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Raposo AC, Caldas P, Jeremias J, Arez M, Cazaux Mateus F, Barbosa P, Sousa-Luís R, Água F, Oxley D, Mupo A, Eckersley-Maslin M, Casanova M, Grosso AR, da Rocha ST. Gene reactivation upon erosion of X chromosome inactivation in female hiPSCs is predictable yet variable and persists through differentiation. Stem Cell Reports 2025; 20:102472. [PMID: 40185090 DOI: 10.1016/j.stemcr.2025.102472] [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: 04/09/2024] [Revised: 03/06/2025] [Accepted: 03/07/2025] [Indexed: 04/07/2025] Open
Abstract
Female human induced pluripotent stem cells frequently undergo X-chromosome inactivation (XCI) erosion, marked by X-inactive specific transcript (XIST) RNA loss and partial reactivation of the inactive X (Xi). This overlooked phenomenon limits our understanding of its impact on stem cell applications. Here, we show that XCI erosion is frequent and heterogeneous, leading to the reactivation of several X-linked genes. These are primarily located on the short arm of the X chromosome, particularly near escape genes and within H3K27me3-enriched domains, with reactivation linked to reduced promoter DNA methylation. Interestingly, escape genes further increase their expression from Xi upon XCI erosion, highlighting the critical role of XIST in their dosage regulation. Importantly, global (hydroxy)methylation levels and imprinted regions remain unaffected, and analysis of trilineage commitment and cardiomyocyte formation reveals that XCI erosion persists across differentiation. These findings underscore the need for greater awareness of the implications of XCI erosion for stem cell research and clinical applications.
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Affiliation(s)
- Ana Cláudia Raposo
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Paulo Caldas
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Department of Life Sciences, UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Joana Jeremias
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Arez
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Francisca Cazaux Mateus
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Barbosa
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal; LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Rui Sousa-Luís
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal; Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Frederico Água
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Department of Life Sciences, UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge, UK
| | - Annalisa Mupo
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Altos Labs, Cambridge, UK
| | - Melanie Eckersley-Maslin
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Miguel Casanova
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Rita Grosso
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Department of Life Sciences, UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Simão Teixeira da Rocha
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
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2
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Zimmerlin L, Angarita A, Park TS, Evans-Moses R, Thomas J, Yan S, Uribe I, Vegas I, Kochendoerfer C, Buys W, Leung AKL, Zambidis ET. Proteogenomic reprogramming to a functional human blastomere-like stem cell state via a PARP-DUX4 regulatory axis. Cell Rep 2025; 44:115671. [PMID: 40338744 DOI: 10.1016/j.celrep.2025.115671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 02/17/2025] [Accepted: 04/16/2025] [Indexed: 05/10/2025] Open
Abstract
Here, we show that conventional human pluripotent stem cells cultured with non-specific tankyrase-PARP1-inhibited conditions underwent proteogenomic reprogramming to functional blastomere-like tankyrase/PARP inhibitor-regulated naive stem cells (TIRN-SC). TIRN-SCs concurrently expressed hundreds of pioneer factors in hybrid 2C-8C-morula-ICM programs that were augmented by induced expression of DUX4. Injection of TIRN-SCs into 8C-staged murine embryos equipotently differentiated human cells to the extra-embryonic and embryonic compartments of chimeric blastocysts and fetuses. Ectopic expression of murine-E-Cadherin in TIRN-SCs further enhanced interspecific chimeric tissue targeting. TIRN-SC-derived trophoblast stem cells efficiently generated placental chimeras. Proteome-ubiquitinome analyses revealed increased TNKS and reduced PARP1 levels and an ADP-ribosylation-deficient, hyper-ubiquitinated proteome that impacted expression of both tankyrase and PARP1 substrates. ChIP-seq of NANOG-SOX2-OCT4 and PARP1 (NSOP) revealed genome-wide NSOP co-binding at DUX4-accessible enhancers of embryonic lineage factors; suggesting a DUX4-NSOP axis regulated TIRN-SC lineage plasticity. TIRN-SCs may serve as valuable models for studying the proteogenomic regulation of pre-lineage human embryogenesis. VIDEO ABSTRACT.
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Affiliation(s)
- Ludovic Zimmerlin
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ariana Angarita
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tea Soon Park
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rebecca Evans-Moses
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Justin Thomas
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sirui Yan
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Isabel Uribe
- Departments of Biochemistry and Molecular Biology, The Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Isabella Vegas
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Clara Kochendoerfer
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Willem Buys
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Anthony K L Leung
- Departments of Biochemistry and Molecular Biology, The Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Elias T Zambidis
- Institute for Cell Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA.
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3
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Hua L, Peng Y, Yan L, Yuan P, Qiao J. Moving toward totipotency: the molecular and cellular features of totipotent and naive pluripotent stem cells. Hum Reprod Update 2025:dmaf006. [PMID: 40299455 DOI: 10.1093/humupd/dmaf006] [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: 05/25/2023] [Revised: 01/06/2025] [Indexed: 04/30/2025] Open
Abstract
BACKGROUND Dissecting the key molecular mechanism of embryonic development provides novel insights into embryogenesis and potential intervention strategies for clinical practices. However, the ability to study the molecular mechanisms of early embryo development in humans, such as zygotic genome activation and lineage segregation, is meaningfully constrained by methodological limitations and ethical concerns. Totipotent stem cells have an extended developmental potential to differentiate into embryonic and extraembryonic tissues, providing a suitable model for studying early embryo development. Recently, a series of ground-breaking results on stem cells have identified totipotent-like cells or induced pluripotent stem cells into totipotent-like cells. OBJECTIVE AND RATIONALE This review followed the PRISMA guidelines, surveys the current works of literature on totipotent, naive, and formative pluripotent stem cells, introduces the molecular and biological characteristics of those stem cells, and gives advice for future research. SEARCH METHODS The search method employed the terms 'totipotent' OR 'naive pluripotent stem cell' OR 'formative pluripotent stem cell' for unfiltered search on PubMed, Web of Science, and Cochrane Library. Papers included were those with information on totipotent stem cells, naive pluripotent stem cells, or formative pluripotent stem cells until June 2024 and were published in the English language. Articles that have no relevance to stem cells, or totipotent, naive pluripotent, or formative pluripotent cells were excluded. OUTCOMES There were 152 records included in this review. These publications were divided into four groups according to the species of the cells included in the studies: 67 human stem cell studies, 70 mouse stem cell studies, 9 porcine stem cell studies, and 6 cynomolgus stem cell studies. Naive pluripotent stem cell models have been established in other species such as porcine and cynomolgus. Human and mouse totipotent stem cells, e.g. human 8-cell-like cells, human totipotent blastomere-like cells, and mouse 2-cell-like cells, have been successfully established and exhibit high developmental potency for both embryonic and extraembryonic contributions. However, the observed discrepancies between these cells and real embryos in terms of epigenetics and transcription suggest that further research is warranted. Our results systematically reviewed the established methods, molecular characteristics, and developmental potency of different naive, formative pluripotent, and totipotent stem cells. Furthermore, we provide a parallel comparison between animal and human models, and offer recommendations for future applications to advance early embryo research and assisted reproduction technologies. WIDER IMPLICATIONS Totipotent cell models provide a valuable resource to understand the underlying mechanisms of embryo development and forge new paths toward future treatment of infertility and regenerative medicine. However, current in vitro cell models exhibit epigenetic and transcriptional differences from in vivo embryos, and many cell models are unstable across passages, thus imperfectly recapitulating embryonic development. In this regard, standardizing and expanding current research on totipotent stem cell models are essential to enhance our capability to resemble and decipher embryogenesis.
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Affiliation(s)
- Lingyue Hua
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Yuyang Peng
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Liying Yan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Peng Yuan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Jie Qiao
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics, Beijing, China
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4
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Ren H, Jia X, Yu L. The building blocks of embryo models: embryonic and extraembryonic stem cells. Cell Discov 2025; 11:40. [PMID: 40258839 PMCID: PMC12012135 DOI: 10.1038/s41421-025-00780-6] [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: 04/24/2024] [Accepted: 01/10/2025] [Indexed: 04/23/2025] Open
Abstract
The process of a single-celled zygote developing into a complex multicellular organism is precisely regulated at spatial and temporal levels in vivo. However, understanding the mechanisms underlying development, particularly in humans, has been constrained by technical and ethical limitations associated with studying natural embryos. Harnessing the intrinsic ability of embryonic stem cells (ESCs) to self-organize when induced and assembled, researchers have established several embryo models as alternative approaches to studying early development in vitro. Recent studies have revealed the critical role of extraembryonic cells in early development; and many groups have created more sophisticated and precise ESC-derived embryo models by incorporating extraembryonic stem cell lines, such as trophoblast stem cells (TSCs), extraembryonic mesoderm cells (EXMCs), extraembryonic endoderm cells (XENs, in rodents), and hypoblast stem cells (in primates). Here, we summarize the characteristics of existing mouse and human embryonic and extraembryonic stem cells and review recent advancements in developing mouse and human embryo models.
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Affiliation(s)
- Hongan Ren
- State Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojie Jia
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Leqian Yu
- State Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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5
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Papetti AV, Jin M, Ma Z, Stillitano AC, Jiang P. Chimeric brain models: Unlocking insights into human neural development, aging, diseases, and cell therapies. Neuron 2025:S0896-6273(25)00256-9. [PMID: 40300597 DOI: 10.1016/j.neuron.2025.03.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2025] [Revised: 03/07/2025] [Accepted: 03/31/2025] [Indexed: 05/01/2025]
Abstract
Human-rodent chimeric brain models serve as a unique platform for investigating the pathophysiology of human cells within a living brain environment. These models are established by transplanting human tissue- or human pluripotent stem cell (hPSC)-derived macroglial, microglial, or neuronal lineage cells, as well as cerebral organoids, into the brains of host animals. This approach has opened new avenues for exploring human brain development, disease mechanisms, and regenerative processes. Here, we highlight recent advancements in using chimeric models to study human neural development, aging, and disease. Additionally, we explore the potential applications of these models for studying human glial cell-replacement therapies, studying in vivo human glial-to-neuron reprogramming, and harnessing single-cell omics and advanced functional assays to uncover detailed insights into human neurobiology. Finally, we discuss strategies to enhance the precision and translational relevance of these models, expanding their impact in stem cell and neuroscience research.
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Affiliation(s)
- Ava V Papetti
- Department of Cell Biology and Neuroscience, Rutgers University-New Brunswick, Piscataway, NJ 08854, USA
| | - Mengmeng Jin
- Department of Cell Biology and Neuroscience, Rutgers University-New Brunswick, Piscataway, NJ 08854, USA
| | - Ziyuan Ma
- Department of Cell Biology and Neuroscience, Rutgers University-New Brunswick, Piscataway, NJ 08854, USA
| | - Alessandro C Stillitano
- Department of Cell Biology and Neuroscience, Rutgers University-New Brunswick, Piscataway, NJ 08854, USA
| | - Peng Jiang
- Department of Cell Biology and Neuroscience, Rutgers University-New Brunswick, Piscataway, NJ 08854, USA.
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6
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Huang T, Radley A, Yanagida A, Ren Z, Carlisle F, Tahajjodi S, Kim D, O'Neill P, Clarke J, Lancaster MA, Heckhausen Z, Zhuo J, de Sousa JPA, Hajkova P, von Meyenn F, Imai H, Nakauchi H, Guo G, Smith A, Masaki H. Inhibition of PRC2 enables self-renewal of blastoid-competent naive pluripotent stem cells from chimpanzee. Cell Stem Cell 2025; 32:627-639.e8. [PMID: 40015279 DOI: 10.1016/j.stem.2025.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 10/11/2024] [Accepted: 02/04/2025] [Indexed: 03/01/2025]
Abstract
Naive pluripotent stem cells (PSCs) are counterparts of early epiblast in the mammalian embryo. Mouse and human naive PSCs differ in self-renewal requirements and extraembryonic lineage potency. Here, we investigated the generation of chimpanzee naive PSCs. Colonies generated by resetting or reprogramming failed to propagate. We discovered that self-renewal is enabled by inhibition of Polycomb repressive complex 2 (PRC2). Expanded cells show global transcriptome proximity to human naive PSCs and embryo pre-implantation epiblast, with shared expression of a subset of pluripotency transcription factors. Chimpanzee naive PSCs can transition to multilineage competence or can differentiate into trophectoderm and hypoblast, forming tri-lineage blastoids. They thus provide a higher primate comparative model for studying pluripotency and early embryogenesis. Genetic deletions confirm that PRC2 mediates growth arrest. Further, inhibition of PRC2 overcomes a roadblock to feeder-free propagation of human naive PSCs. Therefore, excess deposition of chromatin modification H3K27me3 is an unexpected barrier to naive PSC self-renewal.
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Affiliation(s)
- Tao Huang
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Arthur Radley
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Ayaka Yanagida
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo 113-8657, Japan; Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Zhili Ren
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | | | | | - Dongwan Kim
- Stem Cell Therapy Division, Institute of Integrated Research, Institute of Science, Tokyo 113-8510, Japan
| | - Paul O'Neill
- University of Exeter Sequencing Facility, University of Exeter, Exeter EX4 4QD, UK
| | - James Clarke
- Wellcome-MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Zoe Heckhausen
- MRC Laboratory of Medical Sciences (LMS), Du Cane Rd, London W12 0HS, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, W12 0NN, UK
| | - Jingran Zhuo
- Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | | | - Petra Hajkova
- MRC Laboratory of Medical Sciences (LMS), Du Cane Rd, London W12 0HS, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, W12 0NN, UK
| | - Ferdinand von Meyenn
- Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Stem Cell Therapy Division, Institute of Integrated Research, Institute of Science, Tokyo 113-8510, Japan; Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ge Guo
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Austin Smith
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK.
| | - Hideki Masaki
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Stem Cell Therapy Division, Institute of Integrated Research, Institute of Science, Tokyo 113-8510, Japan.
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7
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Fischer LA, Meyer B, Reyes M, Zemke JE, Harrison JK, Park KM, Wang T, Jüppner H, Dietmann S, Theunissen TW. Tracking and mitigating imprint erasure during induction of naive human pluripotency at single-cell resolution. Stem Cell Reports 2025; 20:102419. [PMID: 39952244 PMCID: PMC11960550 DOI: 10.1016/j.stemcr.2025.102419] [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: 06/19/2024] [Revised: 01/14/2025] [Accepted: 01/15/2025] [Indexed: 02/17/2025] Open
Abstract
Naive human pluripotent stem cells (hPSCs) model the pre-implantation epiblast. However, parent-specific epigenetic marks (imprints) are eroded in naive hPSCs, which represents an important deviation from the epiblast in vivo. To track the dynamics of imprint erasure during naive resetting in real time, we established a dual-colored fluorescent reporter at both alleles of the imprinted SNRPN locus. During primed-to-naive resetting, SNRPN expression becomes biallelic in most naive cells, and biallelic SNRPN expression is irreversible upon re-priming. We utilized this live-cell reporter to evaluate chemical and genetic strategies to minimize imprint erasure. Decreasing the level of MEK/ERK inhibition or overexpressing the KRAB zinc-finger protein ZFP57 protected a subset of imprints during naive resetting. Combining these two strategies protected imprint levels to a further extent than either strategy alone. This study offers an experimental tool to track and enhance imprint stability during transitions between human pluripotent states in vitro.
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Affiliation(s)
- Laura A Fischer
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Brittany Meyer
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Monica Reyes
- Endocrine Unit, Department of Medicine and Pediatric Nephrology Unit, Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph E Zemke
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jessica K Harrison
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyoung-Mi Park
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Harald Jüppner
- Endocrine Unit, Department of Medicine and Pediatric Nephrology Unit, Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sabine Dietmann
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA; Institute for Informatics (I(2)), Washington University School of Medicine, St. Louis, MO, USA
| | - Thorold W Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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8
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Zhu J, Li Z, Xue D, Meng Z, Shao S, Pulecio J, Zhang G, Huangfu D, Evans T, Schultz PG, Chen S. A Chemical Epigenetic Probe to Capture the Site-Specific DNA-Binding Protein Complex. RESEARCH SQUARE 2025:rs.3.rs-5915426. [PMID: 40162224 PMCID: PMC11952667 DOI: 10.21203/rs.3.rs-5915426/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Site-specific DNA binding by proteins is critical for regulating genetic activity and cell fate decision. However, identifying proteins bound to specific genomic regions (e.g., promoter or enhancer) remains challenging. To address this, we developed a chemical epigenetic tool, named Site-specific non-canonical amino acid resolved Protein EnRichment (SUPER) system, incorporating a photo-crosslinking amino acid into nuclease-deficient dCas9 mutant. Human pluripotent stem cells (hPSCs) carrying SUPER enables the capture of proteins bound to, in theory, any genomic location, facilitating the study of the cell context-dependent DNA-protein interactions. Using SUPER, we identified OCT4/SOX2/CARHSP1 complex binding to the NANOG promoter to maintain pluripotency in hPSCs. During ectoderm differentiation, ZIC2 acts as a competitive inhibitor, binding the same promoter to downregulate NANOG expression and promote differentiation. Additionally, SUPER identified ZNF8 binding to the distal regulatory region of OCT4 and maintain naïve pluripotency. In summary, SUPER provides a robust system for uncovering the cell context-dependent, site-specific genome regulators, offering valuable insights into gene regulation networks driving cell fate transitions.
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Affiliation(s)
- Jiajun Zhu
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
| | - Zhucui Li
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dongxiang Xue
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
| | - Zihe Meng
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
| | - Sida Shao
- Department of Chemistry, Scripps Research, San Diego, CA, USA
| | - Julian Pulecio
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY 10065, USA
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
| | | | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
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9
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Lea G, Doria-Borrell P, Ferrero-Micó A, Varma A, Simon C, Anderson H, Biggins L, De Clercq K, Andrews S, Niakan KK, Gahurova L, McGovern N, Pérez-García V, Hanna CW. Ectopic expression of DNMT3L in human trophoblast stem cells restores features of the placental methylome. Cell Stem Cell 2025; 32:276-292.e9. [PMID: 39788122 DOI: 10.1016/j.stem.2024.12.007] [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: 05/03/2024] [Revised: 10/07/2024] [Accepted: 12/16/2024] [Indexed: 01/12/2025]
Abstract
The placental DNA methylation landscape is unique, with widespread partially methylated domains (PMDs). The placental "methylome" is conserved across mammals, a shared feature of many cancers, and extensively studied for links with pregnancy complications. Human trophoblast stem cells (hTSCs) offer exciting potential for functional studies to better understand this epigenetic feature; however, whether the hTSC epigenome recapitulates primary trophoblast remains unclear. We find that hTSCs exhibit an atypical methylome compared with trophectoderm and 1st trimester cytotrophoblast. Regardless of cell origin, oxygen levels, or culture conditions, hTSCs show localized DNA methylation within transcribed gene bodies and a complete loss of PMDs. Unlike early human trophoblasts, hTSCs display a notable absence of DNMT3L expression, which is necessary for PMD establishment in mouse trophoblasts. Remarkably, we demonstrate that ectopic expression of DNMT3L in hTSCs restores placental PMDs, supporting a conserved role for DNMT3L in de novo methylation in trophoblast development in human embryogenesis.
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Affiliation(s)
- Georgia Lea
- Loke Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | | | | | - Anakha Varma
- Loke Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Claire Simon
- Loke Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Holly Anderson
- Loke Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Department of Pathology, University of Cambridge, Cambridge, UK
| | - Laura Biggins
- Babraham Bioinformatics, Babraham Institute, Cambridge, UK
| | | | - Simon Andrews
- Babraham Bioinformatics, Babraham Institute, Cambridge, UK
| | - Kathy K Niakan
- Loke Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Lenka Gahurova
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Naomi McGovern
- Loke Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Department of Pathology, University of Cambridge, Cambridge, UK
| | - Vicente Pérez-García
- Centro de Investigación Príncipe Felipe, Valencia, Spain; Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain.
| | - Courtney W Hanna
- Loke Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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10
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Wang LN, Jia JS, Yang XL, Wen YT, Liu JX, Li DK, Chen XR, Wang JH, Li JK, Huang ZX, Yao KT. Foxa1 disruption enhances human cell integration in human-mouse interspecies chimeras. Cell Tissue Res 2025; 399:231-245. [PMID: 39708115 DOI: 10.1007/s00441-024-03941-3] [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: 10/30/2024] [Accepted: 11/25/2024] [Indexed: 12/23/2024]
Abstract
Blastocyst complementation can potentially generate a rodent model with humanized nasopharyngeal epithelium (NE) that supports sustained Epstein-Barr virus (EBV) infection, enabling comprehensive studies of EBV biology in nasopharyngeal carcinoma. However, during this process, the specific gene knockouts required to establish a developmental niche for NE remain unclear. We performed bioinformatics analyses and generated Foxa1 mutant mice to confirm that Foxa1 disruption could potentially create a developmental niche for NE. Subsequently, MYD88-inactivated human pluripotent stem cells (hPSCs) were constructed and complemented with Foxa1-deficient mouse blastocysts, with Nosip-deficient mouse blastocysts as a control. The chimerism of human cells in mouse embryos was evaluated from E8.5 to E12.5 using genomic DNA PCR and immunohistochemistry. Our bioinformatics analysis indicated that the expression patterns of Foxa1 in E8.5 to E16.5 mouse embryos underscore its critical role in NE development. The generated mice with Foxa1 disordered region mutations displayed morphological abnormality in NE, suggesting Foxa1-knockouts could potentially establish a developmental niche for NE. In chimeric assays, human cells integrated into 80.00% of Foxa1-deficient embryos, compared with the 4.17% in controls. Immunohistochemistry results revealed robust proliferation of human cells in Foxa1-deficient mouse embryos. However, chimeras from Foxa1-deficient mouse embryos did not survive beyond E10.5, hindering the evaluation of human cell integration in mouse NE. Foxa1 disruption in mouse embryos significantly enhances the integration of human cells in human-mouse interspecies chimeras, thereby facilitating the generation of endoderm-derived organs through blastocyst complementation. Overcoming chimeras' embryonic lethality is crucial for successfully generating humanized NE in Foxa1-deficient mouse embryos.
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Affiliation(s)
- Li-Na Wang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Department of Oncology, School of Medicine, Guangzhou First People's Hospital, Southern China University of Technology, Guangzhou, 510180, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Jun-Shuang Jia
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Xing-Long Yang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Yue-Ting Wen
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Jing-Xian Liu
- Department of Oncology, Shenzen Hospital of Southern Medical University, Shenzhen, 518110, China
| | - Deng-Ke Li
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Xing-Rui Chen
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Jia-Hong Wang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Ji-Ke Li
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China
| | - Zhong-Xi Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China.
| | - Kai-Tai Yao
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China.
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11
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Ma G, Fu X, Zhou L, Babarinde IA, Shi L, Yang W, Chen J, Xiao Z, Qiao Y, Ma L, Ou Y, Li Y, Chang C, Deng B, Zhang R, Sun L, Tong G, Li D, Li Y, Hutchins AP. The nuclear matrix stabilizes primed-specific genes in human pluripotent stem cells. Nat Cell Biol 2025; 27:232-245. [PMID: 39789220 DOI: 10.1038/s41556-024-01595-5] [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: 12/06/2023] [Accepted: 12/11/2024] [Indexed: 01/12/2025]
Abstract
The nuclear matrix, a proteinaceous gel composed of proteins and RNA, is an important nuclear structure that supports chromatin architecture, but its role in human pluripotent stem cells (hPSCs) has not been described. Here we show that by disrupting heterogeneous nuclear ribonucleoprotein U (HNRNPU) or the nuclear matrix protein, Matrin-3, primed hPSCs adopted features of the naive pluripotent state, including morphology and upregulation of naive-specific marker genes. We demonstrate that HNRNPU depletion leads to increased chromatin accessibility, reduced DNA contacts and increased nuclear size. Mechanistically, HNRNPU acts as a transcriptional co-factor that anchors promoters of primed-specific genes to the nuclear matrix with POLII to promote their expression and their RNA stability. Overall, HNRNPU promotes cell-type stability and when reduced promotes conversion to earlier embryonic states.
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Affiliation(s)
- Gang Ma
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xiuling Fu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Lulu Zhou
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Isaac A Babarinde
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Liyang Shi
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenting Yang
- Department of Reproductive Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jiao Chen
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Zhen Xiao
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yu Qiao
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Lisha Ma
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yuhao Ou
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yuhao Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Chen Chang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Boping Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ran Zhang
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Guoqing Tong
- Department of Reproductive Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dongwei Li
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Yiming Li
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
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12
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Katznelson A, Hernandez B, Fahning H, Tapia K, Burton A, Zhang J, Torres-Padilla ME, Plachta N, Zaret KS, McCarthy RL. ERH Enables Early Embryonic Differentiation and Overlays H3K9me3 Heterochromatin on a Cryptic Pluripotency H3K9me3 Landscape in Somatic Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.06.06.597604. [PMID: 38895478 PMCID: PMC11185749 DOI: 10.1101/2024.06.06.597604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Enhancer of Rudimentary Homolog (ERH) is an evolutionarily conserved protein originally characterized in fission yeast 1 and recently shown to maintain H3K9me3 in human fibroblasts 2 . Here, we find that ERH depletion in fibroblasts reverts the H3K9me3 landscape to an embryonic stem cell (ESC) state and enables activation of naïve and pluripotency genes and transposable elements during induced pluripotent stem cell (iPSC) reprogramming. We find that ERH similarly represses totipotent and alternative lineage programs during mouse preimplantation development and is required for proper segregation of the inner cell mass and trophectoderm cell lineages. During human ESC differentiation into germ layer lineages, ERH silences naïve and pluripotency genes, transposable elements, and alternative lineage somatic genes. As in fission yeast, we find that mammalian ERH interacts with RNA-binding proteins to engage and repress its chromatin targets. Our findings reveal a fundamental role for ERH in cell fate specification via the initiation and maintenance of early developmental gene repression.
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13
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Levin-Ferreyra F, Kodali S, Cui Y, Pashos ARS, Pessina P, Brumbaugh J, Di Stefano B. Transposable element activity captures human pluripotent cell states. EMBO Rep 2025; 26:329-352. [PMID: 39668246 PMCID: PMC11772670 DOI: 10.1038/s44319-024-00343-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: 08/04/2024] [Revised: 11/21/2024] [Accepted: 11/25/2024] [Indexed: 12/14/2024] Open
Abstract
Human pluripotent stem cells (hPSCs) exist in multiple, transcriptionally distinct states and serve as powerful models for studying human development. Despite their significance, the molecular determinants and pathways governing these pluripotent states remain incompletely understood. Here, we demonstrate that transposable elements act as sensitive indicators of distinct pluripotent cell states. We engineered hPSCs with fluorescent reporters to capture the temporal expression dynamics of two state-specific transposable elements, LTR5_Hs, and MER51B. This dual reporter system enables real-time monitoring and isolation of stem cells transitioning from naïve to primed pluripotency and further towards differentiation, serving as a more accurate readout of pluripotency states compared to conventional systems. Unexpectedly, we identified a rare, metastable cell population within primed hPSCs, marked by transcripts related to preimplantation embryo development and which is associated with a DNA damage response. Moreover, our system establishes the chromatin factor NSD1 and the RNA-binding protein FUS as potent molecular safeguards of primed pluripotency. Our study introduces a novel system for investigating cellular potency and provides key insights into the regulation of embryonic development.
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Affiliation(s)
- Florencia Levin-Ferreyra
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Srikanth Kodali
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Yingzhi Cui
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Alison R S Pashos
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Patrizia Pessina
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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14
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Smith ZD, Hetzel S, Meissner A. DNA methylation in mammalian development and disease. Nat Rev Genet 2025; 26:7-30. [PMID: 39134824 DOI: 10.1038/s41576-024-00760-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2024] [Indexed: 12/15/2024]
Abstract
The DNA methylation field has matured from a phase of discovery and genomic characterization to one seeking deeper functional understanding of how this modification contributes to development, ageing and disease. In particular, the past decade has seen many exciting mechanistic discoveries that have substantially expanded our appreciation for how this generic, evolutionarily ancient modification can be incorporated into robust epigenetic codes. Here, we summarize the current understanding of the distinct DNA methylation landscapes that emerge over the mammalian lifespan and discuss how they interact with other regulatory layers to support diverse genomic functions. We then review the rising interest in alternative patterns found during senescence and the somatic transition to cancer. Alongside advancements in single-cell and long-read sequencing technologies, the collective insights made across these fields offer new opportunities to connect the biochemical and genetic features of DNA methylation to cell physiology, developmental potential and phenotype.
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Affiliation(s)
- Zachary D Smith
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA.
| | - Sara Hetzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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15
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van Voorden AJ, Boussata S, Keijser R, Vermij M, Wagner MK, Ganzevoort W, Afink GB. Generation of Bona Fide Human Induced Trophoblast Stem Cells by Direct Reprogramming of Term Umbilical Cord Cells. Int J Mol Sci 2024; 26:271. [PMID: 39796127 PMCID: PMC11719488 DOI: 10.3390/ijms26010271] [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: 11/28/2024] [Revised: 12/23/2024] [Accepted: 12/25/2024] [Indexed: 01/13/2025] Open
Abstract
Placentation disorders, including severe preeclampsia and fetal growth restriction, have their origins in early pregnancy, whereas symptoms typically present later on. To investigate the pathogenesis of these diseases, there is a need for a reliable in vitro model system of early placenta development with known pregnancy outcomes. Therefore, we optimized the generation of human induced trophoblast stem cells (iTSCs) from term umbilical cord, enabling non-invasive collection of patient-derived material immediately after birth. Using a direct reprogramming approach previously described for dermal fibroblasts, we investigated the effects of three supplements (A-485, BMP4, and EPZ-6438) to assess their potential to enhance iTSC induction. The generated iTSCs fulfilled the criteria for bona fide first-trimester trophoblasts and exhibited key functional capacities, including long-term self-renewal, differentiation into hormone-producing syncytiotrophoblasts and invasive extravillous trophoblasts, and the formation of organoids. Furthermore, transcriptomic analysis revealed high similarity between the generated iTSCs and trophoblast stem cells derived from first-trimester placental tissue. The supplements did not improve the generation of iTSCs. In conclusion, we successfully generated bona fide iTSCs from term umbilical cord using a direct reprogramming approach, providing a robust and clinically relevant model to study early placentation mechanisms in patient-derived trophoblasts.
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Affiliation(s)
- A. Jantine van Voorden
- Reproductive Biology Laboratory, Amsterdam University Medical Center Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, 1105 AZ Amsterdam, The Netherlands
| | - Souad Boussata
- Reproductive Biology Laboratory, Amsterdam University Medical Center Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, 1105 AZ Amsterdam, The Netherlands
| | - Remco Keijser
- Reproductive Biology Laboratory, Amsterdam University Medical Center Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, 1105 AZ Amsterdam, The Netherlands
| | - Marloes Vermij
- Reproductive Biology Laboratory, Amsterdam University Medical Center Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, 1105 AZ Amsterdam, The Netherlands
| | - Muriel K. Wagner
- Reproductive Biology Laboratory, Amsterdam University Medical Center Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, 1105 AZ Amsterdam, The Netherlands
| | - Wessel Ganzevoort
- Amsterdam Reproduction and Development Research Institute, 1105 AZ Amsterdam, The Netherlands
- Department of Obstetrics and Gynaecology, Amsterdam University Medical Center Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Gijs B. Afink
- Reproductive Biology Laboratory, Amsterdam University Medical Center Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, 1105 AZ Amsterdam, The Netherlands
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16
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Yun J, So J, Jeong S, Jang J, Han S, Jeon J, Lee K, Jang HR, Lee J. Transcriptome and epigenome dynamics of the clonal heterogeneity of human induced pluripotent stem cells for cardiac differentiation. Cell Mol Life Sci 2024; 82:2. [PMID: 39661125 PMCID: PMC11635083 DOI: 10.1007/s00018-024-05493-9] [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: 06/07/2024] [Revised: 10/22/2024] [Accepted: 11/06/2024] [Indexed: 12/12/2024]
Abstract
Human induced pluripotent stem cells (hiPSCs) generate multiple clones with inherent heterogeneity, leading to variations in their differentiation capacity. Previous studies have primarily addressed line-to-line variations in differentiation capacity, leaving a gap in the comprehensive understanding of clonal heterogeneity. Here, we aimed to profile the heterogeneity of hiPSC clones and identify predictive biomarkers for cardiomyocyte (CM) differentiation capacity by integrating transcriptomic, epigenomic, endogenous retroelement, and protein kinase phosphorylation profiles. We generated multiple clones from a single donor and validated that these clones exhibited comparable levels of pluripotency markers. The clones were classified into two groups based on their differentiation efficiency to CMs-productive clone (PC) and non-productive clone (NPC). We performed RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin with sequencing (ATAC-seq). NPC was enriched in vasculogenesis and cell adhesion, accompanied by elevated levels of phosphorylated ERK1/2. Conversely, PC exhibited enrichment in embryonic organ development and transcription factor activation, accompanied by increased chromatin accessibility near transcription start site (TSS) regions. Integrative analysis of RNA-seq and ATAC-seq revealed 14 candidate genes correlated with cardiac differentiation potential. Notably, TEK and SDR42E1 were upregulated in NPC. Our integrative profiles enhance the understanding of clonal heterogeneity and highlight two novel biomarkers associated with CM differentiation. This insight may facilitate the identification of suboptimal hiPSC clones, thereby mitigating adverse outcomes in clinical applications.
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Affiliation(s)
- Jihye Yun
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaemin So
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seunghee Jeong
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jiye Jang
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Soyoung Han
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Junseok Jeon
- Division of Nephrology, Department of Medicine, Cell and Gene Therapy Institute, Samsung Medical Center, Sungkyunkwan University of Medicine, Seoul, Republic of Korea
| | - Kyungho Lee
- Division of Nephrology, Department of Medicine, Cell and Gene Therapy Institute, Samsung Medical Center, Sungkyunkwan University of Medicine, Seoul, Republic of Korea
| | - Hye Ryoun Jang
- Division of Nephrology, Department of Medicine, Cell and Gene Therapy Institute, Samsung Medical Center, Sungkyunkwan University of Medicine, Seoul, Republic of Korea
| | - Jaecheol Lee
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Epigenome Dynamics Control Research Center (EDCRC), School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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17
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Radisic M. Mechanically constrained into naivety. NATURE MATERIALS 2024; 23:1620-1621. [PMID: 39543231 DOI: 10.1038/s41563-024-02052-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2024]
Affiliation(s)
- Milica Radisic
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
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18
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Tian M, Tang X, Ouyang Z, Li Y, Bai X, Chen B, Yue S, Hu P, Bo X, Ren C, Chen H, Lu M. Long-range transcription factor binding sites clustered regions may mediate transcriptional regulation through phase-separation interactions in early human embryo. Comput Struct Biotechnol J 2024; 23:3514-3526. [PMID: 39435341 PMCID: PMC11492133 DOI: 10.1016/j.csbj.2024.09.017] [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: 02/20/2024] [Revised: 09/19/2024] [Accepted: 09/25/2024] [Indexed: 10/23/2024] Open
Abstract
In mammals, during the post-fertilization pre-implantation phase, the expression of cell type-specific genes is crucial for normal embryonic development, which is regulated by cis-regulatory elements (CREs). TFs control gene expression by interacting with CREs. Research shows that transcription factor binding sites (TFBSs) reflect the general characteristics of the regulatory genome. Here, we identified TFBSs from chromatin accessibility data in five stages of early human embryonic development, and quantified transcription factor binding sites-clustered regions (TFCRs) and their complexity (TC). Assigning TC values to TFCRs has made it possible to assess the functionality of these regulatory elements in a more quantitative way. Our findings reveal a robust correlation between TFCR complexity and gene expression starting from the 8Cell stage, which is when the zygotic genome is activated in humans. Furthermore, we have defined long-range TFCRs (LR-TFCRs) and conjecture that LR-TFCRs may regulate gene expression through phase-separation mechanisms during the early stages of human embryonic development.
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Affiliation(s)
- Mengge Tian
- The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiaohan Tang
- The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Zhangyi Ouyang
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Yaru Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xuemei Bai
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Bijia Chen
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Shutong Yue
- Academy of Military Medical Sciences, Beijing 100850, China
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Pengzhen Hu
- Academy of Military Medical Sciences, Beijing 100850, China
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Xiaochen Bo
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Chao Ren
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hebing Chen
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Meisong Lu
- The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
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19
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Smith A. Propagating pluripotency - The conundrum of self-renewal. Bioessays 2024; 46:e2400108. [PMID: 39180242 PMCID: PMC11589686 DOI: 10.1002/bies.202400108] [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: 04/30/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/26/2024]
Abstract
The discovery of mouse embryonic stem cells in 1981 transformed research in mammalian developmental biology and functional genomics. The subsequent generation of human pluripotent stem cells (PSCs) and the development of molecular reprogramming have opened unheralded avenues for drug discovery and cell replacement therapy. Here, I review the history of PSCs from the perspective that long-term self-renewal is a product of the in vitro signaling environment, rather than an intrinsic feature of embryos. I discuss the relationship between pluripotent states captured in vitro to stages of epiblast in the embryo and suggest key considerations for evaluation of PSCs. A remaining fundamental challenge is to determine whether naïve pluripotency can be propagated from the broad range of mammals by exploiting common principles in gene regulatory architecture.
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Affiliation(s)
- Austin Smith
- Living Systems InstituteUniversity of ExeterExeterUK
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20
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Iyer DP, Khoei HH, van der Weijden VA, Kagawa H, Pradhan SJ, Novatchkova M, McCarthy A, Rayon T, Simon CS, Dunkel I, Wamaitha SE, Elder K, Snell P, Christie L, Schulz EG, Niakan KK, Rivron N, Bulut-Karslioğlu A. mTOR activity paces human blastocyst stage developmental progression. Cell 2024; 187:6566-6583.e22. [PMID: 39332412 PMCID: PMC7617234 DOI: 10.1016/j.cell.2024.08.048] [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: 05/17/2023] [Revised: 06/24/2024] [Accepted: 08/23/2024] [Indexed: 09/29/2024]
Abstract
Many mammals can temporally uncouple conception from parturition by pacing down their development around the blastocyst stage. In mice, this dormant state is achieved by decreasing the activity of the growth-regulating mTOR signaling pathway. It is unknown whether this ability is conserved in mammals in general and in humans in particular. Here, we show that decreasing the activity of the mTOR signaling pathway induces human pluripotent stem cells (hPSCs) and blastoids to enter a dormant state with limited proliferation, developmental progression, and capacity to attach to endometrial cells. These in vitro assays show that, similar to other species, the ability to enter dormancy is active in human cells around the blastocyst stage and is reversible at both functional and molecular levels. The pacing of human blastocyst development has potential implications for reproductive therapies.
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Affiliation(s)
- Dhanur P Iyer
- Stem Cell Chromatin Group, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Heidar Heidari Khoei
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Vera A van der Weijden
- Stem Cell Chromatin Group, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Harunobu Kagawa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Saurabh J Pradhan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Afshan McCarthy
- The Human Embryo and Stem Cell Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Teresa Rayon
- Epigenetics & Signalling Programmes, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Claire S Simon
- The Human Embryo and Stem Cell Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Ilona Dunkel
- Systems Epigenetics, Otto-Warburg-Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sissy E Wamaitha
- The Human Embryo and Stem Cell Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Kay Elder
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | - Phil Snell
- Bourn Hall Clinic, Bourn, Cambridge CB23 2TN, UK
| | | | - Edda G Schulz
- Systems Epigenetics, Otto-Warburg-Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Kathy K Niakan
- The Human Embryo and Stem Cell Laboratory, Francis Crick Institute, London NW1 1AT, UK; Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Nicolas Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| | - Aydan Bulut-Karslioğlu
- Stem Cell Chromatin Group, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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21
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Shahbazi MN, Pasque V. Early human development and stem cell-based human embryo models. Cell Stem Cell 2024; 31:1398-1418. [PMID: 39366361 PMCID: PMC7617107 DOI: 10.1016/j.stem.2024.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/18/2024] [Accepted: 09/02/2024] [Indexed: 10/06/2024]
Abstract
The use of stem cells to model the early human embryo promises to transform our understanding of developmental biology and human reproduction. In this review, we present our current knowledge of the first 2 weeks of human embryo development. We first focus on the distinct cell lineages of the embryo and the derivation of stem cell lines. We then discuss the intercellular crosstalk that guides early embryo development and how this crosstalk is recapitulated in vitro to generate stem cell-based embryo models. We highlight advances in this fast-developing field, discuss current limitations, and provide a vision for the future.
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Affiliation(s)
| | - Vincent Pasque
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium; Leuven Stem Cell Institute & Leuven Institute for Single-Cell Omics (LISCO), Leuven, Belgium.
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22
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Hossain I, Priam P, Reynoso SC, Sahni S, Zhang XX, Côté L, Doumat J, Chik C, Fu T, Lessard JA, Pastor WA. ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency. Nat Commun 2024; 15:8539. [PMID: 39358345 PMCID: PMC11447223 DOI: 10.1038/s41467-024-52431-1] [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: 10/19/2023] [Accepted: 09/03/2024] [Indexed: 10/04/2024] Open
Abstract
The primed epiblast acts as a transitional stage between the relatively homogeneous naïve epiblast and the gastrulating embryo. Its formation entails coordinated changes in regulatory circuits driven by transcription factors and epigenetic modifications. Using a multi-omic approach in human embryonic stem cell models across the spectrum of peri-implantation development, we demonstrate that the transcription factors ZIC2 and ZIC3 have overlapping but essential roles in opening primed-specific enhancers. Together, they are essential to facilitate progression to and maintain primed pluripotency. ZIC2/3 accomplish this by recruiting SWI/SNF to chromatin and loss of ZIC2/3 or degradation of SWI/SNF both prevent enhancer activation. Loss of ZIC2/3 also results in transcriptome changes consistent with perturbed Polycomb activity and a shift towards the expression of genes linked to differentiation towards the mesendoderm. Additionally, we find an intriguing dependency on the transcriptional machinery for sustained recruitment of ZIC2/3 over a subset of primed-hESC specific enhancers. Taken together, ZIC2 and ZIC3 regulate highly dynamic lineage-specific enhancers and collectively act as key regulators of human primed pluripotency.
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Affiliation(s)
| | - Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - Sofia C Reynoso
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Sahil Sahni
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Xiao X Zhang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Laurence Côté
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - Joelle Doumat
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Candus Chik
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Tianxin Fu
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Julie A Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - William A Pastor
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada.
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23
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Yagi M, Horng JE, Hochedlinger K. Manipulating cell fate through reprogramming: approaches and applications. Development 2024; 151:dev203090. [PMID: 39348466 PMCID: PMC11463964 DOI: 10.1242/dev.203090] [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: 05/23/2024] [Accepted: 09/11/2024] [Indexed: 10/02/2024]
Abstract
Cellular plasticity progressively declines with development and differentiation, yet these processes can be experimentally reversed by reprogramming somatic cells to induced pluripotent stem cells (iPSCs) using defined transcription factors. Advances in reprogramming technology over the past 15 years have enabled researchers to study diseases with patient-specific iPSCs, gain fundamental insights into how cell identity is maintained, recapitulate early stages of embryogenesis using various embryo models, and reverse aspects of aging in cultured cells and animals. Here, we review and compare currently available reprogramming approaches, including transcription factor-based methods and small molecule-based approaches, to derive pluripotent cells characteristic of early embryos. Additionally, we discuss our current understanding of mechanisms that resist reprogramming and their role in cell identity maintenance. Finally, we review recent efforts to rejuvenate cells and tissues with reprogramming factors, as well as the application of iPSCs in deriving novel embryo models to study pre-implantation development.
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Affiliation(s)
- Masaki Yagi
- Department of Molecular Biology, Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joy E. Horng
- Department of Molecular Biology, Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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24
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Song Y, Wen H, Zhai X, Jia L, Li L. Functional Bidirectionality of ERV-Derived Long Non-Coding RNAs in Humans. Int J Mol Sci 2024; 25:10481. [PMID: 39408810 PMCID: PMC11476766 DOI: 10.3390/ijms251910481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 09/25/2024] [Accepted: 09/26/2024] [Indexed: 10/20/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are widely recognized as the result of exogenous retroviruses infecting the ancestral germline, stabilizing integration and vertical transmission during human genetic evolution. To date, endogenous retroviruses (ERVs) appear to have been selected for human physiological functions with the loss of retrotransposable capabilities. ERV elements were previously regarded as junk DNA for a long time. Since then, the aberrant activation and expression of ERVs have been observed in the development of many kinds of human diseases, and their role has been explored in a variety of human disorders such as cancer. The results show that specific ERV elements play respective crucial roles. Among them, long non-coding RNAs (lncRNAs) transcribed from specific long-terminal repeat regions of ERVs are often key factors. lncRNAs are over 200 nucleotides in size and typically bind to DNA, RNA, and proteins to perform biological functions. Dysregulated lncRNAs have been implicated in a variety of diseases. In particular, studies have shown that the aberrant expression of some ERV-derived lncRNAs has a tumor-suppressive or oncogenic effect, displaying significant functional bidirectionality. Therefore, theses lncRNAs have a promising future as novel biomarkers and therapeutic targets to explore the concise relationship between ERVs and cancers. In this review, we first summarize the role of ERV-derived lncRNAs in physiological regulation, mainly including immunomodulation, the maintenance of pluripotency, and erythropoiesis. In addition, pathological regulation examples of their aberrant activation and expression leading to carcinogenesis are highlighted, and specific mechanisms of occurrence are discussed.
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Affiliation(s)
- Yanmei Song
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key Laboratory for the Prevention and Control of Emerging Infectious Diseases and Biosafety, Jinan 250012, China; (Y.S.); (H.W.)
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100850, China;
| | - Hongling Wen
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key Laboratory for the Prevention and Control of Emerging Infectious Diseases and Biosafety, Jinan 250012, China; (Y.S.); (H.W.)
| | - Xiuli Zhai
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100850, China;
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230000, China
| | - Lei Jia
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100850, China;
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100850, China;
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25
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Meyer NP, Singh T, Kutys ML, Nystul TG, Barber DL. Arp2/3 complex activity enables nuclear YAP for naïve pluripotency of human embryonic stem cells. eLife 2024; 13:e89725. [PMID: 39319536 PMCID: PMC11509671 DOI: 10.7554/elife.89725] [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: 06/01/2023] [Accepted: 09/04/2024] [Indexed: 09/26/2024] Open
Abstract
Our understanding of the transitions of human embryonic stem cells (hESCs) between distinct stages of pluripotency relies predominantly on regulation by transcriptional and epigenetic programs with limited insight on the role of established morphological changes. We report remodeling of the actin cytoskeleton of hESCs as they transition from primed to naïve pluripotency which includes assembly of a ring of contractile actin filaments encapsulating colonies of naïve hESCs. Activity of the Arp2/3 complex is required for formation of the actin ring, to establish uniform cell mechanics within naïve colonies, to promote nuclear translocation of the Hippo pathway effectors YAP and TAZ, and for effective transition to naïve pluripotency. RNA-sequencing analysis confirms that Arp2/3 complex activity regulates Hippo signaling in hESCs, and impaired naïve pluripotency with inhibited Arp2/3 complex activity is rescued by expressing a constitutively active, nuclear-localized YAP-S127A. Moreover, expression of YAP-S127A partially restores the actin filament fence with Arp2/3 complex inhibition, suggesting that actin filament remodeling is both upstream and downstream of YAP activity. These new findings on the cell biology of hESCs reveal a mechanism for cytoskeletal dynamics coordinating cell mechanics to regulate gene expression and facilitate transitions between pluripotency states.
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Affiliation(s)
- Nathaniel Paul Meyer
- Department of Cell & Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
| | - Tania Singh
- Department of Cell & Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
| | - Matthew L Kutys
- Department of Cell & Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
| | - Todd G Nystul
- Departments of Anatomy and OB-GYN/RS, University of California, San FranciscoSan FranciscoUnited States
| | - Diane L Barber
- Department of Cell & Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
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26
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Shang Y, Wang N, Wang H, An C, Sun W. Modeling X chromosome inactivation using t5iLA naive human pluripotent stem cells. BMC Biol 2024; 22:210. [PMID: 39294757 PMCID: PMC11411763 DOI: 10.1186/s12915-024-01994-y] [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: 01/05/2024] [Accepted: 08/28/2024] [Indexed: 09/21/2024] Open
Abstract
BACKGROUND X chromosome inactivation (XCI) is a critical epigenetic event for dosage compensation of X-linked genes in female mammals, ensuring developmental stability. A robust in vitro model is required for mimicking XCI during the early stages of embryonic development. This methodology article introduces an advanced framework for the in-depth study of XCI using human pluripotent stem cells (hPSCs). By focusing on the transition between naive and primed pluripotent states, we highlight the role of long non-coding RNA X-inactive specific transcript (XIST) and epigenetic alterations in mediating XCI. RESULTS Our methodology enables the distinction between naive and primed hESCs based on XIST expression and the activity of X-linked reporters, facilitating the investigation of XCI initiation and maintenance. Through detailed experimental procedures, we demonstrate the utility of our hESC lines in modeling the process of human XCI, including the establishment of conditions for random XCI induction and the analysis of X chromosome reactivation. METHODS The study outlines a comprehensive approach for characterizing the X chromosome status in hPSCs, employing dual fluorescent reporter hESC lines. These reporter lines enable real-time tracking of XCI dynamics through differentiation processes. We detailed protocols for the induction of X chromosome reactivation and inactivation, as well as the X status characterization methods including cultivation of hESCs, flow cytometric analysis, RNA fluorescence in situ hybridization (FISH), and transcriptome sequencing, providing a step-by-step guide for researchers to investigate XCI mechanisms in vitro. CONCLUSIONS This article provides a detailed, reproducible methodology for studying XCI mechanisms in vitro, employing hPSCs as a model system. It presents a significant advance in our ability to investigate XCI, offering potential applications in developmental biology, disease modeling, and regenerative medicine. By facilitating the study of XCI dynamics, this methodological framework paves the way for deeper understanding and manipulation of this fundamental biological process.
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Affiliation(s)
- Yudan Shang
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory for Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Nannan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Chenrui An
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory for Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
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27
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Na Q, Zhang S, Shao P, Jia Y, Wang Y, Wei M, Chen Y, Chen C, Zhao L, Wang Z, Song Y, Wu B, Bao S, Li X. In vitro generation of trophoblast like stem cells from goat pluripotent stem cells. Theriogenology 2024; 226:120-129. [PMID: 38878464 DOI: 10.1016/j.theriogenology.2024.05.036] [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: 01/05/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 07/24/2024]
Abstract
Since the first mouse induced pluripotent stem cells (iPSCs) was derived, the in vitro culture of domestic iPSCs functionally and molecularly comparable with mouse iPSCs has been a challenge. Here, we established dairy goat iPSCs (giPSCs) from goat ear fibroblast cells with mouse iPSCs morphology, the expression of pluripotent markers and differentiation ability in vitro delivered by piggyBac transposon with nine Dox-inducible exogenous reprogramming factors. These reprogramming factors were bOMSK (bovine OCT4, CMYC, SOX2, and KLF4), pNhL (porcine NANOG and human LIN28), hRL (human RARG and LRH1), and SV40 Large T. Notably, AF-giPSCs (induced in activin A and bFGF condition) were capable of differentiation in embryoid bodies in vitro and could contribute to interspecies chimerism in mouse E6.5 embryos in vitro, demonstrating that AF-giPSCs have the developmental capability to generate some embryonic cell lineages. Moreover, Wnt/β-catenin signaling has an important role in driving goat induced trophoblast-like stem cells (giTLSCs) from Dox-independent giPSCs. This study will support further establishment of the stable giPSC lines without any integration of exogenous genes.
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Affiliation(s)
- Qin Na
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China; College of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Siyu Zhang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China
| | - Peng Shao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China
| | - Yu Jia
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China
| | - Yanqiu Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China
| | - Mengyi Wei
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China
| | - Yanglin Chen
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China
| | - Chen Chen
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China
| | - Lixia Zhao
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Zixin Wang
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, 011517, Hohhot, China
| | - Yongli Song
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China
| | - Baojiang Wu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China
| | - Siqin Bao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China.
| | - Xihe Li
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, 010020, Hohhot, China; Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, 010020, Hohhot, China; Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, 011517, Hohhot, China.
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Du Z, Lin M, Li Q, Guo D, Xue Y, Liu W, Shi H, Chen T, Dan J. The totipotent 2C-like state safeguards genomic stability of mouse embryonic stem cells. J Cell Physiol 2024; 239:e31337. [PMID: 38860420 DOI: 10.1002/jcp.31337] [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: 01/09/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Mouse embryonic stem cells (mESCs) sporadically transition to a transient totipotent state that resembles blastomeres of the two-cell (2C) embryo stage, which has been proposed to contribute to exceptional genomic stability, one of the key features of mESCs. However, the biological significance of the rare population of 2C-like cells (2CLCs) in ESC cultures remains to be tested. Here we generated an inducible reporter cell system for specific elimination of 2CLCs from the ESC cultures to disrupt the equilibrium between ESCs and 2CLCs. We show that removing 2CLCs from the ESC cultures leads to dramatic accumulation of DNA damage, genomic mutations, and rearrangements, indicating impaired genomic instability. Furthermore, 2CLCs removal results in increased apoptosis and reduced proliferation of mESCs in both serum/LIF and 2i/LIF culture conditions. Unexpectedly, p53 deficiency results in defective response to DNA damage, leading to early accumulation of DNA damage, micronuclei, indicative of genomic instability, cell apoptosis, and reduced self-renewal capacity of ESCs when devoid of 2CLCs in cultures. Together, our data reveal that transition to the privileged 2C-like state is a major component of the intrinsic mechanisms that maintain the exceptional genomic stability of mESCs for long-term self-renewal.
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Affiliation(s)
- Zeling Du
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Meiqi Lin
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Qiaohua Li
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Dan Guo
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Yanna Xue
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Wei Liu
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Programs in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Jiameng Dan
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
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29
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Wu J, Fu J. Toward developing human organs via embryo models and chimeras. Cell 2024; 187:3194-3219. [PMID: 38906095 PMCID: PMC11239105 DOI: 10.1016/j.cell.2024.05.027] [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: 05/30/2023] [Revised: 02/02/2024] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
Developing functional organs from stem cells remains a challenging goal in regenerative medicine. Existing methodologies, such as tissue engineering, bioprinting, and organoids, only offer partial solutions. This perspective focuses on two promising approaches emerging for engineering human organs from stem cells: stem cell-based embryo models and interspecies organogenesis. Both approaches exploit the premise of guiding stem cells to mimic natural development. We begin by summarizing what is known about early human development as a blueprint for recapitulating organogenesis in both embryo models and interspecies chimeras. The latest advances in both fields are discussed before highlighting the technological and knowledge gaps to be addressed before the goal of developing human organs could be achieved using the two approaches. We conclude by discussing challenges facing embryo modeling and interspecies organogenesis and outlining future prospects for advancing both fields toward the generation of human tissues and organs for basic research and translational applications.
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Affiliation(s)
- Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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30
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Li S, Yang M, Shen H, Ding L, Lyu X, Lin K, Ong J, Du P. Capturing totipotency in human cells through spliceosomal repression. Cell 2024; 187:3284-3302.e23. [PMID: 38843832 DOI: 10.1016/j.cell.2024.05.010] [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: 06/19/2022] [Revised: 09/01/2023] [Accepted: 05/03/2024] [Indexed: 06/23/2024]
Abstract
The cleavage of zygotes generates totipotent blastomeres. In human 8-cell blastomeres, zygotic genome activation (ZGA) occurs to initiate the ontogenesis program. However, capturing and maintaining totipotency in human cells pose significant challenges. Here, we realize culturing human totipotent blastomere-like cells (hTBLCs). We find that splicing inhibition can transiently reprogram human pluripotent stem cells into ZGA-like cells (ZLCs), which subsequently transition into stable hTBLCs after long-term passaging. Distinct from reported 8-cell-like cells (8CLCs), both ZLCs and hTBLCs widely silence pluripotent genes. Interestingly, ZLCs activate a particular group of ZGA-specific genes, and hTBLCs are enriched with pre-ZGA-specific genes. During spontaneous differentiation, hTBLCs re-enter the intermediate ZLC stage and further generate epiblast (EPI)-, primitive endoderm (PrE)-, and trophectoderm (TE)-like lineages, effectively recapitulating human pre-implantation development. Possessing both embryonic and extraembryonic developmental potency, hTBLCs can autonomously generate blastocyst-like structures in vitro without external cell signaling. In summary, our study provides key criteria and insights into human cell totipotency.
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Affiliation(s)
- Shiyu Li
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Min Yang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Shen
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Li Ding
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuehui Lyu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Kexin Lin
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jennie Ong
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China.
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31
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Tanaka J, Kondo Y, Sakurai M, Sawada A, Hwang Y, Miura A, Shimamura Y, Shimizu D, Hu Y, Sarmah H, Ninish Z, Cai J, Wu J, Mori M. Ephrin Forward Signaling Controls Interspecies Cell Competition in Pluripotent Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597057. [PMID: 38895424 PMCID: PMC11185521 DOI: 10.1101/2024.06.02.597057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
In the animal kingdom, evolutionarily conserved mechanisms known as cell competition eliminate unfit cells during development. Interestingly, cell competition also leads to apoptosis of donor cells upon direct contact with host cells from a different species during interspecies chimera formation. The mechanisms underlying how host animal cells recognize and transmit cell death signals to adjacent xenogeneic human cells remain incompletely understood. In this study, we developed an interspecies cell contact reporter system to dissect the mechanisms underlying competitive interactions between mouse and human pluripotent stem cells (PSCs). Through single-cell RNA-seq analyses, we discovered that Ephrin A ligands in mouse cells play a crucial role in signaling cell death to adjacent human cells that express EPHA receptors during interspecies PSC co-culture. We also demonstrated that blocking the Ephrin A-EPHA receptor interaction pharmacologically, and inhibiting Ephrin forward signaling genetically in the mouse cells, enhances the survival of human PSCs and promotes chimera formation both in vitro and in vivo . Our findings elucidate key mechanisms of interspecies PSC competition during early embryogenesis and open new avenues for generating humanized tissues or organs in animals, potentially revolutionizing regenerative medicine.
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32
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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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33
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Li N, Jin K, Liu B, Yang M, Shi P, Heng D, Wang J, Liu L. Single-cell 3D genome structure reveals distinct human pluripotent states. Genome Biol 2024; 25:122. [PMID: 38741214 PMCID: PMC11089717 DOI: 10.1186/s13059-024-03268-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: 05/23/2023] [Accepted: 05/05/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Pluripotent states of embryonic stem cells (ESCs) with distinct transcriptional profiles affect ESC differentiative capacity and therapeutic potential. Although single-cell RNA sequencing has revealed additional subpopulations and specific features of naive and primed human pluripotent stem cells (hPSCs), the underlying mechanisms that regulate their specific transcription and that control their pluripotent states remain elusive. RESULTS By single-cell analysis of high-resolution, three-dimensional (3D) genomic structure, we herein demonstrate that remodeling of genomic structure is highly associated with the pluripotent states of human ESCs (hESCs). The naive pluripotent state is featured with specialized 3D genomic structures and clear chromatin compartmentalization that is distinct from the primed state. The naive pluripotent state is achieved by remodeling the active euchromatin compartment and reducing chromatin interactions at the nuclear center. This unique genomic organization is linked to enhanced chromatin accessibility on enhancers and elevated expression levels of naive pluripotent genes localized to this region. In contradistinction, the primed state exhibits intermingled genomic organization. Moreover, active euchromatin and primed pluripotent genes are distributed at the nuclear periphery, while repressive heterochromatin is densely concentrated at the nuclear center, reducing chromatin accessibility and the transcription of naive genes. CONCLUSIONS Our data provide insights into the chromatin structure of ESCs in their naive and primed states, and we identify specific patterns of modifications in transcription and chromatin structure that might explain the genes that are differentially expressed between naive and primed hESCs. Thus, the inversion or relocation of heterochromatin to euchromatin via compartmentalization is related to the regulation of chromatin accessibility, thereby defining pluripotent states and cellular identity.
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Affiliation(s)
- Niannian Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Weifang People's Hospital, Shandong, 261041, China
| | - Kairang Jin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Bin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Weifang People's Hospital, Shandong, 261041, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China
| | - Mingzhu Yang
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - PanPan Shi
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Dai Heng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jichang Wang
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China.
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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Su Y, Yu Z, Jin S, Ai Z, Yuan R, Chen X, Xue Z, Guo Y, Chen D, Liang H, Liu Z, Liu W. Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data. Nat Commun 2024; 15:3972. [PMID: 38730241 PMCID: PMC11087464 DOI: 10.1038/s41467-024-48117-3] [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: 10/18/2022] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
The advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing events and isoform expressions. Recently, numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless, there remains a deficiency in comparative studies that systemically evaluate the performance of these tools, which are implemented with different algorithms, under various simulations that encompass potential influencing factors. In this study, we conducted a benchmark analysis of thirteen methods implemented in nine tools capable of identifying isoform structures from long-read RNA-seq data. We evaluated their performances using simulated data, which represented diverse sequencing platforms generated by an in-house simulator, RNA sequins (sequencing spike-ins) data, as well as experimental data. Our findings demonstrate IsoQuant as a highly effective tool for isoform detection with LRS, with Bambu and StringTie2 also exhibiting strong performance. These results offer valuable guidance for future research on alternative splicing analysis and the ongoing improvement of tools for isoform detection using LRS data.
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Affiliation(s)
- Yaqi Su
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Zhejian Yu
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Siqian Jin
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Zhipeng Ai
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Ruihong Yuan
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Xinyi Chen
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Ziwei Xue
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Yixin Guo
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Di Chen
- Center for Reproductive Medicine of the Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China
- Centre for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Hongqing Liang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Zuozhu Liu
- Zhejiang University-Angel Align Inc. R&D Center for Intelligent Healthcare, Zhejiang University-University of Illinois at Urbana-Champaign Institute (ZJU-UIUC Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China
| | - Wanlu Liu
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.
- Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China.
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314100, China.
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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Cerneckis J, Cai H, Shi Y. Induced pluripotent stem cells (iPSCs): molecular mechanisms of induction and applications. Signal Transduct Target Ther 2024; 9:112. [PMID: 38670977 PMCID: PMC11053163 DOI: 10.1038/s41392-024-01809-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 03/09/2024] [Accepted: 03/17/2024] [Indexed: 04/28/2024] Open
Abstract
The induced pluripotent stem cell (iPSC) technology has transformed in vitro research and holds great promise to advance regenerative medicine. iPSCs have the capacity for an almost unlimited expansion, are amenable to genetic engineering, and can be differentiated into most somatic cell types. iPSCs have been widely applied to model human development and diseases, perform drug screening, and develop cell therapies. In this review, we outline key developments in the iPSC field and highlight the immense versatility of the iPSC technology for in vitro modeling and therapeutic applications. We begin by discussing the pivotal discoveries that revealed the potential of a somatic cell nucleus for reprogramming and led to successful generation of iPSCs. We consider the molecular mechanisms and dynamics of somatic cell reprogramming as well as the numerous methods available to induce pluripotency. Subsequently, we discuss various iPSC-based cellular models, from mono-cultures of a single cell type to complex three-dimensional organoids, and how these models can be applied to elucidate the mechanisms of human development and diseases. We use examples of neurological disorders, coronavirus disease 2019 (COVID-19), and cancer to highlight the diversity of disease-specific phenotypes that can be modeled using iPSC-derived cells. We also consider how iPSC-derived cellular models can be used in high-throughput drug screening and drug toxicity studies. Finally, we discuss the process of developing autologous and allogeneic iPSC-based cell therapies and their potential to alleviate human diseases.
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Affiliation(s)
- Jonas Cerneckis
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Hongxia Cai
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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Morey R, Bui T, Cheung VC, Dong C, Zemke JE, Requena D, Arora H, Jackson MG, Pizzo D, Theunissen TW, Horii M. iPSC-based modeling of preeclampsia identifies epigenetic defects in extravillous trophoblast differentiation. iScience 2024; 27:109569. [PMID: 38623329 PMCID: PMC11016801 DOI: 10.1016/j.isci.2024.109569] [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: 11/30/2023] [Revised: 02/20/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Preeclampsia (PE) is a hypertensive pregnancy disorder with increased risk of maternal and fetal morbidity and mortality. Abnormal extravillous trophoblast (EVT) development and function is considered to be the underlying cause of PE, but has not been previously modeled in vitro. We previously derived induced pluripotent stem cells (iPSCs) from placentas of PE patients and characterized abnormalities in formation of syncytiotrophoblast and responses to changes in oxygen tension. In this study, we converted these primed iPSC to naïve iPSC, and then derived trophoblast stem cells (TSCs) and EVT to evaluate molecular mechanisms underlying PE. We found that primed (but not naïve) iPSC-derived PE-EVT have reduced surface HLA-G, blunted invasive capacity, and altered EVT-specific gene expression. These abnormalities correlated with promoter hypermethylation of genes associated with the epithelial-mesenchymal transition pathway, specifically in primed-iPSC derived PE-EVT. Our findings indicate that abnormal epigenetic regulation might play a role in PE pathogenesis.
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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
- Center for Perinatal Discovery, 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
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
| | - Virginia Chu Cheung
- 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
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
| | - Chen Dong
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph E. Zemke
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniela Requena
- 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
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
| | - Harneet Arora
- 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
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
| | - Madeline G. Jackson
- 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
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
| | - Donald Pizzo
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Thorold W. Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, 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
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
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Chen KG, Johnson KR, Park K, Maric D, Yang F, Liu WF, Fann YC, Mallon BS, Robey PG. Resistance to Naïve and Formative Pluripotency Conversion in RSeT Human Embryonic Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580778. [PMID: 38410444 PMCID: PMC10896352 DOI: 10.1101/2024.02.16.580778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
One of the most important properties of human embryonic stem cells (hESCs) is related to their primed and naïve pluripotent states. Our previous meta-analysis indicates the existence of heterogeneous pluripotent states derived from diverse naïve protocols. In this study, we have characterized a commercial medium (RSeT)-based pluripotent state under various growth conditions. Notably, RSeT hESCs can circumvent hypoxic growth conditions as required by naïve hESCs, in which some RSeT cells (e.g., H1 cells) exhibit much lower single cell plating efficiency, having altered or much retarded cell growth under both normoxia and hypoxia. Evidently, hPSCs lack many transcriptomic hallmarks of naïve and formative pluripotency (a phase between naive and primed states). Integrative transcriptome analysis suggests our primed and RSeT hESCs are close to the early stage of post-implantation embryos, similar to the previously reported primary hESCs and early hESC cultures. Moreover, RSeT hESCs did not express naïve surface markers such as CD75, SUSD2, and CD130 at a significant level. Biochemically, RSeT hESCs exhibit a differential dependency of FGF2 and co-independency of both Janus kinase (JAK) and TGFβ signaling in a cell-line-specific manner. Thus, RSeT hESCs represent a previously unrecognized pluripotent state downstream of formative pluripotency. Our data suggest that human naïve pluripotent potentials may be restricted in RSeT medium. Hence, this study provides new insights into pluripotent state transitions in vitro.
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Affiliation(s)
| | - Kory R. Johnson
- Intramural IT and Bioinformatics Program, Bethesda, Maryland 20892, USA
| | - Kyeyoon Park
- NIH Stem Cell Unit, Bethesda, Maryland 20892, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Forest Yang
- NIH Stem Cell Unit, Bethesda, Maryland 20892, USA
| | - Wen Fang Liu
- NIH Stem Cell Unit, Bethesda, Maryland 20892, USA
| | - Yang C. Fann
- Intramural IT and Bioinformatics Program, Bethesda, Maryland 20892, USA
| | | | - Pamela G. Robey
- Skeletal Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA
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38
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Chen C, Liu Q, Chen W, Gong Z, Kang B, Sui M, Huang L, Wang YJ. PRODH safeguards human naive pluripotency by limiting mitochondrial oxidative phosphorylation and reactive oxygen species production. EMBO Rep 2024; 25:2015-2044. [PMID: 38480845 PMCID: PMC11014864 DOI: 10.1038/s44319-024-00110-z] [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: 06/03/2023] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 04/14/2024] Open
Abstract
Naive human embryonic stem cells (hESCs) that resemble the pre-implantation epiblasts are fueled by a combination of aerobic glycolysis and oxidative phosphorylation, but their mitochondrial regulators are poorly understood. Here we report that, proline dehydrogenase (PRODH), a mitochondria-localized proline metabolism enzyme, is dramatically upregulated in naive hESCs compared to their primed counterparts. The upregulation of PRODH is induced by a reduction in c-Myc expression that is dependent on PD0325901, a MEK inhibitor routinely present in naive hESC culture media. PRODH knockdown in naive hESCs significantly promoted mitochondrial oxidative phosphorylation (mtOXPHOS) and reactive oxygen species (ROS) production that triggered autophagy, DNA damage, and apoptosis. Remarkably, MitoQ, a mitochondria-targeted antioxidant, effectively restored the pluripotency and proliferation of PRODH-knockdown naive hESCs, indicating that PRODH maintains naive pluripotency by preventing excessive ROS production. Concomitantly, PRODH knockdown significantly slowed down the proteolytic degradation of multiple key mitochondrial electron transport chain complex proteins. Thus, we revealed a crucial role of PRODH in limiting mtOXPHOS and ROS production, and thereby safeguarding naive pluripotency of hESCs.
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Affiliation(s)
- Cheng Chen
- Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang, 312000, China
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Qianyu Liu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wenjie Chen
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Zhiyuan Gong
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Bo Kang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Meihua Sui
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Liming Huang
- Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang, 312000, China.
| | - Ying-Jie Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Du P, Wu J. Hallmarks of totipotent and pluripotent stem cell states. Cell Stem Cell 2024; 31:312-333. [PMID: 38382531 PMCID: PMC10939785 DOI: 10.1016/j.stem.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Though totipotency and pluripotency are transient during early embryogenesis, they establish the foundation for the development of all mammals. Studying these in vivo has been challenging due to limited access and ethical constraints, particularly in humans. Recent progress has led to diverse culture adaptations of epiblast cells in vitro in the form of totipotent and pluripotent stem cells, which not only deepen our understanding of embryonic development but also serve as invaluable resources for animal reproduction and regenerative medicine. This review delves into the hallmarks of totipotent and pluripotent stem cells, shedding light on their key molecular and functional features.
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Affiliation(s)
- Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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40
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Hosseini SM, Borys B, Karimi-Abdolrezaee S. Neural stem cell therapies for spinal cord injury repair: an update on recent preclinical and clinical advances. Brain 2024; 147:766-793. [PMID: 37975820 DOI: 10.1093/brain/awad392] [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: 07/27/2023] [Revised: 10/22/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Traumatic spinal cord injury (SCI) is a leading cause of lifelong disabilities. Permanent sensory, motor and autonomic impairments after SCI are substantially attributed to degeneration of spinal cord neurons and axons, and disintegration of neural network. To date, minimal regenerative treatments are available for SCI with an unmet need for new therapies to reconstruct the damaged spinal cord neuron-glia network and restore connectivity with the supraspinal pathways. Multipotent neural precursor cells (NPCs) have a unique capacity to generate neurons, oligodendrocytes and astrocytes. Due to this capacity, NPCs have been an attractive cell source for cellular therapies for SCI. Transplantation of NPCs has been extensively tested in preclinical models of SCI in the past two decades. These studies have identified opportunities and challenges associated with NPC therapies. While NPCs have the potential to promote neuroregeneration through various mechanisms, their low long-term survival and integration within the host injured spinal cord limit the functional benefits of NPC-based therapies for SCI. To address this challenge, combinatorial strategies have been developed to optimize the outcomes of NPC therapies by enriching SCI microenvironment through biomaterials, genetic and pharmacological therapies. In this review, we will provide an in-depth discussion on recent advances in preclinical NPC-based therapies for SCI. We will discuss modes of actions and mechanism by which engrafted NPCs contribute to the repair process and functional recovery. We will also provide an update on current clinical trials and new technologies that have facilitated preparation of medical-grade human NPCs suitable for transplantation in clinical studies.
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Affiliation(s)
- Seyed Mojtaba Hosseini
- Department of Physiology and Pathophysiology, Spinal Cord Research Centre, Rady Faculty of Health Sciences, University of Manitoba Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Multiple Sclerosis Research Center, Winnipeg, Manitoba R3E 0J9, Canada
| | - Ben Borys
- Department of Physiology and Pathophysiology, Spinal Cord Research Centre, Rady Faculty of Health Sciences, University of Manitoba Winnipeg, Manitoba R3E 0J9, Canada
| | - Soheila Karimi-Abdolrezaee
- Department of Physiology and Pathophysiology, Spinal Cord Research Centre, Rady Faculty of Health Sciences, University of Manitoba Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Multiple Sclerosis Research Center, Winnipeg, Manitoba R3E 0J9, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
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41
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Fang F, Li Z, Zhang X, Huang Q, Lu S, Wang X. Divergent Roles of KLF4 During Primordial Germ Cell Fate Induction from Human Embryonic Stem Cells. Reprod Sci 2024; 31:727-735. [PMID: 37884729 DOI: 10.1007/s43032-023-01360-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 09/14/2023] [Indexed: 10/28/2023]
Abstract
As a core transcriptional factor regulating pluripotency, Krüppel-like factor 4 (KLF4) has gained much attention in the field of stem cells during the past decades. However, few research have focused on the function of KLF4 during human primordial germ cell (PGC) specification. Here, we induced human PGC-like cells (hPGCLCs) from human embryonic stem cells (hESCs) and the derived hPGCLCs upregulated PGC-related genes, like SOX17, BLIMP1, TFAP2C, NANOS3, and the naïve pluripotency gene KLF4. The KLF4-knockout hESCs formed typical multicellular colonies with clear borders, expressed pluripotency genes, such as NANOG, OCT4, and SOX2, and exhibited no differences in proliferation capacity compared with wild type hESCs. Notably, KLF4 deletion in hESCs did not influence the induction of PGCLCs in vitro. In contrast, overexpression of KLF4 during PGC induction process inhibited the efficiency of PGCLC formation from hESCs in vitro. Overexpression of KLF4 may regenerate the naïve ground state in hESCs and results in repression for PGC specification. Thus, KLF4 could be a downstream target of human PGC program and the upregulation of KLF4 is prepared for late stage of germline development.
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Affiliation(s)
- Fang Fang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Zili Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xiaoke Zhang
- Department of Reproductive Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Qi Huang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Shi Lu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China.
| | - Xiao Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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42
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Blake MJ, Steer CJ. Chimeric Livers: Interspecies Blastocyst Complementation and Xenotransplantation for End-Stage Liver Disease. Hepat Med 2024; 16:11-29. [PMID: 38379783 PMCID: PMC10878318 DOI: 10.2147/hmer.s440697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/10/2024] [Indexed: 02/22/2024] Open
Abstract
Orthotopic liver transplantation (OLT) currently serves as the sole definitive treatment for thousands of patients suffering from end-stage liver disease; and the existing supply of donor livers for OLT is drastically outpaced by the increasing demand. To alleviate this significant gap in treatment, several experimental approaches have been devised with the aim of either offering interim support to patients waiting on the transplant list or bioengineering complete livers for OLT by infusing them with fresh hepatic cells. Recently, interspecies blastocyst complementation has emerged as a promising method for generating complete organs in utero over a short timeframe. When coupled with gene editing technology, it has brought about a potentially revolutionary transformation in regenerative medicine. Blastocyst complementation harbors notable potential for generating complete human livers in large animals, which could be used for xenotransplantation in humans, addressing the scarcity of livers for OLT. Nevertheless, substantial experimental and ethical challenges still need to be overcome to produce human livers in larger domestic animals like pigs. This review compiles the current understanding of interspecies blastocyst complementation and outlines future possibilities for liver xenotransplantation in humans.
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Affiliation(s)
- Madelyn J Blake
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Clifford J Steer
- Departments of Medicine, and Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, MN, USA
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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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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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45
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Li CJ, Chang CC, Tsai LK, Peng M, Lyu WN, Yu JF, Tsai MH, Sung LY. Generation of induced pluripotent stem cells from Bornean orangutans. Front Cell Dev Biol 2024; 11:1331584. [PMID: 38250322 PMCID: PMC10797036 DOI: 10.3389/fcell.2023.1331584] [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: 11/01/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction: Orangutans, classified under the Pongo genus, are an endangered non-human primate (NHP) species. Derivation of induced pluripotent stem cells (iPSCs) represents a promising avenue for conserving the genetic resources of these animals. Earlier studies focused on deriving orangutan iPSCs (o-iPSCs) from Sumatran orangutans (Pongo abelii). To date, no reports specifically target the other Critically Endangered species in the Pongo genus, the Bornean orangutans (Pongo pygmaeus). Methods: Using Sendai virus-mediated Yamanaka factor-based reprogramming of peripheral blood mononuclear cells to generate iPSCs (bo-iPSCs) from a female captive Bornean orangutan. In this study, we evaluate the colony morphology, pluripotent markers, X chromosome activation status, and transcriptomic profile of the bo-iPSCs to demonstrate the pluripotency of iPSCs from Bornean orangutans. Results: The bo-iPSCs were successfully derived from Bornean orangutans, using Sendai virus-mediated Yamanaka factor-based reprogramming of peripheral blood mononuclear cells. When a modified 4i/L/A (m4i/L/A) culture system was applied to activate the WNT signaling pathway in these bo-iPSCs, the derived cells (m-bo-iPSCs) manifested characteristics akin to human naive pluripotent stem cells, including high expression levels of KLF17, DNMT3L, and DPPA3/5, as well as the X chromosome reactivation. Comparative RNA-seq analysis positioned the m-bo-iPSCs between human naive and formative pluripotent states. Furthermore, the m-bo-iPSCs express differentiation capacity into all three germlines, evidenced by controlled in vitro embryoid body formation assay. Discussion: Our work establishes a novel approach to preserve the genetic diversity of endangered Bornean orangutans while offering insights into primate stem cell pluripotency. In the future, derivation of the primordial germ cell-like cells (PGCLCs) from m-bo-iPSCs is needed to demonstrate the further specific application in species preservation and broaden the knowledge of primordial germ cell specification across species.
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Affiliation(s)
- Chia-Jung Li
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Branch, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Chun Chang
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Li-Kuang Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Min Peng
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Wei-Ni Lyu
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Jane-Fang Yu
- Conservation and Research Center, Taipei Zoo, Taipei, Taiwan
| | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Center for Developmental Biology and Regenerative Medicine, Taipei, Taiwan
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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46
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Wilkinson AL, Zorzan I, Rugg-Gunn PJ. Epigenetic regulation of early human embryo development. Cell Stem Cell 2023; 30:1569-1584. [PMID: 37858333 DOI: 10.1016/j.stem.2023.09.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Studies of mammalian development have advanced our understanding of the genetic, epigenetic, and cellular processes that orchestrate embryogenesis and have uncovered new insights into the unique aspects of human embryogenesis. Recent studies have now produced the first epigenetic maps of early human embryogenesis, stimulating new ideas about epigenetic reprogramming, cell fate control, and the potential mechanisms underpinning developmental plasticity in human embryos. In this review, we discuss these new insights into the epigenetic regulation of early human development and the importance of these processes for safeguarding development. We also highlight unanswered questions and key challenges that remain to be addressed.
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Affiliation(s)
| | - Irene Zorzan
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
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47
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Torre D, Fstkchyan YS, Ho JSY, Cheon Y, Patel RS, Degrace EJ, Mzoughi S, Schwarz M, Mohammed K, Seo JS, Romero-Bueno R, Demircioglu D, Hasson D, Tang W, Mahajani SU, Campisi L, Zheng S, Song WS, Wang YC, Shah H, Francoeur N, Soto J, Salfati Z, Weirauch MT, Warburton P, Beaumont K, Smith ML, Mulder L, Villalta SA, Kessenbrock K, Jang C, Lee D, De Rubeis S, Cobos I, Tam O, Hammell MG, Seldin M, Shi Y, Basu U, Sebastiano V, Byun M, Sebra R, Rosenberg BR, Benner C, Guccione E, Marazzi I. Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Mol Cell 2023; 83:4255-4271.e9. [PMID: 37995687 PMCID: PMC10842741 DOI: 10.1016/j.molcel.2023.10.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/28/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Endogenous retroviruses (ERVs) are remnants of ancient parasitic infections and comprise sizable portions of most genomes. Although epigenetic mechanisms silence most ERVs by generating a repressive environment that prevents their expression (heterochromatin), little is known about mechanisms silencing ERVs residing in open regions of the genome (euchromatin). This is particularly important during embryonic development, where induction and repression of distinct classes of ERVs occur in short temporal windows. Here, we demonstrate that transcription-associated RNA degradation by the nuclear RNA exosome and Integrator is a regulatory mechanism that controls the productive transcription of most genes and many ERVs involved in preimplantation development. Disrupting nuclear RNA catabolism promotes dedifferentiation to a totipotent-like state characterized by defects in RNAPII elongation and decreased expression of long genes (gene-length asymmetry). Our results indicate that RNA catabolism is a core regulatory module of gene networks that safeguards RNAPII activity, ERV expression, cell identity, and developmental potency.
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Affiliation(s)
- Denis Torre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yesai S Fstkchyan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jessica Sook Yuin Ho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Youngseo Cheon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea; Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Roosheel S Patel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emma J Degrace
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Slim Mzoughi
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan Schwarz
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kevin Mohammed
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ji-Seon Seo
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Raquel Romero-Bueno
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Deniz Demircioglu
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weijing Tang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sameehan U Mahajani
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura Campisi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Won-Suk Song
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nancy Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan Soto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zelda Salfati
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Peter Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristin Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Lubbertus Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - S Armando Villalta
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, The Mindich Child Health and Development Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Inma Cobos
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oliver Tam
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Marcus Seldin
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Yongsheng Shi
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA; Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Uttiya Basu
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Vittorio Sebastiano
- Institute for Stem Cell Biology and Regenerative Medicine and the Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Minji Byun
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chris Benner
- Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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48
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Kretschmer M, Fischer V, Gapp K. When Dad's Stress Gets under Kid's Skin-Impacts of Stress on Germline Cargo and Embryonic Development. Biomolecules 2023; 13:1750. [PMID: 38136621 PMCID: PMC10742275 DOI: 10.3390/biom13121750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Multiple lines of evidence suggest that paternal psychological stress contributes to an increased prevalence of neuropsychiatric and metabolic diseases in the progeny. While altered paternal care certainly plays a role in such transmitted disease risk, molecular factors in the germline might additionally be at play in humans. This is supported by findings on changes to the molecular make up of germ cells and suggests an epigenetic component in transmission. Several rodent studies demonstrate the correlation between paternal stress induced changes in epigenetic modifications and offspring phenotypic alterations, yet some intriguing cases also start to show mechanistic links in between sperm and the early embryo. In this review, we summarise efforts to understand the mechanism of intergenerational transmission from sperm to the early embryo. In particular, we highlight how stress alters epigenetic modifications in sperm and discuss the potential for these modifications to propagate modified molecular trajectories in the early embryo to give rise to aberrant phenotypes in adult offspring.
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Affiliation(s)
- Miriam Kretschmer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Vincent Fischer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Katharina Gapp
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
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49
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Sarel-Gallily R, Keshet G, Kinreich S, Haim-Abadi G, Benvenisty N. EpiTyping: analysis of epigenetic aberrations in parental imprinting and X-chromosome inactivation using RNA-seq. Nat Protoc 2023; 18:3881-3917. [PMID: 37914783 DOI: 10.1038/s41596-023-00898-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/28/2023] [Indexed: 11/03/2023]
Abstract
Human pluripotent stem cells (hPSCs) hold a central role in studying human development, in disease modeling and in regenerative medicine. These cells not only acquire genetic modifications when kept in culture, but they may also harbor epigenetic aberrations, mainly involving parental imprinting and X-chromosome inactivation. Here we present a detailed bioinformatic protocol for detecting such aberrations using RNA sequencing data. We provide a pipeline designed to process and analyze RNA sequencing data for the identification of abnormal biallelic expression of imprinted genes, and thus detect loss of imprinting. Furthermore, we show how to differentiate among X-chromosome inactivation, full activation and aberrant erosion of X chromosome in female hPSCs. In addition to providing bioinformatic tools, we discuss the impact of such epigenetic variations in hPSCs on their utility for various purposes. This pipeline can be used by any user with basic understanding of the Linux command line. It is available on GitHub as a software container ( https://github.com/Gal-Keshet/EpiTyping ) and produces reliable results in 1-4 d.
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Affiliation(s)
- Roni Sarel-Gallily
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gal Keshet
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Shay Kinreich
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Guy Haim-Abadi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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50
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Verma A, Poondi Krishnan V, Cecere F, D’Angelo E, Lullo V, Strazzullo M, Selig S, Angelini C, Matarazzo MR, Riccio A. ICF1-Syndrome-Associated DNMT3B Mutations Prevent De Novo Methylation at a Subset of Imprinted Loci during iPSC Reprogramming. Biomolecules 2023; 13:1717. [PMID: 38136588 PMCID: PMC10741953 DOI: 10.3390/biom13121717] [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: 08/02/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Parent-of-origin-dependent gene expression of a few hundred human genes is achieved by differential DNA methylation of both parental alleles. This imprinting is required for normal development, and defects in this process lead to human disease. Induced pluripotent stem cells (iPSCs) serve as a valuable tool for in vitro disease modeling. However, a wave of de novo DNA methylation during reprogramming of iPSCs affects DNA methylation, thus limiting their use. The DNA methyltransferase 3B (DNMT3B) gene is highly expressed in human iPSCs; however, whether the hypermethylation of imprinted loci depends on DNMT3B activity has been poorly investigated. To explore the role of DNMT3B in mediating de novo DNA methylation at imprinted DMRs, we utilized iPSCs generated from patients with immunodeficiency, centromeric instability, facial anomalies type I (ICF1) syndrome that harbor biallelic hypomorphic DNMT3B mutations. Using a whole-genome array-based approach, we observed a gain of methylation at several imprinted loci in control iPSCs but not in ICF1 iPSCs compared to their parental fibroblasts. Moreover, in corrected ICF1 iPSCs, which restore DNMT3B enzymatic activity, imprinted DMRs did not acquire control DNA methylation levels, in contrast to the majority of the hypomethylated CpGs in the genome that were rescued in the corrected iPSC clones. Overall, our study indicates that DNMT3B is responsible for de novo methylation of a subset of imprinted DMRs during iPSC reprogramming and suggests that imprinting is unstable during a specific time window of this process, after which the epigenetic state at these regions becomes resistant to perturbation.
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Affiliation(s)
- Ankit Verma
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Varsha Poondi Krishnan
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Emilia D’Angelo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Vincenzo Lullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Maria Strazzullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Sara Selig
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel;
- Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo “Mauro Picone”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy;
| | - Maria R. Matarazzo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
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