, whence trophoblast cells derive. In vitro, naive pluripotent stem cells (PSCs) retain this potential and efficiently generate trophoblast stem cells (TSCs), while conventional PSCs form TSCs at low efficiency. Transient histone deacetylase and MEK inhibition combined with LIF stimulation is used to chemically reset conventional to naive PSCs. Here, we report that chemical resetting induces the expression of both naive and TSC markers and of placental imprinted genes. A modified chemical resetting protocol allows for the fast and efficient conversion of conventional PSCs into TSCs, entailing shutdown of pluripotency genes and full activation of the trophoblast master regulators, without induction of amnion markers. Chemical resetting generates a plastic intermediate state, characterised by co-expression of naive and TSC markers, after which cells steer towards one of the two fates in response to the signalling environment. The efficiency and rapidity of our system will be useful to study cell fate transitions and to generate models of placental disorders.
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Affiliation(s)
- Irene Zorzan
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | | | | | - Mattia Arboit
- Department of Biology, University of Padua, Padua, Italy
| | - Andrea Drusin
- Department of Biology, University of Padua, Padua, Italy
| | | | - Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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44
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Han D, Liu G, Oh Y, Oh S, Yang S, Mandjikian L, Rani N, Almeida MC, Kosik KS, Jang J. ZBTB12 is a molecular barrier to dedifferentiation in human pluripotent stem cells. Nat Commun 2023; 14:632. [PMID: 36759523 PMCID: PMC9911396 DOI: 10.1038/s41467-023-36178-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
Development is generally viewed as one-way traffic of cell state transition from primitive to developmentally advanced states. However, molecular mechanisms that ensure the unidirectional transition of cell fates remain largely unknown. Through exact transcription start site mapping, we report an evolutionarily conserved BTB domain-containing zinc finger protein, ZBTB12, as a molecular barrier for dedifferentiation of human pluripotent stem cells (hPSCs). Single-cell RNA sequencing reveals that ZBTB12 is essential for three germ layer differentiation by blocking hPSC dedifferentiation. Mechanistically, ZBTB12 fine-tunes the expression of human endogenous retrovirus H (HERVH), a primate-specific retrotransposon, and targets specific transcripts that utilize HERVH as a regulatory element. In particular, the downregulation of HERVH-overlapping long non-coding RNAs (lncRNAs) by ZBTB12 is necessary for a successful exit from a pluripotent state and lineage derivation. Overall, we identify ZBTB12 as a molecular barrier that safeguards the unidirectional transition of metastable stem cell fates toward developmentally advanced states.
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Affiliation(s)
- Dasol Han
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Guojing Liu
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.,Novogene Co., Ltd, Beijing, China
| | - Yujeong Oh
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Seyoun Oh
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Seungbok Yang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Lori Mandjikian
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Neha Rani
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.,Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Maria C Almeida
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.,Federal University of ABC, Center for Natural and Human Sciences São Bernardo do Campo, Santo André, Brazil
| | - Kenneth S Kosik
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
| | - Jiwon Jang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea.
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45
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Burgaud M, Bretin B, Reignier A, De Vos J, David L. [New models to study human embryonic development]. Med Sci (Paris) 2023; 39:129-136. [PMID: 36799747 DOI: 10.1051/medsci/2023018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Since 2021, assisted reproductive technologies (ART) are available to infertile couples, but also to single women and female couples. The process of in vitro fertilization (IVF) has allowed to cross the threshold of 5 million births worldwide, between 1978 and 2013. However, the failure rate per each IVF cycle is estimated to be around 75%. Therefore, there is a need to better understand human embryonic development in order to improve the success rate of IVF. Study models have evolved significantly in recent years: development of embryo culture, sequencing of the transcriptome of individualized cells, discovery of culture conditions for naive pluripotent stem cells and generation of blastoids. Here, we review these recent advances in human embryo modeling that establish a new knowledge base for improving ART.
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Affiliation(s)
- Mathilde Burgaud
- Nantes université, CHU Nantes, Inserm, CR2TI, F-44000 Nantes, France
| | - Betty Bretin
- Nantes université, CHU Nantes, Inserm, CR2TI, F-44000 Nantes, France
| | - Arnaud Reignier
- Nantes université, CHU Nantes, Inserm, CR2TI, F-44000 Nantes, France - CHU Nantes, Service de biologie de la reproduction, F-44000 Nantes, France
| | - John De Vos
- IRMB, Univ Montpellier, Inserm, CHU Montpellier, Montpellier, France
| | - Laurent David
- Nantes université, CHU Nantes, Inserm, CR2TI, F-44000 Nantes, France - Nantes université, CHU Nantes, Inserm, CNRS, BioCore, F-44000 Nantes, France
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46
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Guallar D. Roadmap of the Early Events of In Vivo Somatic Cell Reprogramming. Cell Reprogram 2023; 25:7-8. [PMID: 36695734 DOI: 10.1089/cell.2022.0160] [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: 01/26/2023] Open
Abstract
Single-cell transcriptomics and in situ imaging of murine pancreas upon partial reprogramming in vivo reveal transcriptional dynamics upon Oct4, Sox2, Klf4, and cMyc (OSKM) induction. Interestingly, transcriptomic signatures of partial reprogramming observed in pancreas are shared by several tissues upon OSKM induction as well as during in vitro reprogramming of fibroblasts, pointing to the existence of conserved pathways critical for early reprogramming, regeneration, and rejuvenation.
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Affiliation(s)
- Diana Guallar
- Epitranscriptomics & Ageing Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
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47
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Ouyang JF, Chothani S, Rackham OJ. Deep learning models will shape the future of stem cell research. Stem Cell Reports 2023; 18:6-12. [PMID: 36630908 PMCID: PMC9860061 DOI: 10.1016/j.stemcr.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 01/12/2023] Open
Abstract
Our ability to understand and control stem cell biology is being augmented by developments on two fronts, our ability to collect more data describing cell state and our capability to comprehend these data using deep learning models. Here we consider the impact deep learning will have in the future of stem cell research. We explore the importance of generating data suitable for these methods, the requirement for close collaboration between experimental and computational researchers, and the challenges we face to do this fairly and effectively. Achieving this will ensure that the resulting deep learning models are biologically meaningful and computationally tractable.
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Affiliation(s)
- John F. Ouyang
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Singapore, Singapore
| | - Sonia Chothani
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Singapore, Singapore
| | - Owen J.L. Rackham
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders (CVMD) and Centre for Computational Biology (CCB), Singapore, Singapore,School of Biological Sciences, University of Southampton, Southampton, UK,The Alan Turing Institute, The British Library, London, UK,Corresponding author
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48
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Li H, Peng H, Hong W, Wei Y, Tian H, Huang X, Jia L, Zheng J, Duan T, He Q, Wang K. Human Placental Endothelial Cell and Trophoblast Heterogeneity and Differentiation Revealed by Single-Cell RNA Sequencing. Cells 2022; 12:cells12010087. [PMID: 36611882 PMCID: PMC9818681 DOI: 10.3390/cells12010087] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The placenta is an important organ for fetal and maternal health during pregnancy and impacts offspring health late in life. Defects in placental vasculature and trophoblast have been identified in several pregnancy complications. Thus, the detailed molecular profile and heterogeneity of endothelial cells and trophoblasts in placentas will aid us in better understanding placental behaviors and improving pregnancy outcomes. METHODS Single-cell RNA sequencing (scRNA-seq) was performed to profile the transcriptomics of human placental villous tissues from eleven patients with normal pregnancies in the first and second trimesters (6-16 weeks of gestation). RESULTS The transcriptomic landscape of 52,179 single cells was obtained, and the cells were classified as trophoblasts, fibroblasts, endothelial cells, erythroid cells, Hofbauer cells, and macrophages. Our analysis further revealed the three subtypes of placental endothelial cells, with distinct metabolic signatures and transcription factor regulatory networks. We also determined the transcriptomic features of the trophoblast subpopulations and characterized two distinct populations of progenitor cells in cytotrophoblasts, which were capable of differentiating to extravillous trophoblasts and syncytiotrophoblasts, respectively. CONCLUSIONS Our study provided a high-resolution molecular profile of the human placenta between 6 and 16 weeks of gestation. Our data revealed the placental cell complexity and demonstrated the transcriptional networks and signaling involved in placental endothelial and trophoblast differentiation during early pregnancy, which will be a resource for future studies of the human placental development.
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Affiliation(s)
- Han Li
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Hao Peng
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Wei Hong
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Yingying Wei
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Haojun Tian
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Xiaojie Huang
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Linyan Jia
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Jing Zheng
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Tao Duan
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Qizhi He
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
- Correspondence: (Q.H.); (K.W.)
| | - Kai Wang
- Clinical and Translational Research Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 201204, China
- Correspondence: (Q.H.); (K.W.)
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49
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Moya-Jódar M, Ullate-Agote A, Barlabé P, Rodríguez-Madoz JR, Abizanda G, Barreda C, Carvajal-Vergara X, Vilas-Zornoza A, Romero JP, Garate L, Agirre X, Coppiello G, Prósper F, Aranguren XL. Revealing cell populations catching the early stages of human embryo development in naive pluripotent stem cell cultures. Stem Cell Reports 2022; 18:64-80. [PMID: 36563688 PMCID: PMC9860119 DOI: 10.1016/j.stemcr.2022.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022] Open
Abstract
Naive human pluripotent stem cells (hPSCs) are defined as the in vitro counterpart of the human preimplantation embryo's epiblast and are used as a model system to study developmental processes. In this study, we report the discovery and characterization of distinct cell populations coexisting with epiblast-like cells in 5iLAF naive human induced PSC (hiPSC) cultures. It is noteworthy that these populations closely resemble different cell types of the human embryo at early developmental stages. While epiblast-like cells represent the main cell population, interestingly we detect a cell population with gene and transposable element expression profile closely resembling the totipotent eight-cell (8C)-stage human embryo, and three cell populations analogous to trophectoderm cells at different stages of their maturation process: transition, early, and mature stages. Moreover, we reveal the presence of cells resembling primitive endoderm. Thus, 5iLAF naive hiPSC cultures provide an excellent opportunity to model the earliest events of human embryogenesis, from the 8C stage to the peri-implantation period.
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Affiliation(s)
- Marta Moya-Jódar
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Asier Ullate-Agote
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Paula Barlabé
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Juan Roberto Rodríguez-Madoz
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Gloria Abizanda
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Carolina Barreda
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Xonia Carvajal-Vergara
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Amaia Vilas-Zornoza
- Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Juan Pablo Romero
- Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain,10x Genomics, 6230 Stoneridge Mall Road, Pleasanton, CA 94588, USA
| | - Leire Garate
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Giulia Coppiello
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Felipe Prósper
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain; Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain; Hematology Department, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain.
| | - Xabier L. Aranguren
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain,Corresponding author
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50
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Larcombe MR, Hsu S, Polo JM, Knaupp AS. Indirect Mechanisms of Transcription Factor-Mediated Gene Regulation during Cell Fate Changes. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2200015. [PMID: 36911290 PMCID: PMC9993476 DOI: 10.1002/ggn2.202200015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Indexed: 06/18/2023]
Abstract
Transcription factors (TFs) are the master regulators of cellular identity, capable of driving cell fate transitions including differentiations, reprogramming, and transdifferentiations. Pioneer TFs recognize partial motifs exposed on nucleosomal DNA, allowing for TF-mediated activation of repressed chromatin. Moreover, there is evidence suggesting that certain TFs can repress actively expressed genes either directly through interactions with accessible regulatory elements or indirectly through mechanisms that impact the expression, activity, or localization of other regulatory factors. Recent evidence suggests that during reprogramming, the reprogramming TFs initiate opening of chromatin regions rich in somatic TF motifs that are inaccessible in the initial and final cellular states. It is postulated that analogous to a sponge, these transiently accessible regions "soak up" somatic TFs, hence lowering the initial barriers to cell fate changes. This indirect TF-mediated gene regulation event, which is aptly named the "sponge effect," may play an essential role in the silencing of the somatic transcriptional network during different cellular conversions.
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Affiliation(s)
- Michael R. Larcombe
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
| | - Sheng Hsu
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
| | - Jose M. Polo
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
- South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical SciencesUniversity of AdelaideAdelaideSouth Australia5005Australia
- Adelaide Centre for Epigenetics, Faculty of Health and Medical SciencesUniversity of AdelaideAdelaideSouth Australia5005Australia
| | - Anja S. Knaupp
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
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