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Wang S, Leng L, Wang Q, Gu Y, Li J, An Y, Deng Q, Xie P, Cheng C, Chen X, Zhou Q, Lu J, Chen F, Liu L, Yang H, Wang J, Xu X, Hou Y, Gong F, Hu L, Lu G, Shang Z, Lin G. A single-cell transcriptome atlas of human euploid and aneuploid blastocysts. Nat Genet 2024; 56:1468-1481. [PMID: 38839885 DOI: 10.1038/s41588-024-01788-6] [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: 03/24/2023] [Accepted: 05/06/2024] [Indexed: 06/07/2024]
Abstract
Aneuploidy is frequently detected in early human embryos as a major cause of early pregnancy failure. However, how aneuploidy affects cellular function remains elusive. Here, we profiled the transcriptomes of 14,908 single cells from 203 human euploid and aneuploid blastocysts involving autosomal and sex chromosomes. Nearly all of the blastocysts contained four lineages. In aneuploid chromosomes, 19.5% ± 1.2% of the expressed genes showed a dosage effect, and 90 dosage-sensitive domains were identified. Aneuploidy leads to prevalent genome-wide transcriptome alterations. Common effects, including apoptosis, were identified, especially in monosomies, partially explaining the lower cell numbers in autosomal monosomies. We further identified lineage-specific effects causing unstable epiblast development in aneuploidies, which was accompanied by the downregulation of TGF-β and FGF signaling, which resulted in insufficient trophectoderm maturation. Our work provides crucial insights into the molecular basis of human aneuploid blastocysts and may shed light on the cellular interaction during blastocyst development.
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Affiliation(s)
- Shengpeng Wang
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lizhi Leng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | | | - Yifan Gu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | | | | | - Qiuting Deng
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Pingyuan Xie
- Hunan Normal University School of Medicine, Changsha, China
- National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Can Cheng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
| | - Xueqin Chen
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
| | - Qinwei Zhou
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | - Jia Lu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
| | - Fang Chen
- BGI Research, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, BGI Research, Shenzhen, China
| | - Longqi Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huanming Yang
- BGI Research, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Jian Wang
- BGI Research, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Xun Xu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Yong Hou
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fei Gong
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | - Guangxiu Lu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
- National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Zhouchun Shang
- BGI Research, Shenzhen, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China.
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China.
- National Engineering and Research Center of Human Stem Cell, Changsha, China.
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Vendrell X, de Castro P, Escrich L, Grau N, Gonzalez-Martin R, Quiñonero A, Escribá MJ, Domínguez F. Longitudinal profiling of human androgenotes through single-cell analysis unveils paternal gene expression dynamics in early embryo development. Hum Reprod 2024; 39:1186-1196. [PMID: 38622061 PMCID: PMC11145015 DOI: 10.1093/humrep/deae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/12/2024] [Indexed: 04/17/2024] Open
Abstract
STUDY QUESTION How do transcriptomics vary in haploid human androgenote embryos at single cell level in the first four cell cycles of embryo development? SUMMARY ANSWER Gene expression peaks at the fourth cell cycle, however some androcytes exhibit unique transcriptional behaviors. WHAT IS KNOWN ALREADY The developmental potential of an embryo is determined by the competence of the oocyte and the sperm. However, studies of the contribution of the paternal genome using pure haploid androgenotes are very scarce. STUDY DESIGN, SIZE, DURATION This study was performed analyzing the single-cell transcriptomic sequencing of 38 androcytes obtained from 10 androgenote bioconstructs previously produced in vitro (de Castro et al., 2023). These results were analyzed through different bioinformatics software such as g: Profiler, GSEA, Cytoscape, and Reactome. PARTICIPANTS/MATERIALS, SETTING, METHODS Single cell sequencing was used to obtain the transcriptomic profiles of the different androcytes. The results obtained were compared between the different cycles studied using the DESeq2 program and functional enrichment pathways using g: Profiler, Cytoscape, and Reactome. MAIN RESULTS AND THE ROLE OF CHANCE A wave of paternally driven transcriptomic activation was found during the third-cell cycle, with 1128 upregulated and 225 downregulated genes and the fourth-cell cycle, with 1373 upregulated and 286 downregulated genes, compared to first-cell cycle androcytes. Differentially expressed routes related to cell differentiation, DNA-binding transcription, RNA biosynthesis and RNA polymerase II transcription regulatory complex, and cell death were found in the third and fourth with respect to the first-cell cycle. Conversely, in the fourth cell cycle, 153 downregulated and 332 upregulated genes were found compared with third cell cycle, associated with differentially expressed processes related to E-box binding and zinc finger protein 652 (ZNF652) transcription factor. Further, significant overexpression of LEUTX, PRAMEF1, DUXA, RFPL4A, TRIM43, and ZNF675 found in androgenotes, compared to biparental embryos, highlights the paternal contributions to zygote genome activation. LARGE SCALE DATA All raw sequencing data are available through the Gene Expression Omnibus (GEO) under accessions number: GSE216501. LIMITATIONS, REASONS FOR CAUTION Extrapolation of biological events from uniparental constructs to biparental embryos should be done with caution. Maternal and paternal genomes do not act independently of each other in a natural condition. The absence of one genome may affect gene transcription of the other. In this sense, the haploid condition of the bioconstructs could mask the transcriptomic patterns of the single cells. WIDER IMPLICATIONS OF THE FINDINGS The results obtained demonstrated the level of involvement of the human paternal haploid genome in the early stages of embryo development as well as its evolution at the transcriptomic level, laying the groundwork for the use of these bioconstructs as reliable models to dispel doubts about the genetic role played by the paternal genome in the early cycles of embryo development. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by Instituto de Salud Carlos III (ISCIII) through the project 'PI22/00924', co-funded by European Regional Development Fund (ERDF); 'A way to make Europe'. F.D. was supported by the Spanish Ministry of Economy and Competitiveness through the Miguel Servet program (CPII018/00002). M.J.E. was supported by Instituto de Salud Carlos III (PI19/00577 [M.J.E.]) and FI20/00086. P.dC. was supported by a predoctoral grant for training in research into health (PFIS PI19/00577) from the Instituto de Salud Carlos III. All authors declare having no conflict of interest with regard to this trial.
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Affiliation(s)
- X Vendrell
- Reproductive Genetics Department, Sistemas Genómicos-Synlab, Valencia, Spain
| | - P de Castro
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - L Escrich
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - N Grau
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - R Gonzalez-Martin
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - A Quiñonero
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - M J Escribá
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - F Domínguez
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
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Radley A, Boeing S, Smith A. Branching topology of the human embryo transcriptome revealed by Entropy Sort Feature Weighting. Development 2024; 151:dev202832. [PMID: 38691188 PMCID: PMC11213519 DOI: 10.1242/dev.202832] [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: 02/26/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Analysis of single cell transcriptomics (scRNA-seq) data is typically performed after subsetting to highly variable genes (HVGs). Here, we show that Entropy Sorting provides an alternative mathematical framework for feature selection. On synthetic datasets, continuous Entropy Sort Feature Weighting (cESFW) outperforms HVG selection in distinguishing cell-state-specific genes. We apply cESFW to six merged scRNA-seq datasets spanning human early embryo development. Without smoothing or augmenting the raw counts matrices, cESFW generates a high-resolution embedding displaying coherent developmental progression from eight-cell to post-implantation stages and delineating 15 distinct cell states. The embedding highlights sequential lineage decisions during blastocyst development, while unsupervised clustering identifies branch point populations obscured in previous analyses. The first branching region, where morula cells become specified for inner cell mass or trophectoderm, includes cells previously asserted to lack a developmental trajectory. We quantify the relatedness of different pluripotent stem cell cultures to distinct embryo cell types and identify marker genes of naïve and primed pluripotency. Finally, by revealing genes with dynamic lineage-specific expression, we provide markers for staging progression from morula to blastocyst.
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Affiliation(s)
- Arthur Radley
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Austin Smith
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
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Azagury M, Buganim Y. Unlocking trophectoderm mysteries: In vivo and in vitro perspectives on human and mouse trophoblast fate induction. Dev Cell 2024; 59:941-960. [PMID: 38653193 DOI: 10.1016/j.devcel.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/10/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
In recent years, the pursuit of inducing the trophoblast stem cell (TSC) state has gained prominence as a compelling research objective, illuminating the establishment of the trophoblast lineage and unlocking insights into early embryogenesis. In this review, we examine how advancements in diverse technologies, including in vivo time course transcriptomics, cellular reprogramming to TSC state, chemical induction of totipotent stem-cell-like state, and stem-cell-based embryo-like structures, have enriched our insights into the intricate molecular mechanisms and signaling pathways that define the mouse and human trophectoderm/TSC states. We delve into disparities between mouse and human trophectoderm/TSC fate establishment, with a special emphasis on the intriguing role of pluripotency in this context. Additionally, we re-evaluate recent findings concerning the potential of totipotent-stem-like cells and embryo-like structures to fully manifest the trophectoderm/trophoblast lineage's capabilities. Lastly, we briefly discuss the potential applications of induced TSCs in pregnancy-related disease modeling.
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Affiliation(s)
- Meir Azagury
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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5
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Sotomayor-Lugo F, Iglesias-Barrameda N, Castillo-Aleman YM, Casado-Hernandez I, Villegas-Valverde CA, Bencomo-Hernandez AA, Ventura-Carmenate Y, Rivero-Jimenez RA. The Dynamics of Histone Modifications during Mammalian Zygotic Genome Activation. Int J Mol Sci 2024; 25:1459. [PMID: 38338738 PMCID: PMC10855761 DOI: 10.3390/ijms25031459] [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: 12/29/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Mammalian fertilization initiates the reprogramming of oocytes and sperm, forming a totipotent zygote. During this intricate process, the zygotic genome undergoes a maternal-to-zygotic transition (MZT) and subsequent zygotic genome activation (ZGA), marking the initiation of transcriptional control and gene expression post-fertilization. Histone modifications are pivotal in shaping cellular identity and gene expression in many mammals. Recent advances in chromatin analysis have enabled detailed explorations of histone modifications during ZGA. This review delves into conserved and unique regulatory strategies, providing essential insights into the dynamic changes in histone modifications and their variants during ZGA in mammals. The objective is to explore recent advancements in leading mechanisms related to histone modifications governing this embryonic development phase in depth. These considerations will be useful for informing future therapeutic approaches that target epigenetic regulation in diverse biological contexts. It will also contribute to the extensive areas of evolutionary and developmental biology and possibly lay the foundation for future research and discussion on this seminal topic.
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Affiliation(s)
| | | | | | | | | | | | | | - Rene Antonio Rivero-Jimenez
- Abu Dhabi Stem Cells Center, Abu Dhabi P.O. Box 4600, United Arab Emirates; (F.S.-L.); (N.I.-B.); (Y.M.C.-A.); (I.C.-H.); (C.A.V.-V.); (A.A.B.-H.); (Y.V.-C.)
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6
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Lee M, Oh JN, Choe GC, Choi KH, Lee DK, Kim SH, Jeong J, Ahn Y, Lee CK. NANOG expression in parthenogenetic porcine blastocysts is required for intact lineage specification and pluripotency. Anim Biosci 2023; 36:1905-1917. [PMID: 37641830 PMCID: PMC10623019 DOI: 10.5713/ab.23.0210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVE Nanog homeobox (NANOG) is a core transcription factor that contributes to pluripotency along with octamer binding transcription factor-4 (OCT4) and sex determining region-Y box-2 (SOX2). It is an epiblast lineage marker in mammalian pre-implantation embryos and exhibits a species-specific expression pattern. Therefore, it is important to understand the lineage of NANOG, the trophectoderm, and the primitive endoderm in the pig embryo. METHODS A loss- and gain-of-function analysis was done to determine the role of NANOG in lineage specification in parthenogenetic porcine blastocysts. We analyzed the relationship between NANOG and pluripotent core transcription factors and other lineage makers. RESULTS In NANOG-null late blastocysts, OCT4-, SOX2-, and SOX17-positive cells were decreased, whereas GATA binding protein 6 (GATA6)-positive cells were increased. Quantitative real-time polymerase chain reaction revealed that the expression of SOX2 was decreased in NANOG-null blastocysts, whereas that of primitive endoderm makers, except SOX17, was increased. In NANOG-overexpressing blastocysts, caudal type homeobox 2 (CDX2-), SOX17-, and GATA6-positive cells were decreased. The results indicated that the expression of primitive endoderm markers and trophectoderm-related genes was decreased. CONCLUSION Taken together, the results demonstrate that NANOG is involved in the epiblast and primitive endoderm differentiation and is essential for maintaining pluripotency within the epiblast.
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Affiliation(s)
- Mingyun Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Jong-Nam Oh
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06510,
USA
| | - Gyung Cheol Choe
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Kwang-Hwan Choi
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Dong-Kyung Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Seung-Hun Kim
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Jinsol Jeong
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Yelim Ahn
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354,
Korea
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7
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Wei X, Fang X, Yu X, Li H, Guo Y, Qi Y, Sun C, Han D, Liu X, Li N, Hu H. Integrative analysis of single-cell embryo data reveals transcriptome signatures for the human pre-implantation inner cell mass. Dev Biol 2023; 502:39-49. [PMID: 37437860 DOI: 10.1016/j.ydbio.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/14/2023]
Abstract
As the source of embryonic stem cells (ESCs), inner cell mass (ICM) can form all tissues of the embryo proper, however, its role in early human lineage specification remains controversial. Although a stepwise differentiation model has been proposed suggesting the existence of ICM as a distinct developmental stage, the underlying molecular mechanism remains unclear. In the present study, we perform an integrated analysis on the public human preimplantation embryonic single-cell transcriptomic data and apply a trajectory inference algorithm to measure the cell plasticity. In our results, ICM population can be clearly discriminated on the dimension-reduced graph and confirmed by compelling evidences, thus validating the two-step hypothesis of lineage commitment. According to the branch probabilities and differentiation potential, we determine the precise time points for two lineage segregations. Further analysis on gene expression dynamics and regulatory network indicates that transcription factors including GSC, PRDM1, and SPIC may underlie the decisions of ICM fate. In addition, new human ICM marker genes, such as EPHA4 and CCR8 are discovered and validated by immunofluorescence. Given the potential clinical applications of ESCs, our analysis provides a further understanding of human ICM cells and facilitates the exploration of more unique characteristics in early human development.
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Affiliation(s)
- Xinshu Wei
- School of Medicine, South China University of Technology, Guangzhou, China; Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Xiang Fang
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, China
| | - Xiu Yu
- School of Medicine, Jiaying University, Meizhou, 514015, China; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
| | - Hong Li
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Yuyang Guo
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Yifei Qi
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Dingding Han
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Xiaonan Liu
- Department of Assisted Reproductive Technology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Na Li
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
| | - Hao Hu
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China; Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China; Third Affiliatied Hospital of Zhengzhou University, Zhengzhou, China.
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8
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Gahurova L, Tomankova J, Cerna P, Bora P, Kubickova M, Virnicchi G, Kovacovicova K, Potesil D, Hruska P, Zdrahal Z, Anger M, Susor A, Bruce AW. Spatial positioning of preimplantation mouse embryo cells is regulated by mTORC1 and m 7G-cap-dependent translation at the 8- to 16-cell transition. Open Biol 2023; 13:230081. [PMID: 37553074 PMCID: PMC10409569 DOI: 10.1098/rsob.230081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
Preimplantation mouse embryo development involves temporal-spatial specification and segregation of three blastocyst cell lineages: trophectoderm, primitive endoderm and epiblast. Spatial separation of the outer-trophectoderm lineage from the two other inner-cell-mass (ICM) lineages starts with the 8- to 16-cell transition and concludes at the 32-cell stages. Accordingly, the ICM is derived from primary and secondary contributed cells; with debated relative EPI versus PrE potencies. We report generation of primary but not secondary ICM populations is highly dependent on temporal activation of mammalian target of Rapamycin (mTOR) during 8-cell stage M-phase entry, mediated via regulation of the 7-methylguanosine-cap (m7G-cap)-binding initiation complex (EIF4F) and linked to translation of mRNAs containing 5' UTR terminal oligopyrimidine (TOP-) sequence motifs, as knockdown of identified TOP-like motif transcripts impairs generation of primary ICM founders. However, mTOR inhibition-induced ICM cell number deficits in early blastocysts can be compensated by the late blastocyst stage, after inhibitor withdrawal; compensation likely initiated at the 32-cell stage when supernumerary outer cells exhibit molecular characteristics of inner cells. These data identify a novel mechanism specifically governing initial spatial segregation of mouse embryo blastomeres, that is distinct from those directing subsequent inner cell formation, contributing to germane segregation of late blastocyst lineages.
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Affiliation(s)
- Lenka Gahurova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic
| | - Jana Tomankova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Pavlina Cerna
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Pablo Bora
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Michaela Kubickova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Giorgio Virnicchi
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Kristina Kovacovicova
- Laboratory of Cell Division Control, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic
- Department of Genetics and Reproduction, Central European Institute of Technology, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic
| | - David Potesil
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Pavel Hruska
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Zbynek Zdrahal
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Martin Anger
- Laboratory of Cell Division Control, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic
- Department of Genetics and Reproduction, Central European Institute of Technology, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic
| | - Andrej Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic
| | - Alexander W Bruce
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
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9
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The Human Early Maternal–Embryonic Interactome. REPRODUCTIVE MEDICINE 2023. [DOI: 10.3390/reprodmed4010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Background: Single cell transcriptomics offers an avenue for predicting, with improved accuracy, the gene networks that are involved in the establishment of the first direct cell–cell interactions between the blastocyst and the maternal luminal epithelium. We hypothesised that in silico modelling of the maternal–embryonic interface may provide a causal model of these interactions, leading to the identification of genes associated with a successful initiation of implantation. Methods: Bulk and single cell RNA-sequencing of endometrial epithelium and scRNAseq of day 6 and 7 trophectoderm (TE) were used to model the initial encounter between the blastocyst and the maternal uterine lining epithelium in silico. In silico modelling of the maternal–embryonic interface was performed using hypernetwork (HN) analysis of genes mediating endometrial–TE interactions and the wider endometrial epithelial transcriptome. A hypernetwork analysis identifies genes that co-ordinate the expression of many other genes to derive a higher order interaction likely to be causally linked to the function. Potential interactions of TE with non-ciliated luminal cells, ciliated cells, and glandular cells were examined. Results: Prominent epithelial activities include secretion, endocytosis, ion transport, adhesion, and immune modulation. Three highly correlated clusters of 25, 22 and 26 TE-interacting epithelial surface genes were identified, each with distinct properties. Genes in both ciliated and non-ciliated luminal epithelial cells and glandular cells exhibit significant functional associations. Ciliated cells are predicted to bind to TE via galectin–glycan interaction. Day 6 and day 7 embryonic–epithelial interactomes are largely similar. The removal of aneuploid TE-derived mRNA invoked only subtle differences. No direct interaction with the maternal gland epithelial cell surface is predicted. These functional differences validate the in silico segregation of phenotypes. Single cell analysis of the epithelium revealed significant change with the cycle phase, but differences in the cell phenotype between individual donors were also present. Conclusions: A hypernetwork analysis can identify epithelial gene clusters that show correlated change during the menstrual cycle and can be interfaced with TE genes to predict pathways and processes occurring during the initiation of embryo–epithelial interaction in the mid-secretory phase. The data are on a scale that is realistic for functional dissection using current ex vivo human implantation models. A focus on luminal epithelial cells may allow a resolution to the current bottleneck of endometrial receptivity testing based on tissue lysates, which is confounded by noise from multiple diverse cell populations.
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10
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Schnirman RE, Kuo SJ, Kelly RC, Yamaguchi TP. The role of Wnt signaling in the development of the epiblast and axial progenitors. Curr Top Dev Biol 2023; 153:145-180. [PMID: 36967193 DOI: 10.1016/bs.ctdb.2023.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Understanding how the body plan is established during embryogenesis remains a fundamental biological question. The Wnt/β-catenin signaling pathway plays a crucial and highly conserved role in body plan formation, functioning to polarize the primary anterior-posterior (AP) or head-to-tail body axis in most metazoans. In this chapter, we focus on the roles that the mammalian Wnt/β-catenin pathway plays to prepare the pluripotent epiblast for gastrulation, and to elicit the emergence of multipotent axial progenitors from the caudal epiblast. Interactions between Wnt and retinoic acid (RA), another powerful family of developmental signaling molecules, in axial progenitors will also be discussed. Gastrulation movements and somitogenesis result in the anterior displacement of the RA source (the rostral somites and lateral plate mesoderm (LPM)), from the posterior Wnt source (the primitive streak (PS)), leading to the establishment of antiparallel gradients of RA and Wnt that control the self-renewal and successive differentiation of neck, trunk and tail progenitors.
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Affiliation(s)
| | - Samuel J Kuo
- NCI-Frederick, NIH, Frederick, MD, United States
| | - Ryan C Kelly
- NCI-Frederick, NIH, Frederick, MD, United States
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11
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Robert C, Prista von Bonhorst F, De Decker Y, Dupont G, Gonze D. Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo. Interface Focus 2022; 12:20220010. [PMID: 35865503 PMCID: PMC9184963 DOI: 10.1098/rsfs.2022.0010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/12/2022] [Indexed: 08/30/2024] Open
Abstract
During development, cells from a population of common progenitors evolve towards different fates characterized by distinct levels of specific transcription factors, a process known as cell differentiation. This evolution is governed by gene regulatory networks modulated by intercellular signalling. In order to evolve towards distinct fates, cells forming the population of common progenitors must display some heterogeneity. We applied a modelling approach to obtain insights into the possible sources of cell-to-cell variability initiating the specification of cells of the inner cell mass into epiblast or primitive endoderm cells in early mammalian embryo. At the single-cell level, these cell fates correspond to three possible steady states of the model. A combination of numerical simulations and bifurcation analyses predicts that the behaviour of the model is preserved with respect to the source of variability and that cell-cell coupling induces the emergence of multiple steady states associated with various cell fate configurations, and to a distribution of the levels of expression of key transcription factors. Statistical analysis of these time-dependent distributions reveals differences in the evolutions of the variance-to-mean ratios of key variables of the system, depending on the simulated source of variability, and, by comparison with experimental data, points to the rate of synthesis of the key transcription factor NANOG as a likely initial source of heterogeneity.
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Affiliation(s)
- Corentin Robert
- Unit of Theoretical Chronobiology and Université Libre de Bruxelles (ULB), Brussels CP 231, Belgium
- Nonlinear Physical Chemistry Unit, Université Libre de Bruxelles (ULB), Brussels CP 231, Belgium
| | | | - Yannick De Decker
- Nonlinear Physical Chemistry Unit, Université Libre de Bruxelles (ULB), Brussels CP 231, Belgium
| | - Geneviève Dupont
- Unit of Theoretical Chronobiology and Université Libre de Bruxelles (ULB), Brussels CP 231, Belgium
| | - Didier Gonze
- Unit of Theoretical Chronobiology and Université Libre de Bruxelles (ULB), Brussels CP 231, Belgium
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12
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Minchiotti G, D’Aniello C, Fico A, De Cesare D, Patriarca EJ. Capturing Transitional Pluripotency through Proline Metabolism. Cells 2022; 11:cells11142125. [PMID: 35883568 PMCID: PMC9323356 DOI: 10.3390/cells11142125] [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: 06/10/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 12/03/2022] Open
Abstract
In this paper, we summarize the current knowledge of the role of proline metabolism in the control of the identity of Embryonic Stem Cells (ESCs). An imbalance in proline metabolism shifts mouse ESCs toward a stable naïve-to-primed intermediate state of pluripotency. Proline-induced cells (PiCs), also named primitive ectoderm-like cells (EPLs), are phenotypically metastable, a trait linked to a rapid and reversible relocalization of E-cadherin from the plasma membrane to intracellular membrane compartments. The ESC-to-PiC transition relies on the activation of Erk and Tgfβ/Activin signaling pathways and is associated with extensive remodeling of the transcriptome, metabolome and epigenome. PiCs maintain several properties of naïve pluripotency (teratoma formation, blastocyst colonization and 3D gastruloid development) and acquire a few traits of primed cells (flat-shaped colony morphology, aerobic glycolysis metabolism and competence for primordial germ cell fate). Overall, the molecular and phenotypic features of PiCs resemble those of an early-primed state of pluripotency, providing a robust model to study the role of metabolic perturbations in pluripotency and cell fate decisions.
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