1
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Campos G, Nel-Themaat L. Blastocoel fluid as an alternative source of DNA for minimally invasive PGT and biomarker of embryo competence. Reprod Biomed Online 2024; 49:104322. [PMID: 39121560 DOI: 10.1016/j.rbmo.2024.104322] [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: 02/16/2024] [Revised: 04/26/2024] [Accepted: 06/05/2024] [Indexed: 08/12/2024]
Abstract
The discovery of DNA in blastocoel fluid (BF-DNA) generated new perspectives in the potential development of simpler and safer alternative non-invasive tests in reproductive genetics. Short DNA fragments of apoptotic origin, together with specific expression patterns of pro- and anti-apoptotic genes in the blastocoel fluid of euploid and aneuploid embryos, suggest a self-correction mechanism to preferentially eliminate aneuploid cells, and purge defective and non-viable cells. The correlation of blastocoel fluid content with the genetic status of the whole embryo, and therefore its potential use in minimally invasive preimplantation genetic testing (miPGT), or as an indicator of embryo potential, remains uncertain and needs to be determined. The limited amount and compromised integrity of BF-DNA, with likely apoptotic origination, constrains its amplification, leading to low concordance and reproducibility rates for both aneuploidy screening and monogenic testing. While embryo genotyping constitutes a more ambitious goal, the presence of analysable DNA after amplification in blastocoel fluid may be used as a clinical biomarker of embryo competency to select the most viable embryo(s) for transfer, and potentially improve the implantation rate. Although blastocentesis remains a promising area for future research, several technical and methodological limitations are currently constraining its consideration for clinical practice.
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Affiliation(s)
- Gerard Campos
- Geisinger Medical Centre, Women's Health Fertility Clinic, Danville, Pennsylvania, USA; Girexx Fertility Clinics, Barcelona, Spain.
| | - Liesl Nel-Themaat
- Stanford Fertility and Reproductive Health Services, Stanford Medicine Children's Health, Sunnyvale, California, USA
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2
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Skory RM. Revisiting trophectoderm-inner cell mass lineage segregation in the mammalian preimplantation embryo. Hum Reprod 2024; 39:1889-1898. [PMID: 38926157 DOI: 10.1093/humrep/deae142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
In the first days of life, cells of the mammalian embryo segregate into two distinct lineages, trophectoderm and inner cell mass. Unlike nonmammalian species, mammalian development does not proceed from predetermined factors in the oocyte. Rather, asymmetries arise de novo in the early embryo incorporating cues from cell position, contractility, polarity, and cell-cell contacts. Molecular heterogeneities, including transcripts and non-coding RNAs, have now been characterized as early as the 2-cell stage. However, it's debated whether these early heterogeneities bias cells toward one fate or the other or whether lineage identity arises stochastically at the 16-cell stage. This review summarizes what is known about early blastomere asymmetries and our understanding of lineage allocation in the context of historical models. Preimplantation development is reviewed coupled with what is known about changes in morphology, contractility, and transcription factor networks. The addition of single-cell atlases of human embryos has begun to reveal key differences between human and mouse, including the timing of events and core transcription factors. Furthermore, the recent generation of blastoid models will provide valuable tools to test and understand fate determinants. Lastly, new techniques are reviewed, which may better synthesize existing knowledge with emerging data sets and reconcile models with the regulative capacity unique to the mammalian embryo.
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Affiliation(s)
- Robin M Skory
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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3
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Sun M, Chang L, He L, Wang L, Jiang Z, Si Y, Yu J, Ma Y. Combining single-cell profiling and functional analysis explores the role of pseudogenes in human early embryonic development. J Genet Genomics 2024:S1673-8527(24)00189-9. [PMID: 39032861 DOI: 10.1016/j.jgg.2024.07.013] [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: 03/25/2024] [Revised: 07/12/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
More and more studies have demonstrated that pseudogenes possess coding ability, and the functions of their transcripts in the development of diseases have been partially revealed. However, the role of pseudogenes in maintenance of normal physiological states and life activities has long been neglected. Here, we identify pseudogenes that are dynamically expressed during human early embryogenesis, showing different expression pattern from that of adult tissues. We explore the expression correlation between pseudogenes and the parent genes, part due to their shared gene regulatory elements or the potential regulation network between them. The essential role of three pseudogenes, PI4KAP1, TMED10P1, and FBXW4P1, in maintaining self-renewal of human embryonic stem cells is demonstrated. We further find that the three pseudogenes might perform their regulatory functions by binding to proteins or microRNAs. The pseudogene-related single-nucleotide polymorphisms are significantly associated with human congenital disease, further illustrating their importance during early embryonic development. Overall, this study is an excavation and exploration of functional pseudogenes during early human embryonic development, suggesting that pseudogenes are not only capable of being specifically activated in pathological states, but also play crucial roles in the maintenance of normal physiological states.
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Affiliation(s)
- Mengyao Sun
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China
| | - Le Chang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Liu He
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Li Wang
- Department of Obstetrics, Haidian District Maternity and Child Health Hospital, Beijing 100080, China
| | - Zhengyang Jiang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yanmin Si
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
| | - Yanni Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China.
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4
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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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5
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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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6
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Indana D, Zakharov A, Lim Y, Dunn AR, Bhutani N, Shenoy VB, Chaudhuri O. Lumen expansion is initially driven by apical actin polymerization followed by osmotic pressure in a human epiblast model. Cell Stem Cell 2024; 31:640-656.e8. [PMID: 38701758 PMCID: PMC11323070 DOI: 10.1016/j.stem.2024.03.016] [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: 09/29/2023] [Revised: 02/08/2024] [Accepted: 03/27/2024] [Indexed: 05/05/2024]
Abstract
Post-implantation, the pluripotent epiblast in a human embryo forms a central lumen, paving the way for gastrulation. Osmotic pressure gradients are considered the drivers of lumen expansion across development, but their role in human epiblasts is unknown. Here, we study lumenogenesis in a pluripotent-stem-cell-based epiblast model using engineered hydrogels. We find that leaky junctions prevent osmotic pressure gradients in early epiblasts and, instead, forces from apical actin polymerization drive lumen expansion. Once the lumen reaches a radius of ∼12 μm, tight junctions mature, and osmotic pressure gradients develop to drive further growth. Computational modeling indicates that apical actin polymerization into a stiff network mediates initial lumen expansion and predicts a transition to pressure-driven growth in larger epiblasts to avoid buckling. Human epiblasts show transcriptional signatures consistent with these mechanisms. Thus, actin polymerization drives lumen expansion in the human epiblast and may serve as a general mechanism of early lumenogenesis.
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Affiliation(s)
- Dhiraj Indana
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Andrei Zakharov
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Youngbin Lim
- Cell Sciences Imaging Facility (CSIF), Beckman Center, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander R Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Nidhi Bhutani
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vivek B Shenoy
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA.
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7
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Azagury M, Buganim Y. Unlocking trophectoderm mysteries: In vivo and in vitro perspectives on human and mouse trophoblast fate induction. Dev Cell 2024; 59:941-960. [PMID: 38653193 DOI: 10.1016/j.devcel.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/10/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
In recent years, the pursuit of inducing the trophoblast stem cell (TSC) state has gained prominence as a compelling research objective, illuminating the establishment of the trophoblast lineage and unlocking insights into early embryogenesis. In this review, we examine how advancements in diverse technologies, including in vivo time course transcriptomics, cellular reprogramming to TSC state, chemical induction of totipotent stem-cell-like state, and stem-cell-based embryo-like structures, have enriched our insights into the intricate molecular mechanisms and signaling pathways that define the mouse and human trophectoderm/TSC states. We delve into disparities between mouse and human trophectoderm/TSC fate establishment, with a special emphasis on the intriguing role of pluripotency in this context. Additionally, we re-evaluate recent findings concerning the potential of totipotent-stem-like cells and embryo-like structures to fully manifest the trophectoderm/trophoblast lineage's capabilities. Lastly, we briefly discuss the potential applications of induced TSCs in pregnancy-related disease modeling.
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Affiliation(s)
- Meir Azagury
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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8
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Carvalho S, Zea-Redondo L, Tang TCC, Stachel-Braum P, Miller D, Caldas P, Kukalev A, Diecke S, Grosswendt S, Grosso AR, Pombo A. SRRM2 splicing factor modulates cell fate in early development. Biol Open 2024; 13:bio060415. [PMID: 38656788 PMCID: PMC11070786 DOI: 10.1242/bio.060415] [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: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Embryo development is an orchestrated process that relies on tight regulation of gene expression to guide cell differentiation and fate decisions. The Srrm2 splicing factor has recently been implicated in developmental disorders and diseases, but its role in early mammalian development remains unexplored. Here, we show that Srrm2 dosage is critical for maintaining embryonic stem cell pluripotency and cell identity. Srrm2 heterozygosity promotes loss of stemness, characterised by the coexistence of cells expressing naive and formative pluripotency markers, together with extensive changes in gene expression, including genes regulated by serum-response transcription factor (SRF) and differentiation-related genes. Depletion of Srrm2 by RNA interference in embryonic stem cells shows that the earliest effects of Srrm2 heterozygosity are specific alternative splicing events on a small number of genes, followed by expression changes in metabolism and differentiation-related genes. Our findings unveil molecular and cellular roles of Srrm2 in stemness and lineage commitment, shedding light on the roles of splicing regulators in early embryogenesis, developmental diseases and tumorigenesis.
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Affiliation(s)
- Silvia Carvalho
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
- Graduate Program in Areas of Basic and Applied Biology (GABBA), ICBAS, University of Porto, 4050-313 Porto, Portugal
| | - Luna Zea-Redondo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
| | - Tsz Ching Chloe Tang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
| | - Philipp Stachel-Braum
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Exploratory Diagnostic Sciences (EDS) 10178 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), From Cell State to Function Group, 10115 Berlin, Germany
| | - Duncan Miller
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Pluripotent Stem Cells Platform, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10785 Berlin, Germany
| | - Paulo Caldas
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Alexander Kukalev
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
| | - Sebastian Diecke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Pluripotent Stem Cells Platform, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10785 Berlin, Germany
| | - Stefanie Grosswendt
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Exploratory Diagnostic Sciences (EDS) 10178 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), From Cell State to Function Group, 10115 Berlin, Germany
| | - Ana Rita Grosso
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
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9
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Liang P, Li H, Long C, Liu M, Zhou J, Zuo Y. Chromatin region binning of gene expression for improving embryo cell subtype identification. Comput Biol Med 2024; 170:108049. [PMID: 38290319 DOI: 10.1016/j.compbiomed.2024.108049] [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: 10/10/2023] [Revised: 01/01/2024] [Accepted: 01/26/2024] [Indexed: 02/01/2024]
Abstract
Mammalian embryonic development is a complex process, characterized by intricate spatiotemporal dynamics and distinct chromatin preferences. However, the quick diversification in early embryogenesis leads to significant cellular diversity and the sparsity of scRNA-seq data, posing challenges in accurately determining cell fate decisions. In this study, we introduce a chromatin region binning method using scChrBin, designed to identify chromatin regions that elucidate the dynamics of embryonic development and lineage differentiation. This method transforms scRNA-seq data into a chromatin-based matrix, leveraging genomic annotations. Our results showed that the scChrBin method achieves high accuracy, with 98.0% and 89.2% on two single-cell embryonic datasets, demonstrating its effectiveness in analyzing complex developmental processes. We also systematically and comprehensively analysis of these key chromatin binning regions and their associated genes, focusing on their roles in lineage and stage development. The perspective of chromatin region binning method enables a comprehensive analysis of transcriptome data at the chromatin level, allowing us to unveil the dynamic expression of chromatin regions across temporal and spatial development. The tool is available as an application at https://github.com/liameihao/scChrBin.
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Affiliation(s)
- Pengfei Liang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Hanshuang Li
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Chunshen Long
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Mingzhu Liu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Jian Zhou
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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10
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Nakanoh S, Sham K, Ghimire S, Mohorianu I, Rayon T, Vallier L. Human surface ectoderm and amniotic ectoderm are sequentially specified according to cellular density. SCIENCE ADVANCES 2024; 10:eadh7748. [PMID: 38427729 PMCID: PMC10906920 DOI: 10.1126/sciadv.adh7748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024]
Abstract
Mechanisms specifying amniotic ectoderm and surface ectoderm are unresolved in humans due to their close similarities in expression patterns and signal requirements. This lack of knowledge hinders the development of protocols to accurately model human embryogenesis. Here, we developed a human pluripotent stem cell model to investigate the divergence between amniotic and surface ectoderms. In the established culture system, cells differentiated into functional amnioblast-like cells. Single-cell RNA sequencing analyses of amnioblast differentiation revealed an intermediate cell state with enhanced surface ectoderm gene expression. Furthermore, when the differentiation started at the confluent condition, cells retained the expression profile of surface ectoderm. Collectively, we propose that human amniotic ectoderm and surface ectoderm are specified along a common nonneural ectoderm trajectory based on cell density. Our culture system also generated extraembryonic mesoderm-like cells from the primed pluripotent state. Together, this study provides an integrative understanding of the human nonneural ectoderm development and a model for embryonic and extraembryonic human development around gastrulation.
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Affiliation(s)
- Shota Nakanoh
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge CB22 3AT, UK
| | - Kendig Sham
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Sabitri Ghimire
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Teresa Rayon
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge CB22 3AT, UK
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
- Berlin Institute of Health Centre for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany
- Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
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11
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Zheng Y. Stem Cell-Derived Microfluidic Amniotic Sac Embryoid (μPASE). Methods Mol Biol 2024; 2767:75-84. [PMID: 36749485 DOI: 10.1007/7651_2022_470] [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] [Indexed: 02/08/2023]
Abstract
The microfluidic amniotic sac embryoid (μPASE) is a human pluripotent stem cell (hPSC)-derived multicellular human embryo-like structure with molecular and morphological features resembling the progressive development of the early post-implantation human embryonic sac. The microfluidic device is specifically designed to control the formation of hPSC clusters and expose the clusters to different morphogen environments, allowing the development of μPASEs in a highly controllable, reproducible, and scalable fashion. The μPASE model displays human embryonic developmental landmarks such as lumenogenesis of the epiblast, amniotic cavity formation, and the specification of primordial germ cells and gastrulating cells (or mesendoderm cells). Here, we provide detailed instructions needed to reproduce μPASEs, including the immunofluorescence staining and cell retrieval protocols for characterizing μPASEs obtained under different experimental conditions.
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Affiliation(s)
- Yi Zheng
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA
- BioInspired Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, NY, USA
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12
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Xiang L, Yin Y, Shi G, Li T. Human Pre-gastrulation Embryo Culture in 3D Condition. Methods Mol Biol 2024; 2767:19-25. [PMID: 36515895 DOI: 10.1007/7651_2022_466] [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] [Indexed: 12/15/2022]
Abstract
The development process of human embryo until blastocyst is well understood during the past 30 years, however, embryogenesis from blastocyst to pre-gastrulation was still remained a "black box". Limited by research materials and culture technologies, the "black box" is still unopened. We recently established an extended three-dimensional (3D) culture system of human blastocysts (Xiang et al., Nature 577(7791):537-542, 2020). The 3D embryo culture system could enable human blastocyst growing up to early primitive streak anlage stage in vitro. Here, we introduce the detail protocol and notes of culturing human 3D embryos.
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Affiliation(s)
- Lifeng Xiang
- Department of Reproductive Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yu Yin
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Gaohui Shi
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Tianqing Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
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13
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Campos G, Sciorio R, Fleming S. Healthy Live Births after the Transfer of Mosaic Embryos: Self-Correction or PGT-A Overestimation? Genes (Basel) 2023; 15:18. [PMID: 38275600 PMCID: PMC10815078 DOI: 10.3390/genes15010018] [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: 12/04/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
The implementation of next generation sequencing (NGS) in preimplantation genetic testing for aneuploidy (PGT-A) has led to a higher prevalence of mosaic diagnosis within the trophectoderm (TE) sample. Regardless, mosaicism could potentially increase the rate of live-born children with chromosomic syndromes, though available data from the transfer of embryos with putative PGT-A mosaicism are scarce but reassuring. Even with lower implantation and higher miscarriage rates, mosaic embryos can develop into healthy live births. Therefore, this urges an explanation for the disappearance of aneuploid cells throughout development, to provide guidance in the management of mosaicism in clinical practice. Technical overestimation of mosaicism, together with some sort of "self-correction" mechanisms during the early post-implantation stages, emerged as potential explanations. Unlike the animal model, in which the elimination of genetically abnormal cells from the future fetal lineage has been demonstrated, in human embryos this capability remains unverified even though the germ layer displays an aneuploidy-induced cell death lineage preference with higher rates of apoptosis in the inner cell mass (ICM) than in the TE cells. Moreover, the reported differential dynamics of cell proliferation and apoptosis between euploid, mosaic, and aneuploid embryos, together with pro-apoptosis gene products (cfDNA and mRNA) and extracellular vesicles identified in the blastocoel fluid, may support the hypothesis of apoptosis as a mechanism to purge the preimplantation embryo of aneuploid cells. Alternative hypotheses, like correction of aneuploidy by extrusion of a trisomy chromosome or by monosomic chromosome duplication, are even, though they represent an extremely rare phenomenon. On the other hand, the technical limitations of PGT-A analysis may lead to inaccuracy in embryo diagnoses, identifying as "mosaic" those embryos that are uniformly euploid or aneuploid. NGS assumption of "intermediate copy number profiles" as evidence of a mixture of euploid and aneuploid cells in a single biopsy has been reported to be poorly predictive in cases of mosaicism diagnosis. Additionally, the concordance found between the TE and the ICM in cases of TE biopsies displaying mosaicism is lower than expected, and it correlates differently depending on the type (whole chromosome versus segmental) and the level of mosaicism reported. Thus, in cases of low-/medium-level mosaicism (<50%), aneuploid cells would rarely involve the ICM and other regions. However, in high-level mosaics (≥50%), abnormal cells in the ICM should display higher prevalence, revealing more uniform aneuploidy in most embryos, representing a technical variation in the uniform aneuploidy range, and therefore might impair the live birth rate.
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Affiliation(s)
- Gerard Campos
- Geisinger Medical Center, Women’s Health Fertility Clinic, Danville, PA 17821, USA;
- GIREXX Fertility Clinics, C. de Cartagena, 258, 08025 Girona, Spain
| | - Romualdo Sciorio
- Fertility Medicine and Gynaecological Endocrinology Unit, Department Woman-Mother-Child, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Steven Fleming
- Discipline of Anatomy & Histology, School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia;
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14
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Li L, Lai F, Hu X, Liu B, Lu X, Lin Z, Liu L, Xiang Y, Frum T, Halbisen MA, Chen F, Fan Q, Ralston A, Xie W. Multifaceted SOX2-chromatin interaction underpins pluripotency progression in early embryos. Science 2023; 382:eadi5516. [PMID: 38096290 DOI: 10.1126/science.adi5516] [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: 05/04/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
Pioneer transcription factors (TFs), such as OCT4 and SOX2, play crucial roles in pluripotency regulation. However, the master TF-governed pluripotency regulatory circuitry was largely inferred from cultured cells. In this work, we investigated SOX2 binding from embryonic day 3.5 (E3.5) to E7.5 in the mouse. In E3.5 inner cell mass (ICM), SOX2 regulates the ICM-trophectoderm program but is dispensable for opening global enhancers. Instead, SOX2 occupies preaccessible enhancers in part opened by early-stage expressing TFs TFAP2C and NR5A2. SOX2 then widely redistributes when cells adopt naive and formative pluripotency by opening enhancers or poising them for rapid future activation. Hence, multifaceted pioneer TF-enhancer interaction underpins pluripotency progression in embryos, including a distinctive state in E3.5 ICM that bridges totipotency and pluripotency.
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Affiliation(s)
- Lijia Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, New Cornerstone Science Laboratory, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Fangnong Lai
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, New Cornerstone Science Laboratory, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaoyu Hu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, New Cornerstone Science Laboratory, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, New Cornerstone Science Laboratory, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xukun Lu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, New Cornerstone Science Laboratory, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Zili Lin
- College of Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, New Cornerstone Science Laboratory, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yunlong Xiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Tristan Frum
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael A Halbisen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Fengling Chen
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, New Cornerstone Science Laboratory, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, New Cornerstone Science Laboratory, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Amy Ralston
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, New Cornerstone Science Laboratory, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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15
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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: 10] [Impact Index Per Article: 10.0] [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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16
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Perera M, Brickman JM. In vitro models of human hypoblast and mouse primitive endoderm. Curr Opin Genet Dev 2023; 83:102115. [PMID: 37783145 DOI: 10.1016/j.gde.2023.102115] [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: 03/23/2023] [Revised: 07/28/2023] [Accepted: 08/24/2023] [Indexed: 10/04/2023]
Abstract
The primitive endoderm (PrE, also named hypoblast), a predominantly extraembryonic epithelium that arises from the inner cell mass (ICM) of the mammalian pre-implantation blastocyst, plays a fundamental role in embryonic development, giving rise to the yolk sac, establishing the anterior-posterior axis and contributing to the gut. PrE is specified from the ICM at the same time as the epiblast (Epi) that will form the embryo proper. While in vitro cell lines resembling the pluripotent Epi have been derived from a variety of conditions, only one model system currently exists for the PrE, naïve extraembryonic endoderm (nEnd). As a result, considerably more is known about the gene regulatory networks and signalling requirements of pluripotent stem cells than nEnd. In this review, we describe the ontogeny and differentiation of the PrE or hypoblast in mouse and primate and then discuss in vitro cell culture models for different extraembryonic endodermal cell types.
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Affiliation(s)
- Marta Perera
- reNEW UCPH - The Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark. https://twitter.com/@MartaPrera
| | - Joshua M Brickman
- reNEW UCPH - The Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
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17
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Chang Y, Hummel SN, Jung J, Jin G, Deng Q, Bao X. Engineered hematopoietic and immune cells derived from human pluripotent stem cells. Exp Hematol 2023; 127:14-27. [PMID: 37611730 PMCID: PMC10615717 DOI: 10.1016/j.exphem.2023.08.006] [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: 05/31/2023] [Revised: 08/09/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
For the past decade, significant advances have been achieved in human hematopoietic stem cell (HSC) transplantation for treating various blood diseases and cancers. However, challenges remain with the quality control, amount, and cost of HSCs and HSC-derived immune cells. The advent of human pluripotent stem cells (hPSCs) may transform HSC transplantation and cancer immunotherapy by providing a cost-effective and scalable cell source for fundamental studies and translational applications. In this review, we discuss the current developments in the field of stem cell engineering for hematopoietic stem and progenitor cell (HSPC) differentiation and further differentiation of HSPCs into functional immune cells. The key advances in stem cell engineering include the generation of HSPCs from hPSCs, genetic modification of hPSCs, and hPSC-derived HSPCs for improved function, further differentiation of HPSCs into functional immune cells, and applications of cell culture platforms for hematopoietic cell manufacturing. Current challenges impeding the translation of hPSC-HSPCs and immune cells as well as further directions to address these challenges are also discussed.
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Affiliation(s)
- Yun Chang
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana; Purdue University Institute for Cancer Research, West Lafayette, Indiana
| | - Sydney N Hummel
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana; Purdue University Institute for Cancer Research, West Lafayette, Indiana
| | - Juhyung Jung
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana; Purdue University Institute for Cancer Research, West Lafayette, Indiana
| | - Gyuhyung Jin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana; Purdue University Institute for Cancer Research, West Lafayette, Indiana
| | - Qing Deng
- Purdue University Institute for Cancer Research, West Lafayette, Indiana; Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Xiaoping Bao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana; Purdue University Institute for Cancer Research, West Lafayette, Indiana.
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18
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Agostinho de Sousa J, Wong CW, Dunkel I, Owens T, Voigt P, Hodgson A, Baker D, Schulz EG, Reik W, Smith A, Rostovskaya M, von Meyenn F. Epigenetic dynamics during capacitation of naïve human pluripotent stem cells. SCIENCE ADVANCES 2023; 9:eadg1936. [PMID: 37774033 PMCID: PMC10541016 DOI: 10.1126/sciadv.adg1936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are of fundamental relevance in regenerative medicine. Naïve hPSCs hold promise to overcome some of the limitations of conventional (primed) hPSCs, including recurrent epigenetic anomalies. Naïve-to-primed transition (capacitation) follows transcriptional dynamics of human embryonic epiblast and is necessary for somatic differentiation from naïve hPSCs. We found that capacitated hPSCs are transcriptionally closer to postimplantation epiblast than conventional hPSCs. This prompted us to comprehensively study epigenetic and related transcriptional changes during capacitation. Our results show that CpG islands, gene regulatory elements, and retrotransposons are hotspots of epigenetic dynamics during capacitation and indicate possible distinct roles of specific epigenetic modifications in gene expression control between naïve and primed hPSCs. Unexpectedly, PRC2 activity appeared to be dispensable for the capacitation. We find that capacitated hPSCs acquire an epigenetic state similar to conventional hPSCs. Significantly, however, the X chromosome erosion frequently observed in conventional female hPSCs is reversed by resetting and subsequent capacitation.
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Affiliation(s)
- João Agostinho de Sousa
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | - Chee-Wai Wong
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | - Ilona Dunkel
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Thomas Owens
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Philipp Voigt
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Adam Hodgson
- School of Biosciences, The Julia Garnham Centre, University of Sheffield, S10 2TN Sheffield, UK
| | - Duncan Baker
- Sheffield Diagnostic Genetics Services, Sheffield Children’s NHS Foundation Trust, S5 7AU Sheffield, UK
| | - Edda G. Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1QR, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Altos Labs Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Austin Smith
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Living Systems Institute, University of Exeter, EX4 4QD Exeter, UK
| | - Maria Rostovskaya
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
- Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, SE1 9RT London, UK
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19
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Lee DK, Kim M, Jeong J, Lee YS, Yoon JW, An MJ, Jung HY, Kim CH, Ahn Y, Choi KH, Jo C, Lee CK. Unlocking the potential of stem cells: Their crucial role in the production of cultivated meat. Curr Res Food Sci 2023; 7:100551. [PMID: 37575132 PMCID: PMC10412782 DOI: 10.1016/j.crfs.2023.100551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/05/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
Cellular agriculture is an emerging research field of agribiotechnology that aims to produce agricultural products using stem cells, without sacrificing animals or cultivating crops. Cultivated meat, as a representative cellular product of cellular agriculture, is being actively researched due to global food insecurity, environmental, and ethical concerns. This review focuses on the application of stem cells, which are the seeds of cellular agriculture, for the production of cultivated meat, with emphasis on deriving and culturing muscle and adipose stem cells for imitating fresh meat. Establishing standards and safety regulations for culturing stem cells is crucial for the market entry of cultured muscle tissue-based biomaterials. Understanding stem cells is a prerequisite for creating reliable cultivated meat and other cellular agricultural biomaterials. The techniques and regulations from the cultivated meat industry could pave the way for new cellular agriculture industries in the future.
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Affiliation(s)
- Dong-Kyung Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Research and Development Center, Space F Corporation, Hwasung, 18471, Gyeonggi-do, Republic of Korea
| | - Minsu Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jinsol Jeong
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Young-Seok Lee
- Research and Development Center, Space F Corporation, Hwasung, 18471, Gyeonggi-do, Republic of Korea
| | - Ji Won Yoon
- Research and Development Center, Space F Corporation, Hwasung, 18471, Gyeonggi-do, Republic of Korea
| | - Min-Jeong An
- Research and Development Center, Space F Corporation, Hwasung, 18471, Gyeonggi-do, Republic of Korea
| | - Hyun Young Jung
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Cho Hyun Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yelim Ahn
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kwang-Hwan Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Research and Development Center, Space F Corporation, Hwasung, 18471, Gyeonggi-do, Republic of Korea
| | - Cheorun Jo
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Gangwon-do, Republic of Korea
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Gangwon-do, Republic of Korea
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20
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Varzideh F, Gambardella J, Kansakar U, Jankauskas SS, Santulli G. Molecular Mechanisms Underlying Pluripotency and Self-Renewal of Embryonic Stem Cells. Int J Mol Sci 2023; 24:8386. [PMID: 37176093 PMCID: PMC10179698 DOI: 10.3390/ijms24098386] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Embryonic stem cells (ESCs) are derived from the inner cell mass (ICM) of the blastocyst. ESCs have two distinctive properties: ability to proliferate indefinitely, a feature referred as "self-renewal", and to differentiate into different cell types, a peculiar characteristic known as "pluripotency". Self-renewal and pluripotency of ESCs are finely orchestrated by precise external and internal networks including epigenetic modifications, transcription factors, signaling pathways, and histone modifications. In this systematic review, we examine the main molecular mechanisms that sustain self-renewal and pluripotency in both murine and human ESCs. Moreover, we discuss the latest literature on human naïve pluripotency.
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Affiliation(s)
- Fahimeh Varzideh
- Department of Medicine (Division of Cardiology), Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Institute for Neuroimmunology and Inflammation (INI), Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Jessica Gambardella
- Department of Molecular Pharmacology, Einstein-Mount Sinai Diabetes Research Center (ES-DRC), Fleischer Institute for Diabetes and Metabolism (FIDAM), Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Urna Kansakar
- Department of Medicine (Division of Cardiology), Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Institute for Neuroimmunology and Inflammation (INI), Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Stanislovas S. Jankauskas
- Department of Medicine (Division of Cardiology), Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Institute for Neuroimmunology and Inflammation (INI), Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Gaetano Santulli
- Department of Medicine (Division of Cardiology), Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Institute for Neuroimmunology and Inflammation (INI), Albert Einstein College of Medicine, New York, NY 10461, USA
- Department of Molecular Pharmacology, Einstein-Mount Sinai Diabetes Research Center (ES-DRC), Fleischer Institute for Diabetes and Metabolism (FIDAM), Albert Einstein College of Medicine, New York, NY 10461, USA
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21
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Pinzón-Arteaga CA, Wang Y, Wei Y, Ribeiro Orsi AE, Li L, Scatolin G, Liu L, Sakurai M, Ye J, Hao Ming, Yu L, Li B, Jiang Z, Wu J. Bovine blastocyst-like structures derived from stem cell cultures. Cell Stem Cell 2023; 30:611-616.e7. [PMID: 37146582 PMCID: PMC10230549 DOI: 10.1016/j.stem.2023.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/23/2023] [Accepted: 04/05/2023] [Indexed: 05/07/2023]
Abstract
Understanding the mechanisms of blastocyst formation and implantation is critical for improving farm animal reproduction but is hampered by a limited supply of embryos. Here, we developed an efficient method to generate bovine blastocyst-like structures (termed blastoids) via assembling bovine trophoblast stem cells and expanded potential stem cells. Bovine blastoids resemble blastocysts in morphology, cell composition, single-cell transcriptomes, in vitro growth, and the ability to elicit maternal recognition of pregnancy following transfer to recipient cows. Bovine blastoids represent an accessible in vitro model for studying embryogenesis and improving reproductive efficiency in livestock species.
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Affiliation(s)
- Carlos A Pinzón-Arteaga
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yinjuan Wang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70810, USA
| | - Yulei Wei
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China, Agricultural University, Beijing 100193, China
| | - Ana E Ribeiro Orsi
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Leijie Li
- SJTU-Yale Joint Center for Biostatistics and Data Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Giovanna Scatolin
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70810, USA; Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lizhong Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Masahiro Sakurai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jianfeng Ye
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hao Ming
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70810, USA
| | - Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Li
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zongliang Jiang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70810, USA; Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 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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22
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Extracellular vesicles throughout development: A potential roadmap for emerging glioblastoma therapies. Semin Cell Dev Biol 2023; 133:32-41. [PMID: 35697594 DOI: 10.1016/j.semcdb.2022.05.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 12/15/2022]
Abstract
Extracellular vesicles (EVs) are membrane-delimited vesicular bodies carrying different molecules, classified according to their size, density, cargo, and origin. Research on this topic has been actively growing through the years, as EVs are associated with critical pathological processes such as neurodegenerative diseases and cancer. Despite that, studies exploring the physiological functions of EVs are sparse, with particular emphasis on their role in organismal development, initial cell differentiation, and morphogenesis. In this review, we explore the topic of EVs from a developmental perspective, discussing their role in the earliest cell-fate decisions and neural tissue morphogenesis. We focus on the function of EVs through development to highlight possible conserved or novel processes that can impact disease progression. Specifically, we take advantage of what was learned about their role in development so far to discuss EVs impact on glioblastoma, a particular brain tumor of stem-cell origin and poor prognosis, and how their function can be hijacked to improve current therapies.
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23
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Matsumoto S, Okamura E, Muto M, Ema M. Similarities and differences in placental development between humans and cynomolgus monkeys. Reprod Med Biol 2023; 22:e12522. [PMID: 37377753 PMCID: PMC10292683 DOI: 10.1002/rmb2.12522] [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: 05/10/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Background The placenta is an extraembryonic organ, which is essential to maintain a normal pregnancy. However, placental development in humans is poorly understood because of technical and ethical reasons. Methods We analyzed the anatomical localization of each trophoblastic subtype in the cynomolgus monkey placenta by immunohistochemistry in the early second trimester. Histological differences among the mouse, cynomolgus monkey, and human placenta were compared. The PubMed database was used to search for studies on placentation in rodents and primates. Main findings The anatomical structures and subtypes of the placenta in cynomolgus monkeys are highly similar to those in humans, with the exception of fewer interstitial extravillous trophoblasts in cynomolgus monkeys. Conclusion The cynomolgus monkey appears to be a good animal model to investigate human placentation.
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Affiliation(s)
- Shoma Matsumoto
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Eiichi Okamura
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Masanaga Muto
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
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24
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Cesare E, Urciuolo A, Stuart HT, Torchio E, Gesualdo A, Laterza C, Gagliano O, Martewicz S, Cui M, Manfredi A, Di Filippo L, Sabatelli P, Squarzoni S, Zorzan I, Betto RM, Martello G, Cacchiarelli D, Luni C, Elvassore N. 3D ECM-rich environment sustains the identity of naive human iPSCs. Cell Stem Cell 2022; 29:1703-1717.e7. [PMID: 36459970 DOI: 10.1016/j.stem.2022.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/07/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022]
Abstract
The establishment of in vitro naive human pluripotent stem cell cultures opened new perspectives for the study of early events in human development. The role of several transcription factors and signaling pathways have been characterized during maintenance of human naive pluripotency. However, little is known about the role exerted by the extracellular matrix (ECM) and its three-dimensional (3D) organization. Here, using an unbiased and integrated approach combining microfluidic cultures with transcriptional, proteomic, and secretome analyses, we found that naive, but not primed, hiPSC colonies are characterized by a self-organized ECM-rich microenvironment. Based on this, we developed a 3D culture system that supports robust long-term feeder-free self-renewal of naive hiPSCs and also allows direct and timely developmental morphogenesis simply by modulating the signaling environment. Our study opens new perspectives for future applications of naive hiPSCs to study critical stages of human development in 3D starting from a single cell.
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Affiliation(s)
- Elisa Cesare
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy; Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy
| | - Anna Urciuolo
- University College London Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; Institute of Pediatric Research IRP, Corso Stati Uniti, Padova 35127, Italy; Department of Molecular Medicine, University of Padova, Via G. Colombo 3, 35131 Padova, Italy
| | - Hannah T Stuart
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy; Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Erika Torchio
- Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy
| | - Alessia Gesualdo
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy
| | - Cecilia Laterza
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy; Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy
| | - Onelia Gagliano
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy; Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy
| | - Sebastian Martewicz
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Meihua Cui
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Anna Manfredi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy; Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Lucio Di Filippo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy; Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Patrizia Sabatelli
- CNR - Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" - Unit of Bologna, Bologna, Italy; IRCCS-Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Stefano Squarzoni
- CNR - Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" - Unit of Bologna, Bologna, Italy; IRCCS-Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Irene Zorzan
- Epigenetics Programme, Babraham Institute, CB22 3AT Cambridge, UK
| | - Riccardo M Betto
- Department of Molecular Medicine, University of Padova, Via G. Colombo 3, 35131 Padova, Italy
| | - Graziano Martello
- Department of Biology, University of Padova, Via G. Colombo 3, Padova 35131, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy; Department of Translational Medicine, University of Naples "Federico II", Naples, Italy; School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples "Federico II", Naples, Italy
| | - Camilla Luni
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China; Department of Civil, Chemical, Environmental, and Materials Engineering (DICAM), University of Bologna, Via Terracini 28, Bologna 40131, Italy
| | - Nicola Elvassore
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy; Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy; University College London Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK.
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25
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Moris N, Shahbazi M. Unravelling the mysteries of human embryogenesis. Semin Cell Dev Biol 2022; 131:1-3. [PMID: 35753909 DOI: 10.1016/j.semcdb.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Naomi Moris
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Marta Shahbazi
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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26
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Medina-Cano D, Corrigan EK, Glenn RA, Islam MT, Lin Y, Kim J, Cho H, Vierbuchen T. Rapid and robust directed differentiation of mouse epiblast stem cells into definitive endoderm and forebrain organoids. Development 2022; 149:dev200561. [PMID: 35899604 PMCID: PMC10655922 DOI: 10.1242/dev.200561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022]
Abstract
Directed differentiation of pluripotent stem cells (PSCs) is a powerful model system for deconstructing embryonic development. Although mice are the most advanced mammalian model system for genetic studies of embryonic development, state-of-the-art protocols for directed differentiation of mouse PSCs into defined lineages require additional steps and generates target cell types with lower purity than analogous protocols for human PSCs, limiting their application as models for mechanistic studies of development. Here, we examine the potential of mouse epiblast stem cells cultured in media containing Wnt pathway inhibitors as a starting point for directed differentiation. As a proof of concept, we focused our efforts on two specific cell/tissue types that have proven difficult to generate efficiently and reproducibly from mouse embryonic stem cells: definitive endoderm and neural organoids. We present new protocols for rapid generation of nearly pure definitive endoderm and forebrain-patterned neural organoids that model the development of prethalamic and hippocampal neurons. These differentiation models present new possibilities for combining mouse genetic tools with in vitro differentiation to characterize molecular and cellular mechanisms of embryonic development.
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Affiliation(s)
- Daniel Medina-Cano
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Emily K. Corrigan
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Rachel A. Glenn
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Cell and Developmental Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Mohammed T. Islam
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Yuan Lin
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Juliet Kim
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Hyunwoo Cho
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
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27
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Abstract
The complex process by which a single-celled zygote develops into a viable embryo is nothing short of a miraculous wonder of the natural world. Elucidating how this process is orchestrated in humans has long eluded the grasp of scientists due to ethical and practical limitations. Thankfully, pluripotent stem cells that resemble early developmental cell types possess the ability to mimic specific embryonic events. As such, murine and human stem cells have been leveraged by scientists to create in vitro models that aim to recapitulate different stages of early mammalian development. Here, we examine the wide variety of stem cell-based embryo models that have been developed to recapitulate and study embryonic events, from pre-implantation development through to early organogenesis. We discuss the applications of these models, key considerations regarding their importance within the field, and how such models are expected to grow and evolve to achieve exciting new milestones in the future.
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Affiliation(s)
- Aidan H. Terhune
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeyoon Bok
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shiyu Sun
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, 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 and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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28
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Pladevall-Morera D, Zylicz JJ. Chromatin as a sensor of metabolic changes during early development. Front Cell Dev Biol 2022; 10:1014498. [PMID: 36299478 PMCID: PMC9588933 DOI: 10.3389/fcell.2022.1014498] [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] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Cellular metabolism is a complex network of biochemical reactions fueling development with energy and biomass; however, it can also shape the cellular epigenome. Indeed, some intermediates of metabolic reactions exert a non-canonical function by acting as co-factors, substrates or inhibitors of chromatin modifying enzymes. Therefore, fluctuating availability of such molecules has the potential to regulate the epigenetic landscape. Thanks to this functional coupling, chromatin can act as a sensor of metabolic changes and thus impact cell fate. Growing evidence suggest that both metabolic and epigenetic reprogramming are crucial for ensuring a successful embryo development from the zygote until gastrulation. In this review, we provide an overview of the complex relationship between metabolism and epigenetics in regulating the early stages of mammalian embryo development. We report on recent breakthroughs in uncovering the non-canonical functions of metabolism especially when re-localized to the nucleus. In addition, we identify the challenges and outline future perspectives to advance the novel field of epi-metabolomics especially in the context of early development.
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Affiliation(s)
| | - Jan J. Zylicz
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
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29
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Zheng L, Liang P, Long C, Li H, Li H, Liang Y, He X, Xi Q, Xing Y, Zuo Y. EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis. Nucleic Acids Res 2022; 51:D924-D932. [PMID: 36189903 PMCID: PMC9825456 DOI: 10.1093/nar/gkac848] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/06/2022] [Accepted: 09/21/2022] [Indexed: 01/30/2023] Open
Abstract
The emerging importance of embryonic development research rapidly increases the volume for a professional resource related to multi-omics data. However, the lack of global embryogenesis repository and systematic analysis tools limits the preceding in stem cell research, human congenital diseases and assisted reproduction. Here, we developed the EmAtlas, which collects the most comprehensive multi-omics data and provides multi-scale tools to explore spatiotemporal activation during mammalian embryogenesis. EmAtlas contains data on multiple types of gene expression, chromatin accessibility, DNA methylation, nucleosome occupancy, histone modifications, and transcription factors, which displays the complete spatiotemporal landscape in mouse and human across several time points, involving gametogenesis, preimplantation, even fetus and neonate, and each tissue involves various cell types. To characterize signatures involved in the tissue, cell, genome, gene and protein levels during mammalian embryogenesis, analysis tools on these five scales were developed. Additionally, we proposed EmRanger to deliver extensive development-related biological background annotations. Users can utilize these tools to analyze, browse, visualize, and download data owing to the user-friendly interface. EmAtlas is freely accessible at http://bioinfor.imu.edu.cn/ematlas.
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Affiliation(s)
- Lei Zheng
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Pengfei Liang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Chunshen Long
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Haicheng Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Hanshuang Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yuchao Liang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Xiang He
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Qilemuge Xi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yongqiang Xing
- Correspondence may also be addressed to Yongqiang Xing. Tel: +86 472 5951944; Fax: +86 472 5951944;
| | - Yongchun Zuo
- To whom correspondence should be addressed. Tel: +86 471 5227683; Fax: +86 471 5227683;
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30
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Puscheck EE, Ruden X, Singh A, Abdulhasan M, Ruden DM, Awonuga AO, Rappolee DA. Using high throughput screens to predict miscarriages with placental stem cells and long-term stress effects with embryonic stem cells. Birth Defects Res 2022; 114:1014-1036. [PMID: 35979652 PMCID: PMC10108263 DOI: 10.1002/bdr2.2079] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022]
Abstract
A problem in developmental toxicology is the massive loss of life from fertilization through gastrulation, and the surprising lack of knowledge of causes of miscarriage. Half to two-thirds of embryos are lost, and environmental and genetic causes are nearly equal. Simply put, it can be inferred that this is a difficult period for normal embryos, but that environmental stresses may cause homeostatic responses that move from adaptive to maladaptive with increasing exposures. At the lower 50% estimate, miscarriage causes greater loss-of-life than all cancers combined or of all cardio- and cerebral-vascular accidents combined. Surprisingly, we do not know if miscarriage rates are increasing or decreasing. Overshadowed by the magnitude of miscarriages, are insufficient data on teratogenic or epigenetic imbalances in surviving embryos and their stem cells. Superimposed on the difficult normal trajectory for peri-gastrulation embryos are added malnutrition, hormonal, and environmental stresses. An overarching hypothesis is that high throughput screens (HTS) using cultured viable reporter embryonic and placental stem cells (e.g., embryonic stem cells [ESC] and trophoblast stem cells [TSC] that report status using fluorescent reporters in living cells) from the pre-gastrulation embryo will most rapidly test a range of hormonal, environmental, nutritional, drug, and diet supplement stresses that decrease stem cell proliferation and imbalance stemness/differentiation. A second hypothesis is that TSC respond with greater sensitivity in magnitude to stress that would cause miscarriage, but ESC are stress-resistant to irreversible stemness loss and are best used to predict long-term health defects. DevTox testing needs more ESC and TSC HTS to model environmental stresses leading to miscarriage or teratogenesis and more research on epidemiology of stress and miscarriage. This endeavor also requires a shift in emphasis on pre- and early gastrulation events during the difficult period of maximum loss by miscarriage.
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Affiliation(s)
- Elizabeth E Puscheck
- CS Mott Center for Human Growth and Development, Department of Ob/Gyn, Reproductive Endocrinology and Infertility, Wayne State University School of Medicine, Detroit, Michigan, USA
- Reproductive Stress 3M Inc, Grosse Pointe Farms, Michigan, USA
- Invia Fertility Clinics, Hoffman Estates, Illinois, USA
| | - Ximena Ruden
- CS Mott Center for Human Growth and Development, Department of Ob/Gyn, Reproductive Endocrinology and Infertility, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Aditi Singh
- CS Mott Center for Human Growth and Development, Department of Ob/Gyn, Reproductive Endocrinology and Infertility, Wayne State University School of Medicine, Detroit, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Mohammed Abdulhasan
- CS Mott Center for Human Growth and Development, Department of Ob/Gyn, Reproductive Endocrinology and Infertility, Wayne State University School of Medicine, Detroit, Michigan, USA
- Reproductive Stress 3M Inc, Grosse Pointe Farms, Michigan, USA
| | - Douglas M Ruden
- CS Mott Center for Human Growth and Development, Department of Ob/Gyn, Reproductive Endocrinology and Infertility, Wayne State University School of Medicine, Detroit, Michigan, USA
- Invia Fertility Clinics, Hoffman Estates, Illinois, USA
- Institute for Environmental Health Science, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Awoniyi O Awonuga
- CS Mott Center for Human Growth and Development, Department of Ob/Gyn, Reproductive Endocrinology and Infertility, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Daniel A Rappolee
- CS Mott Center for Human Growth and Development, Department of Ob/Gyn, Reproductive Endocrinology and Infertility, Wayne State University School of Medicine, Detroit, Michigan, USA
- Reproductive Stress 3M Inc, Grosse Pointe Farms, Michigan, USA
- Invia Fertility Clinics, Hoffman Estates, Illinois, USA
- Institute for Environmental Health Science, Wayne State University School of Medicine, Detroit, Michigan, USA
- Program for Reproductive Sciences and Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Biology, University of Windsor, Windsor, Ontario, Canada
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31
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Zheng Y, Yan RZ, Sun S, Kobayashi M, Xiang L, Yang R, Goedel A, Kang Y, Xue X, Esfahani SN, Liu Y, Resto Irizarry AM, Wu W, Li Y, Ji W, Niu Y, Chien KR, Li T, Shioda T, Fu J. Single-cell analysis of embryoids reveals lineage diversification roadmaps of early human development. Cell Stem Cell 2022; 29:1402-1419.e8. [PMID: 36055194 PMCID: PMC9499422 DOI: 10.1016/j.stem.2022.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 06/08/2022] [Accepted: 08/11/2022] [Indexed: 01/03/2023]
Abstract
Despite its clinical and fundamental importance, our understanding of early human development remains limited. Stem cell-derived, embryo-like structures (or embryoids) allowing studies of early development without using natural embryos can potentially help fill the knowledge gap of human development. Herein, transcriptome at the single-cell level of a human embryoid model was profiled at different time points. Molecular maps of lineage diversifications from the pluripotent human epiblast toward the amniotic ectoderm, primitive streak/mesoderm, and primordial germ cells were constructed and compared with in vivo primate data. The comparative transcriptome analyses reveal a critical role of NODAL signaling in human mesoderm and primordial germ cell specification, which is further functionally validated. Through comparative transcriptome analyses and validations with human blastocysts and in vitro cultured cynomolgus embryos, we further proposed stringent criteria for distinguishing between human blastocyst trophectoderm and early amniotic ectoderm cells.
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Affiliation(s)
- Yi Zheng
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Robin Zhexuan Yan
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shiyu Sun
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mutsumi Kobayashi
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA
| | - Lifeng Xiang
- Department of Reproductive Medicine, the First People's Hospital of Yunnan Province, Kunming, China
| | - Ran Yang
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Alexander Goedel
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Yu Kang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Xufeng Xue
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sajedeh Nasr Esfahani
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yue Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Weisheng Wu
- BRCF Bioinformatics Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yunxiu Li
- Department of Reproductive Medicine, the First People's Hospital of Yunnan Province, Kunming, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Kenneth R Chien
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Tianqing Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Toshihiro Shioda
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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32
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Wang X, Wu Q. The Divergent Pluripotent States in Mouse and Human Cells. Genes (Basel) 2022; 13:genes13081459. [PMID: 36011370 PMCID: PMC9408542 DOI: 10.3390/genes13081459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022] Open
Abstract
Pluripotent stem cells (PSCs), which can self-renew and give rise to all cell types in all three germ layers, have great potential in regenerative medicine. Recent studies have shown that PSCs can have three distinct but interrelated pluripotent states: naive, formative, and primed. The PSCs of each state are derived from different stages of the early developing embryo and can be maintained in culture by different molecular mechanisms. In this review, we summarize the current understanding on features of the three pluripotent states and review the underlying molecular mechanisms of maintaining their identities. Lastly, we discuss the interrelation and transition among these pluripotency states. We believe that comprehending the divergence of pluripotent states is essential to fully harness the great potential of stem cells in regenerative medicine.
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Affiliation(s)
| | - Qiang Wu
- Correspondence: ; Tel.: +853-8897-2708
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33
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Epigenetics as "conductor" in "orchestra" of pluripotent states. Cell Tissue Res 2022; 390:141-172. [PMID: 35838826 DOI: 10.1007/s00441-022-03667-0] [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: 12/30/2021] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
Pluripotent character is described as the potency of cells to differentiate into all three germ layers. The best example to reinstate the term lies in the context of embryonic stem cells (ESCs). Pluripotent ESC describes the in vitro status of those cells that originate during the complex process of embryogenesis. Pre-implantation to post-implantation development of embryo embrace cells with different levels of stemness. Currently, four states of pluripotency have been recognized, in the progressing order of "naïve," "poised," "formative," and "primed." Epigenetics act as the "conductor" in this "orchestra" of transition in pluripotent states. With a distinguishable gene expression profile, these four states associate with different epigenetic signatures, sometimes distinct while otherwise overlapping. The present review focuses on how epigenetic factors, including DNA methylation, bivalent chromatin, chromatin remodelers, chromatin/nuclear architecture, and microRNA, could dictate pluripotent states and their transition among themselves.
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34
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Palacios Martínez S, Greaney J, Zenker J. Beyond the centrosome: The mystery of microtubule organising centres across mammalian preimplantation embryos. Curr Opin Cell Biol 2022; 77:102114. [PMID: 35841745 DOI: 10.1016/j.ceb.2022.102114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/25/2022] [Accepted: 06/11/2022] [Indexed: 11/18/2022]
Abstract
Mammalian preimplantation embryogenesis depends on the spatio-temporal dynamics of the microtubule cytoskeleton to enable exceptionally fast changes in cell number, function, architecture, and fate. Microtubule organising centres (MTOCs), which coordinate the remodelling of microtubules, are therefore of fundamental significance during the first days of a new life. Despite its indispensable role during early mammalian embryogenesis, the origin of microtubule growth remains poorly understood. In this review, we summarise the most recent discoveries on microtubule organisation and function during early human embryogenesis and compare these to innovative studies conducted in alternative mammalian models. We emphasise the differences and analogies of centriole inheritance and their role during the first cleavage. Furthermore, we highlight the significance of non-centrosomal MTOCs for embryo viability and discuss the potential of novel in vitro models and light-inducible approaches towards unravelling microtubule formation in research and assisted reproductive technologies.
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Affiliation(s)
| | - Jessica Greaney
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Jennifer Zenker
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.
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35
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Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model. Cell Rep 2022; 39:110973. [PMID: 35732132 DOI: 10.1016/j.celrep.2022.110973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 03/21/2022] [Accepted: 05/24/2022] [Indexed: 11/20/2022] Open
Abstract
Human primed embryonic stem cells (ESCs) are known to be converted to cells with several trophoblast properties, but it has remained controversial whether this phenomenon represents the inherent differentiation competence of human primed ESCs to trophoblast lineages. In this study, we report that chemical blockage of ACTIVIN/NODAL and FGF signals is sufficient to steer human primed ESCs into GATA3-expressing cells that give rise to placental hormone-producing syncytia analogous to syncytiotrophoblasts of the post-implantation stage of the human embryo. Despite their cytological similarity to syncytiotrophoblasts, these syncytia arise from the non-trophoblastic differentiation trajectory that recapitulates amniogenesis. These results provide insights into the possible extraembryonic differentiation pathway that is unique in primate embryogenesis.
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36
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Soncin F, Morey R, Bui T, Requena DF, Cheung VC, Kallol S, Kittle R, Jackson MG, Farah O, Chousal J, Meads M, Pizzo D, Horii M, Fisch KM, Parast MM. Derivation of functional trophoblast stem cells from primed human pluripotent stem cells. Stem Cell Reports 2022; 17:1303-1317. [PMID: 35594858 PMCID: PMC9214048 DOI: 10.1016/j.stemcr.2022.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/25/2022] Open
Abstract
Trophoblast stem cells (TSCs) have recently been derived from human embryos and early-first-trimester placenta; however, aside from ethical challenges, the unknown disease potential of these cells limits their scientific utility. We have previously established a bone morphogetic protein 4 (BMP4)-based two-step protocol for differentiation of primed human pluripotent stem cells (hPSCs) into functional trophoblasts; however, those trophoblasts could not be maintained in a self-renewing TSC-like state. Here, we use the first step from this protocol, followed by a switch to newly developed TSC medium, to derive bona fide TSCs. We show that these cells resemble placenta- and naive hPSC-derived TSCs, based on their transcriptome as well as their in vitro and in vivo differentiation potential. We conclude that primed hPSCs can be used to generate functional TSCs through a simple protocol, which can be applied to a widely available set of existing hPSCs, including induced pluripotent stem cells, derived from patients with known birth outcomes.
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Affiliation(s)
- Francesca Soncin
- 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
| | - Robert Morey
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, 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
| | - Daniela F 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
| | - 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; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sampada Kallol
- 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
| | - Ryan Kittle
- 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
| | - 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
| | - Omar Farah
- 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
| | - Jennifer Chousal
- 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
| | - Morgan Meads
- 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
| | - Donald Pizzo
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Mariko Horii
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Mana M Parast
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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37
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Zhang C, Wen H, Liu S, Fu E, Yu L, Chen S, Han Q, Li Z, Liu N. Maternal Factor Dppa3 Activates 2C-Like Genes and Depresses DNA Methylation in Mouse Embryonic Stem Cells. Front Cell Dev Biol 2022; 10:882671. [PMID: 35721479 PMCID: PMC9203971 DOI: 10.3389/fcell.2022.882671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Mouse embryonic stem cells (ESCs) contain a rare cell population of “two-cell embryonic like” cells (2CLCs) that display similar features to those found in the two-cell (2C) embryo and thus represent an in vitro model for studying the progress of zygotic genome activation (ZGA). However, the positive regulator determinants of the 2CLCs’ conversion and ZGA have not been completely elucidated. Here, we identify a new regulator promoting 2CLCs and ZGA transcripts. Through a combination of overexpression (OE), knockdown (KD), together with transcriptional analysis and methylome analysis, we find that Dppa3 regulates the 2CLC-associated transcripts, DNA methylation, and 2CLC population in ESCs. The differentially methylated regions (DMRs) analysis identified 6,920 (98.2%) hypomethylated, whilst only 129 (1.8%) hypermethylated, regions in Dppa3 OE ESCs, suggesting that Dppa3 facilitates 2CLCs reprogramming. The conversion to 2CLCs by overexpression of Dppa3 is also associated with DNA damage response. Dppa3 knockdown manifest impairs transition into the 2C-like state. Global DNA methylome and chromatin state analysis of Dppa3 OE ESCs reveal that Dppa3 facilitates the chromatin configuration to 2CLCs reversion. Our finding for the first time elucidates a novel role of Dppa3 in mediating the 2CLC conversion, and suggests that Dppa3 is a new regulator for ZGA progress.
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Affiliation(s)
- Chuanyu Zhang
- School of Medicine, Nankai University, Tianjin, China
| | - Hang Wen
- School of Medicine, Nankai University, Tianjin, China
| | - Siying Liu
- School of Medicine, Nankai University, Tianjin, China
| | - Enze Fu
- School of Medicine, Nankai University, Tianjin, China
| | - Lu Yu
- School of Medicine, Nankai University, Tianjin, China
| | - Shang Chen
- School of Medicine, Nankai University, Tianjin, China
| | - Qingsheng Han
- School of Medicine, Nankai University, Tianjin, China
| | - Zongjin Li
- School of Medicine, Nankai University, Tianjin, China
- Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences Nankai University, Tianjin, China
- *Correspondence: Zongjin Li, ; Na Liu,
| | - Na Liu
- School of Medicine, Nankai University, Tianjin, China
- Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences Nankai University, Tianjin, China
- *Correspondence: Zongjin Li, ; Na Liu,
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38
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Kobayashi N, Okae H, Hiura H, Kubota N, Kobayashi EH, Shibata S, Oike A, Hori T, Kikutake C, Hamada H, Kaji H, Suyama M, Bortolin-Cavaillé ML, Cavaillé J, Arima T. The microRNA cluster C19MC confers differentiation potential into trophoblast lineages upon human pluripotent stem cells. Nat Commun 2022; 13:3071. [PMID: 35654791 PMCID: PMC9163035 DOI: 10.1038/s41467-022-30775-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 05/13/2022] [Indexed: 02/08/2023] Open
Abstract
The first cell fate commitment during mammalian development is the specification of the inner cell mass and trophectoderm. This irreversible cell fate commitment should be epigenetically regulated, but the precise mechanism is largely unknown in humans. Here, we show that naïve human embryonic stem (hES) cells can transdifferentiate into trophoblast stem (hTS) cells, but primed hES cells cannot. Our transcriptome and methylome analyses reveal that a primate-specific miRNA cluster on chromosome 19 (C19MC) is active in naïve hES cells but epigenetically silenced in primed ones. Moreover, genome and epigenome editing using CRISPR/Cas systems demonstrate that C19MC is essential for hTS cell maintenance and C19MC-reactivated primed hES cells can give rise to hTS cells. Thus, we reveal that C19MC activation confers differentiation potential into trophoblast lineages on hES cells. Our findings are fundamental to understanding the epigenetic regulation of human early development and pluripotency. Little is known about the epigenetic mechanisms of the first cell fate commitment in humans. Here, the authors show that activation of the miRNA cluster C19MC confers differentiation potential into trophoblast lineages on human embryonic stem cells.
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Affiliation(s)
- Norio Kobayashi
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan.
| | - Hitoshi Hiura
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Naoto Kubota
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Eri H Kobayashi
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Shun Shibata
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Akira Oike
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Takeshi Hori
- Department of Biomechanics, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, 101-0062, Japan
| | - Chie Kikutake
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hirotaka Hamada
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Hirokazu Kaji
- Department of Biomechanics, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, 101-0062, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Marie-Line Bortolin-Cavaillé
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Jérôme Cavaillé
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan.
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39
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Ai Z, Yin Y, Niu B, Li T. Deconstructing human peri-implantation embryogenesis based on embryos and embryoids. Biol Reprod 2022; 107:212-225. [PMID: 35552636 DOI: 10.1093/biolre/ioac096] [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: 12/31/2021] [Revised: 04/11/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022] Open
Abstract
The peri-implantation period from blastula to gastrula is one of the crucial stages of human embryo and stem cell development. During development, human embryos undergo many crucial events, such as embryonic lineage differentiation and development, structural self-assembly, pluripotency state transition, cell communication between lineages, and crosstalk between the embryo and uterus. Abnormalities in these developmental events will result in implantation failure or pregnancy loss. However, because of ethical and technical limits, the developmental dynamics of human peri-implantation embryos and the underlying mechanisms of abnormal development remain in a "black box". In this review, we summarize recent progress made towards our understanding of human peri-implantation embryogenesis based on extended in vitro cultured embryos and stem cell-based embryoids. These findings lay an important foundation for understanding early life, promoting research into human stem cells and their application, and preventing and treating infertility. We also propose key scientific issues regarding peri-implantation embryogenesis and provide an outlook on future study directions. Finally, we sum up China's contribution to the field and future opportunities.
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Affiliation(s)
- Zongyong Ai
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.,Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
| | - Yu Yin
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.,Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
| | - Baohua Niu
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.,Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
| | - Tianqing Li
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.,Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan, 650500, China
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40
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Quan Y, Wang M, Xu C, Wang X, Wu Y, Qin D, Lin Y, Lu X, Lu F, Li L. Cnot8 eliminates naïve regulation networks and is essential for naïve-to-formative pluripotency transition. Nucleic Acids Res 2022; 50:4414-4435. [PMID: 35390160 PMCID: PMC9071485 DOI: 10.1093/nar/gkac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 03/11/2022] [Accepted: 03/26/2022] [Indexed: 11/14/2022] Open
Abstract
Mammalian early epiblasts at different phases are characterized by naïve, formative, and primed pluripotency states, involving extensive transcriptome changes. Here, we report that deadenylase Cnot8 of Ccr4-Not complex plays essential roles during the transition from naïve to formative state. Knock out (KO) Cnot8 resulted in early embryonic lethality in mice, but Cnot8 KO embryonic stem cells (ESCs) could be established. Compared with the cells differentiated from normal ESCs, Cnot8 KO cells highly expressed a great many genes during their differentiation into the formative state, including several hundred naïve-like genes enriched in lipid metabolic process and gene expression regulation that may form the naïve regulation networks. Knockdown expression of the selected genes of naïve regulation networks partially rescued the differentiation defects of Cnot8 KO ESCs. Cnot8 depletion led to the deadenylation defects of its targets, increasing their poly(A) tail lengths and half-life, eventually elevating their expression levels. We further found that Cnot8 was involved in the clearance of targets through its deadenylase activity and the binding of Ccr4-Not complex, as well as the interacting with Tob1 and Pabpc1. Our results suggest that Cnot8 eliminates naïve regulation networks through mRNA clearance, and is essential for naïve-to-formative pluripotency transition.
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Affiliation(s)
- Yujun Quan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meijiao Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengpeng Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dandan Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuxuan Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xukun Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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41
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Cloutier M, Kumar S, Buttigieg E, Keller L, Lee B, Williams A, Mojica-Perez S, Erliandri I, Rocha AMD, Cadigan K, Smith GD, Kalantry S. Preventing erosion of X-chromosome inactivation in human embryonic stem cells. Nat Commun 2022; 13:2516. [PMID: 35523820 PMCID: PMC9076865 DOI: 10.1038/s41467-022-30259-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/11/2022] [Indexed: 12/12/2022] Open
Abstract
X-chromosome inactivation is a paradigm of epigenetic transcriptional regulation. Female human embryonic stem cells (hESCs) often undergo erosion of X-inactivation upon prolonged culture. Here, we investigate the sources of X-inactivation instability by deriving new primed pluripotent hESC lines. We find that culture media composition dramatically influenced the expression of XIST lncRNA, a key regulator of X-inactivation. hESCs cultured in a defined xenofree medium stably maintained XIST RNA expression and coating, whereas hESCs cultured in the widely used mTeSR1 medium lost XIST RNA expression. We pinpointed lithium chloride in mTeSR1 as a cause of XIST RNA loss. The addition of lithium chloride or inhibitors of GSK-3 proteins that are targeted by lithium to the defined hESC culture medium impeded XIST RNA expression. GSK-3 inhibition in differentiating female mouse embryonic stem cells and epiblast stem cells also resulted in a loss of XIST RNA expression. Together, these data may reconcile observed variations in X-inactivation in hESCs and inform the faithful culture of pluripotent stem cells.
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Affiliation(s)
- Marissa Cloutier
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Surinder Kumar
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Emily Buttigieg
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Laura Keller
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Brandon Lee
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Aaron Williams
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sandra Mojica-Perez
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Indri Erliandri
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Andre Monteiro Da Rocha
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine & Cardiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kenneth Cadigan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Gary D Smith
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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42
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Abstract
Embryoids and organoids hold great promise for human biology and medicine. Herein, we discuss conceptual and technological frameworks useful for developing high-fidelity embryoids and organoids that display tissue- and organ-level phenotypes and functions, which are critically needed for decoding developmental programs and improving translational applications. Through dissecting the layers of inputs controlling mammalian embryogenesis, we review recent progress in reconstructing multiscale structural orders in embryoids and organoids. Bioengineering tools useful for multiscale, multimodal structural engineering of tissue- and organ-level cellular organization and microenvironment are also discussed to present integrative, bioengineering-directed approaches to achieve next-generation, high-fidelity embryoids and organoids.
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Affiliation(s)
- Yue Shao
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China; State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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43
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Collier AJ, Bendall A, Fabian C, Malcolm AA, Tilgner K, Semprich CI, Wojdyla K, Nisi PS, Kishore K, Roamio Franklin VN, Mirshekar-Syahkal B, D’Santos C, Plath K, Yusa K, Rugg-Gunn PJ. Genome-wide screening identifies Polycomb repressive complex 1.3 as an essential regulator of human naïve pluripotent cell reprogramming. SCIENCE ADVANCES 2022; 8:eabk0013. [PMID: 35333572 PMCID: PMC8956265 DOI: 10.1126/sciadv.abk0013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Uncovering the mechanisms that establish naïve pluripotency in humans is crucial for the future applications of pluripotent stem cells including the production of human blastoids. However, the regulatory pathways that control the establishment of naïve pluripotency by reprogramming are largely unknown. Here, we use genome-wide screening to identify essential regulators as well as major impediments of human primed to naïve pluripotent stem cell reprogramming. We discover that factors essential for cell state change do not typically undergo changes at the level of gene expression but rather are repurposed with new functions. Mechanistically, we establish that the variant Polycomb complex PRC1.3 and PRDM14 jointly repress developmental and gene regulatory factors to ensure naïve cell reprogramming. In addition, small-molecule inhibitors of reprogramming impediments improve naïve cell reprogramming beyond current methods. Collectively, this work defines the principles controlling the establishment of human naïve pluripotency and also provides new insights into mechanisms that destabilize and reconfigure cell identity during cell state transitions.
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Affiliation(s)
- Amanda J. Collier
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Adam Bendall
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | | | - Andrew A. Malcolm
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Katarzyna Tilgner
- Stem Cell Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | | | - Kamal Kishore
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | - Clive D’Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Kosuke Yusa
- Stem Cell Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Stem Cell Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Peter J. Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
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44
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Luijkx D, Shankar V, van Blitterswijk C, Giselbrecht S, Vrij E. From Mice to Men: Generation of Human Blastocyst-Like Structures In Vitro. Front Cell Dev Biol 2022; 10:838356. [PMID: 35359453 PMCID: PMC8963787 DOI: 10.3389/fcell.2022.838356] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/26/2022] [Indexed: 01/04/2023] Open
Abstract
Advances in the field of stem cell-based models have in recent years lead to the development of blastocyst-like structures termed blastoids. Blastoids can be used to study key events in mammalian pre-implantation development, as they mimic the blastocyst morphologically and transcriptionally, can progress to the post-implantation stage and can be generated in large numbers. Blastoids were originally developed using mouse pluripotent stem cells, and since several groups have successfully generated blastocyst models of the human system. Here we provide a comparison of the mouse and human protocols with the aim of deriving the core requirements for blastoid formation, discuss the models’ current ability to mimic blastocysts and give an outlook on potential future applications.
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Affiliation(s)
| | | | | | | | - Erik Vrij
- *Correspondence: Erik Vrij, ; Stefan Giselbrecht,
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45
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Ozturk H, Saribal D, Gelmez YM, Deniz G, Yilmaz A, Kirectepe A, Ercan AM. Extremely low frequency electromagnetic fields exposure during the prenatal and postnatal periods alters pro-inflammatory cytokines levels by gender. Electromagn Biol Med 2022; 41:163-173. [PMID: 35232334 DOI: 10.1080/15368378.2022.2046045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Maternal exposure to the excessive electromagnetic fields is considered harmful to infants and associated with several health problems in life, such as neurological or immune diseases. In this present study we aimed to investigate the potential effects of extremely low-frequency electromagnetic field (ELF-EMF) exposure during the gestational and lactational period of dams on immune system parameters. The development of white blood cells (WBC), lymphocyte subpopulations (CD4+ T cells, CD8+ T cells, Natural Killer (NK) cells, and B cells) and production of T cell related cytokines were explored in the offsprings. Significant changes were found in WBC and lymphocyte counts. Although no changes in lymphocyte subunits were observed among groups, CD4+ cells were significantly increased in the female group exposed to ELF-EMF. Also, IL-17A and IFN-γ levels increased in plasma and spleen. The mean IL-4 level and the expression level of the IL-4 gene were not changed, in the experimental groups. But the expression of the IL-17A gene was also upregulated, which supports cytokine quantification analyses. In conclusion, ELF-EMF exposure in the prenatal and postnatal period increases the level of IL-17A in the spleen and blood of young female rats, and it upregulates IL-17 gene expression in the spleen, resulting in CD4+ cell proliferation and inflammation.
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Affiliation(s)
- Hilal Ozturk
- Faculty of Medicine, Department of Biophysics, Karadeniz Technical Unicersity, Trabzon, Turkey.,Faculty of Medicine, Department of Biophysics, Istanbul University/Cerrahpaşa, İstanbul, Turkey
| | - Devrim Saribal
- Faculty of Medicine, Department of Biophysics, Istanbul University/Cerrahpaşa, İstanbul, Turkey
| | - Yusuf Metin Gelmez
- Faculty of Medicine, Department of Immunology, Istanbul University, İstanbul, Turkey
| | - Gunnur Deniz
- Faculty of Medicine, Department of Immunology, Istanbul University, İstanbul, Turkey
| | - Abdullah Yilmaz
- Faculty of Medicine, Department of Immunology, Istanbul University, İstanbul, Turkey
| | - Asli Kirectepe
- Faculty of Medicine, Department of Medical Biology, Nisantasi University, İstanbul, Turkey
| | - Alev Meltem Ercan
- Faculty of Medicine, Department of Biophysics, Istanbul University/Cerrahpaşa, İstanbul, Turkey
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46
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Effects of fibrin matrix and Ishikawa cells on in vitro 3D uterine tissue cultures on a rat model: A controlled study. JOURNAL OF SURGERY AND MEDICINE 2022. [DOI: 10.28982/josam.1054556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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47
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Carter T, Singh M, Dumbovic G, Chobirko JD, Rinn JL, Feschotte C. Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo. eLife 2022; 11:76257. [PMID: 35179489 PMCID: PMC8912925 DOI: 10.7554/elife.76257] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/17/2022] [Indexed: 12/05/2022] Open
Abstract
The human endogenous retrovirus type-H (HERVH) family is expressed in the preimplantation embryo. A subset of these elements are specifically transcribed in pluripotent stem cells where they appear to exert regulatory activities promoting self-renewal and pluripotency. How HERVH elements achieve such transcriptional specificity remains poorly understood. To uncover the sequence features underlying HERVH transcriptional activity, we performed a phyloregulatory analysis of the long terminal repeats (LTR7) of the HERVH family, which harbor its promoter, using a wealth of regulatory genomics data. We found that the family includes at least eight previously unrecognized subfamilies that have been active at different timepoints in primate evolution and display distinct expression patterns during human embryonic development. Notably, nearly all HERVH elements transcribed in ESCs belong to one of the youngest subfamilies we dubbed LTR7up. LTR7 sequence evolution was driven by a mixture of mutational processes, including point mutations, duplications, and multiple recombination events between subfamilies, that led to transcription factor binding motif modules characteristic of each subfamily. Using a reporter assay, we show that one such motif, a predicted SOX2/3 binding site unique to LTR7up, is essential for robust promoter activity in induced pluripotent stem cells. Together these findings illuminate the mechanisms by which HERVH diversified its expression pattern during evolution to colonize distinct cellular niches within the human embryo.
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Affiliation(s)
- Thomas Carter
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States [US]
| | - Manvendra Singh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Gabrijela Dumbovic
- Department of Biochemistry, University of Colorado Boulder, Boulder, United States
| | - Jason D Chobirko
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, United States
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
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48
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Cerrizuela S, Vega-Lopez GA, Méndez-Maldonado K, Velasco I, Aybar MJ. The crucial role of model systems in understanding the complexity of cell signaling in human neurocristopathies. WIREs Mech Dis 2022; 14:e1537. [PMID: 35023327 DOI: 10.1002/wsbm.1537] [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: 03/30/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 11/07/2022]
Abstract
Animal models are useful to study the molecular, cellular, and morphogenetic mechanisms underlying normal and pathological development. Cell-based study models have emerged as an alternative approach to study many aspects of human embryonic development and disease. The neural crest (NC) is a transient, multipotent, and migratory embryonic cell population that generates a diverse group of cell types that arises during vertebrate development. The abnormal formation or development of the NC results in neurocristopathies (NCPs), which are characterized by a broad spectrum of functional and morphological alterations. The impaired molecular mechanisms that give rise to these multiphenotypic diseases are not entirely clear yet. This fact, added to the high incidence of these disorders in the newborn population, has led to the development of systematic approaches for their understanding. In this article, we have systematically reviewed the ways in which experimentation with different animal and cell model systems has improved our knowledge of NCPs, and how these advances might contribute to the development of better diagnostic and therapeutic tools for the treatment of these pathologies. This article is categorized under: Congenital Diseases > Genetics/Genomics/Epigenetics Congenital Diseases > Stem Cells and Development Congenital Diseases > Molecular and Cellular Physiology Neurological Diseases > Genetics/Genomics/Epigenetics.
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Affiliation(s)
- Santiago Cerrizuela
- Division of Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina
| | - Guillermo A Vega-Lopez
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina.,Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Karla Méndez-Maldonado
- Instituto de Fisiología Celular - Neurociencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Departamento de Fisiología y Farmacología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Iván Velasco
- Instituto de Fisiología Celular - Neurociencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Laboratorio de Reprogramación Celular del Instituto de Fisiología Celular, UNAM en el Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Ciudad de México, Mexico
| | - Manuel J Aybar
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina.,Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
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49
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Rossant J, Tam PP. Early human embryonic development: Blastocyst formation to gastrulation. Dev Cell 2022; 57:152-165. [DOI: 10.1016/j.devcel.2021.12.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/29/2021] [Accepted: 12/22/2021] [Indexed: 12/13/2022]
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50
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Abstract
Human pluripotent stem cells exist in naïve and primed states that recapitulate the distinct molecular and cellular properties of pre- and post-implantation epiblast cells, respectively. Naïve pluripotent stem cells can be captured directly from blastocysts but, more commonly, the cells are reprogrammed from primed cells in a process called "resetting". Several methods to achieve resetting have been described. Chemical resetting of primed cells to a naïve pluripotent state is one such method and has come to the forefront as a simple, efficient, and transgene-free method to induce naïve pluripotency. The process involves the transient application of a histone deacetylase inhibitor to initiate resetting, followed by the emergence of nascent naïve pluripotent stem cells in supportive conditions, and finally the stabilization and expansion of naïve pluripotent stem cell cultures. Here, a detailed protocol is provided for chemical resetting starting from plating primed cells until a stable culture of naïve pluripotent stem cells is established.
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