1
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Murase Y, Yokogawa R, Yabuta Y, Nagano M, Katou Y, Mizuyama M, Kitamura A, Puangsricharoen P, Yamashiro C, Hu B, Mizuta K, Tsujimura T, Yamamoto T, Ogata K, Ishihama Y, Saitou M. In vitro reconstitution of epigenetic reprogramming in the human germ line. Nature 2024; 631:170-178. [PMID: 38768632 PMCID: PMC11222161 DOI: 10.1038/s41586-024-07526-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Epigenetic reprogramming resets parental epigenetic memories and differentiates primordial germ cells (PGCs) into mitotic pro-spermatogonia or oogonia. This process ensures sexually dimorphic germ cell development for totipotency1. In vitro reconstitution of epigenetic reprogramming in humans remains a fundamental challenge. Here we establish a strategy for inducing epigenetic reprogramming and differentiation of pluripotent stem-cell-derived human PGC-like cells (hPGCLCs) into mitotic pro-spermatogonia or oogonia, coupled with their extensive amplification (about >1010-fold). Bone morphogenetic protein (BMP) signalling is a key driver of these processes. BMP-driven hPGCLC differentiation involves attenuation of the MAPK (ERK) pathway and both de novo and maintenance DNA methyltransferase activities, which probably promote replication-coupled, passive DNA demethylation. hPGCLCs deficient in TET1, an active DNA demethylase abundant in human germ cells2,3, differentiate into extraembryonic cells, including amnion, with de-repression of key genes that bear bivalent promoters. These cells fail to fully activate genes vital for spermatogenesis and oogenesis, and their promoters remain methylated. Our study provides a framework for epigenetic reprogramming in humans and an important advance in human biology. Through the generation of abundant mitotic pro-spermatogonia and oogonia-like cells, our results also represent a milestone for human in vitro gametogenesis research and its potential translation into reproductive medicine.
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Affiliation(s)
- Yusuke Murase
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryuta Yokogawa
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Nagano
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshitaka Katou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manami Mizuyama
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ayaka Kitamura
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Pimpitcha Puangsricharoen
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Chika Yamashiro
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Bo Hu
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Mizuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Taro Tsujimura
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Medical-Risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan
| | - Kosuke Ogata
- Department of Molecular Systems BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yasushi Ishihama
- Department of Molecular Systems BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
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2
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Cheng K, Seita Y, Whelan EC, Yokomizo R, Hwang YS, Rotolo A, Krantz ID, Ginsberg JP, Kolon TF, Lal P, Luo X, Pierorazio PM, Linn RL, Ryeom S, Sasaki K. Defining the cellular origin of seminoma by transcriptional and epigenetic mapping to the normal human germline. Cell Rep 2024; 43:114323. [PMID: 38861385 DOI: 10.1016/j.celrep.2024.114323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/26/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024] Open
Abstract
Aberrant male germline development can lead to the formation of seminoma, a testicular germ cell tumor. Seminomas are biologically similar to primordial germ cells (PGCs) and many bear an isochromosome 12p [i(12p)] with two additional copies of the short arm of chromosome 12. By mapping seminoma transcriptomes and open chromatin landscape onto a normal human male germline trajectory, we find that seminoma resembles premigratory/migratory PGCs; however, it exhibits enhanced germline and pluripotency programs and upregulation of genes involved in apoptosis, angiogenesis, and MAPK/ERK pathways. Using pluripotent stem cell-derived PGCs from Pallister-Killian syndrome patients mosaic for i(12p), we model seminoma and identify gene dosage effects that may contribute to transformation. As murine seminoma models do not exist, our analyses provide critical insights into genetic, cellular, and signaling programs driving seminoma transformation, and the in vitro platform developed herein permits evaluation of additional signals required for seminoma tumorigenesis.
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Affiliation(s)
- Keren Cheng
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Yasunari Seita
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Eoin C Whelan
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Ryo Yokomizo
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Young Sun Hwang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Antonia Rotolo
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Ian D Krantz
- Division of Human Genetics, The Roberts Individualized Medical Genetics Center, The Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Jill P Ginsberg
- Department of Pediatrics, The Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Thomas F Kolon
- Division of Urology, The Children's Hospital of Philadelphia, 3500 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Priti Lal
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Xunda Luo
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Presbyterian Medical Center, 51 North 39th Street, Philadelphia, PA 19104, USA
| | - Phillip M Pierorazio
- Division of Urology, University of Pennsylvania Presbyterian Medical Center, 3737 Market St. 4th Floor, Philadelphia, PA 19104, USA
| | - Rebecca L Linn
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, Philadelphia, PA 19104, USA; Department of Pathology, The Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Sandra Ryeom
- Department of Surgery, Columbia University Irving Medical Center, 630 W. 168th Street, P&S 17-409, New York, NY 10032, USA
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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3
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Ikeda H, Miyao S, Yamada N, Sugimoto S, Kimura F, Kurimoto K. Protocol for high-quality single-cell RNA-seq from tissue sections with DRaqL. STAR Protoc 2024; 5:103050. [PMID: 38703368 PMCID: PMC11088347 DOI: 10.1016/j.xpro.2024.103050] [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: 02/20/2024] [Revised: 03/27/2024] [Accepted: 04/16/2024] [Indexed: 05/06/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) combined with laser capture microdissection (LCM) offers a versatile framework for comprehensive transcriptomics from tissue sections. Here, we present a detailed protocol for DRaqL (direct RNA recovery and quenching for LCM) in combination with Smart-seq2 (DRaqL-Smart-seq2), which enables high-quality RNA sequencing for single cells obtained from alcohol-fixed murine ovarian sections. Additionally, we provide an optional procedure for scRNA-seq from formalin-fixed sections (DRaqL-Protease-Smart-seq2). We outline key steps for cell lysis, cDNA amplification, and sequencing library preparation. For complete details on the use and execution of this protocol, please refer to Ikeda et al.1.
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Affiliation(s)
- Hiroki Ikeda
- Department of Embryology, School of Medicine, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Shintaro Miyao
- Department of Embryology, School of Medicine, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Nanami Yamada
- Department of Embryology, School of Medicine, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Sumire Sugimoto
- Department of Obstetrics and Gynecology, School of Medicine, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Fuminori Kimura
- Department of Obstetrics and Gynecology, School of Medicine, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Kazuki Kurimoto
- Department of Embryology, School of Medicine, Nara Medical University, Kashihara, Nara 634-8521, Japan.
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4
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Sakurai J, Oka S, Higuchi Y, Ohsawa S, Fujimori T. Effects of blastocyst elongation and implantation chamber formation on the alignment of the embryonic axis and uterine axis in mice. Front Cell Dev Biol 2024; 12:1421222. [PMID: 38946796 PMCID: PMC11211524 DOI: 10.3389/fcell.2024.1421222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/17/2024] [Indexed: 07/02/2024] Open
Abstract
Embryo implantation involves a series of events that bring the embryo and maternal tissues into contact to support post-implantation development in mammals. During implantation, alignment of the embryonic-abembryonic (E-Ab) axis of the blastocyst with the mesometrial-antimesometrial (M-AM) axis of the uterus precedes post-implantation embryonic development and placentation. In the present study, we observed the morphological changes in blastocysts and the endometrial luminal epithelium (LE) that occur during the alignment of the embryonic and the uterine axes. We found that at the time that the blastocysts attached to the LE at the mural trophectoderm, the embryonic axis was not aligned with the uterine axis. Alignment of the embryonic E-Ab axis with the uterine M-AM axis occurred after E4.0, and the embryo was significantly elongated during the process. The depth of the implantation chamber (IC) correlated with the degree of alignment, suggesting that elongated embryos are oriented along the M-AM axis during IC formation. Transplantation of the Concanavalin A (Con A)-coated beads induced IC formation, and the alignment of two Con A-coated beads present in the same IC in the M-AM direction suggested that elongated materials can align along the M-AM axis. These data suggest that an elongated shape of the embryo and IC formation coordinate the alignment of the embryonic and uterine axes.
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Affiliation(s)
- Jun Sakurai
- Division of Embryology, National Institute for Basic Biology, Okazaki, Japan
- Deapartment of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
| | - Sanae Oka
- Division of Embryology, National Institute for Basic Biology, Okazaki, Japan
| | - Yoko Higuchi
- Division of Embryology, National Institute for Basic Biology, Okazaki, Japan
| | - Sonoko Ohsawa
- Model Organisms Facility, Trans-Scale Biology Center, National Institute for Basic Biology, Okazaki, Japan
| | - Toshihiko Fujimori
- Division of Embryology, National Institute for Basic Biology, Okazaki, Japan
- Deapartment of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
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5
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Hwang YS, Seita Y, Blanco MA, Sasaki K. CRISPR loss of function screening to identify genes involved in human primordial germ cell-like cell development. PLoS Genet 2023; 19:e1011080. [PMID: 38091369 PMCID: PMC10752514 DOI: 10.1371/journal.pgen.1011080] [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: 09/05/2023] [Revised: 12/27/2023] [Accepted: 11/22/2023] [Indexed: 12/28/2023] Open
Abstract
Despite our increasing knowledge of molecular mechanisms guiding various aspects of human reproduction, those underlying human primordial germ cell (PGC) development remain largely unknown. Here, we conducted custom CRISPR screening in an in vitro system of human PGC-like cells (hPGCLCs) to identify genes required for acquisition and maintenance of PGC fate. Amongst our candidates, we identified TCL1A, an AKT coactivator. Functional assessment in our in vitro hPGCLCs system revealed that TCL1A played a critical role in later stages of hPGCLC development. Moreover, we found that TCL1A loss reduced AKT-mTOR signaling, downregulated expression of genes related to translational control, and subsequently led to a reduction in global protein synthesis and proliferation. Together, our study highlights the utility of CRISPR screening for human in vitro-derived germ cells and identifies novel translational regulators critical for hPGCLC development.
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Affiliation(s)
- Young Sun Hwang
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yasunari Seita
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - M. Andrés Blanco
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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6
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Wang HQ, Liu Y, Li D, Liu JY, Jiang Y, He Y, Zhou JD, Wang ZL, Tang XY, Zhang Y, Zhen X, Cao ZW, Sheng XQ, Yang CF, Yue QL, Ding LJ, Hu YL, Hu ZB, Li CJ, Yan GJ, Sun HX. Maternal and embryonic signals cause functional differentiation of luminal epithelial cells and receptivity establishment. Dev Cell 2023; 58:2376-2392.e6. [PMID: 37643613 DOI: 10.1016/j.devcel.2023.08.004] [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: 06/20/2022] [Revised: 04/11/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
Embryo implantation requires temporospatial maternal-embryonic dialog. Using single-cell RNA sequencing for the uterus from 2.5 to 4.5 days post-coitum (DPC) and bulk sequencing for the corresponding embryos of 3.5 and 4.0 DPC pregnant mice, we found that estrogen-responsive luminal epithelial cells (EECs) functionally differentiated into adhesive epithelial cells (AECs) and supporting epithelial cells (SECs), promoted by progesterone. Along with maternal signals, embryonic Pdgfa and Efna3/4 signaling activated AECs and SECs, respectively, enhancing the attachment of embryos to the endometrium and furthering embryo development. This differentiation process was largely conserved between humans and mice. Notably, the developmental defects of SOX9-positive human endometrial epithelial cells (similar to mouse EEC) were related to thin endometrium, whereas functional defects of SEC-similar unciliated epithelial cells were related to recurrent implantation failure (RIF). Our findings provide insights into endometrial luminal epithelial cell development directed by maternal and embryonic signaling, which is crucial for endometrial receptivity.
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Affiliation(s)
- Hai-Quan Wang
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Yang Liu
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Department of Reproductive Medicine Center, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Dong Li
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Jing-Yu Liu
- State Key Laboratory of Reproductive Medicine and Offspring Health Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Yue Jiang
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Yuanlin He
- State Key Laboratory of Reproductive Medicine and Offspring Health Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ji-Dong Zhou
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Zhi-Long Wang
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Xin-Yi Tang
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Yang Zhang
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Xin Zhen
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Zhi-Wen Cao
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Xiao-Qiang Sheng
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Chao-Fan Yang
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Qiu-Ling Yue
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Li-Jun Ding
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Ya-Li Hu
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China
| | - Zhi-Bin Hu
- State Key Laboratory of Reproductive Medicine and Offspring Health Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Chao-Jun Li
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; State Key Laboratory of Reproductive Medicine and Offspring Health Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Gui-Jun Yan
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Department of Reproductive Medicine Center, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China.
| | - Hai-Xiang Sun
- Center for Reproductive Medicine and Obstetrics & Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; State Key Laboratory of Reproductive Medicine and Offspring Health Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, China.
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7
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Ikeda H, Miyao S, Nagaoka S, Takashima T, Law SM, Yamamoto T, Kurimoto K. High-quality single-cell transcriptomics from ovarian histological sections during folliculogenesis. Life Sci Alliance 2023; 6:e202301929. [PMID: 37722727 PMCID: PMC10507249 DOI: 10.26508/lsa.202301929] [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: 01/16/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
High-quality, straightforward single-cell RNA sequencing (RNA-seq) with spatial resolution remains challenging. Here, we developed DRaqL (direct RNA recovery and quenching for laser capture microdissection), an experimental approach for efficient cell lysis of tissue sections, directly applicable to cDNA amplification. Single-cell RNA-seq combined with DRaqL allowed transcriptomic profiling from alcohol-fixed sections with efficiency comparable with that of profiling from freshly dissociated cells, together with effective exon-exon junction profiling. The combination of DRaqL with protease treatment enabled robust and efficient single-cell transcriptome analysis from formalin-fixed tissue sections. Applying this method to mouse ovarian sections, we were able to predict the transcriptome of oocytes by their size and identified an anomaly in the size-transcriptome relationship relevant to growth retardation of oocytes, in addition to detecting oocyte-specific splice isoforms. Furthermore, we identified differentially expressed genes in granulosa cells in association with their proximity to the oocytes, suggesting distinct epigenetic regulations and cell-cycle activities governing the germ-soma relationship. Thus, DRaqL is a versatile, efficient approach for high-quality single-cell RNA-seq from tissue sections, thereby revealing histological heterogeneity in folliculogenic transcriptome.
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Affiliation(s)
- Hiroki Ikeda
- https://ror.org/045ysha14 Department of Embryology, School of Medicine, Nara Medical University, Kashihara, Japan
| | - Shintaro Miyao
- https://ror.org/045ysha14 Department of Embryology, School of Medicine, Nara Medical University, Kashihara, Japan
| | - So Nagaoka
- https://ror.org/045ysha14 Department of Embryology, School of Medicine, Nara Medical University, Kashihara, Japan
| | - Tomoya Takashima
- https://ror.org/045ysha14 Department of Embryology, School of Medicine, Nara Medical University, Kashihara, Japan
| | - Sze-Ming Law
- https://ror.org/045ysha14 Department of Embryology, School of Medicine, Nara Medical University, Kashihara, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan
| | - Kazuki Kurimoto
- https://ror.org/045ysha14 Department of Embryology, School of Medicine, Nara Medical University, Kashihara, Japan
- https://ror.org/045ysha14 Advanced Medical Research Center, Nara Medical University, Kashihara, Japan
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8
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Gyobu‐Motani S, Yabuta Y, Mizuta K, Katou Y, Okamoto I, Kawasaki M, Kitamura A, Tsukiyama T, Iwatani C, Tsuchiya H, Tsujimura T, Yamamoto T, Nakamura T, Saitou M. Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys. EMBO J 2023; 42:e112962. [PMID: 36929479 PMCID: PMC10152148 DOI: 10.15252/embj.2022112962] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/18/2023] Open
Abstract
Human in vitro oogenesis provides a framework for clarifying the mechanism of human oogenesis. To create its benchmark, it is vital to promote in vitro oogenesis using a model physiologically close to humans. Here, we establish a foundation for in vitro oogenesis in cynomolgus (cy) monkeys (Macaca fascicularis): cy female embryonic stem cells harboring one active and one inactive X chromosome (Xa and Xi, respectively) differentiate robustly into primordial germ cell-like cells, which in xenogeneic reconstituted ovaries develop efficiently into oogonia and, remarkably, further into meiotic oocytes at the zygotene stage. This differentiation entails comprehensive epigenetic reprogramming, including Xi reprogramming, yet Xa and Xi remain epigenetically asymmetric with, as partly observed in vivo, incomplete Xi reactivation. In humans and monkeys, the Xi epigenome in pluripotent stem cells functions as an Xi-reprogramming determinant. We further show that developmental pathway over-activations with suboptimal up-regulation of relevant meiotic genes impede in vitro meiotic progression. Cy in vitro oogenesis exhibits critical homology with the human system, including with respect to bottlenecks, providing a salient model for advancing human in vitro oogenesis.
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Affiliation(s)
- Sayuri Gyobu‐Motani
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Ken Mizuta
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Yoshitaka Katou
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Ikuhiro Okamoto
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Masanori Kawasaki
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Ayaka Kitamura
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Tomoyuki Tsukiyama
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Chizuru Iwatani
- Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Hideaki Tsuchiya
- Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Taro Tsujimura
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
- Center for Advanced Intelligence Project, RIKENTokyoJapan
| | - Tomonori Nakamura
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
- The Hakubi Center for Advanced ResearchKyoto UniversityKyotoJapan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
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9
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Imai A, Matsuda K, Niimi Y, Suzuki A. Loss of Dead end1 induces testicular teratomas from primordial germ cells that failed to undergo sexual differentiation in embryonic testes. Sci Rep 2023; 13:6398. [PMID: 37076592 PMCID: PMC10115811 DOI: 10.1038/s41598-023-33706-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/18/2023] [Indexed: 04/21/2023] Open
Abstract
Spontaneous testicular teratomas (STTs) are tumours comprising a diverse array of cell and tissue types, which are derived from pluripotent stem-like cells called embryonal carcinoma cells (ECCs). Although mouse ECCs originate from primordial germ cells (PGCs) in embryonic testes, the molecular basis underlying ECC development remains unclear. This study shows that the conditional deletion of mouse Dead end1 (Dnd1) from migrating PGCs leads to STT development. In Dnd1-conditional knockout (Dnd1-cKO) embryos, PGCs colonise the embryonic testes but fail to undergo sexual differentiation; subsequently, ECCs develop from a portion of the PGCs. Transcriptomic analyses reveal that PGCs not only fail to undergo sexual differentiation but are also prone to transformation into ECCs by upregulating the expression of marker genes for primed pluripotency in the testes of Dnd1-cKO embryos. Thus, our results clarify the role of Dnd1 in developing STTs and developmental process of ECC from PGC, providing novel insights into pathogenic mechanisms of STTs.
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Affiliation(s)
- Atsuki Imai
- Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Kazuya Matsuda
- Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Yuki Niimi
- Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
- Research & Development Group, Center for Exploratory Research, Hitachi, Ltd., Kobe, Hyogo, Japan
| | - Atsushi Suzuki
- Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan.
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan.
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10
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Wang S, Sun ST, Zhang XY, Ding HR, Yuan Y, He JJ, Wang MS, Yang B, Li YB. The Evolution of Single-Cell RNA Sequencing Technology and Application: Progress and Perspectives. Int J Mol Sci 2023; 24:ijms24032943. [PMID: 36769267 PMCID: PMC9918030 DOI: 10.3390/ijms24032943] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/01/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
As an emerging sequencing technology, single-cell RNA sequencing (scRNA-Seq) has become a powerful tool for describing cell subpopulation classification and cell heterogeneity by achieving high-throughput and multidimensional analysis of individual cells and circumventing the shortcomings of traditional sequencing for detecting the average transcript level of cell populations. It has been applied to life science and medicine research fields such as tracking dynamic cell differentiation, revealing sensitive effector cells, and key molecular events of diseases. This review focuses on the recent technological innovations in scRNA-Seq, highlighting the latest research results with scRNA-Seq as the core technology in frontier research areas such as embryology, histology, oncology, and immunology. In addition, this review outlines the prospects for its innovative application in traditional Chinese medicine (TCM) research and discusses the key issues currently being addressed by scRNA-Seq and its great potential for exploring disease diagnostic targets and uncovering drug therapeutic targets in combination with multiomics technologies.
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Affiliation(s)
| | | | | | | | | | | | | | - Bin Yang
- Correspondence: (B.Y.); (Y.-B.L.)
| | - Yu-Bo Li
- Correspondence: (B.Y.); (Y.-B.L.)
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11
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Seita Y, Cheng K, McCarrey JR, Yadu N, Cheeseman IH, Bagwell A, Ross CN, Santana Toro I, Yen LH, Vargas S, Navara CS, Hermann BP, Sasaki K. Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells. eLife 2023; 12:e82263. [PMID: 36719274 PMCID: PMC9937652 DOI: 10.7554/elife.82263] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/31/2023] [Indexed: 02/01/2023] Open
Abstract
Reconstitution of germ cell fate from pluripotent stem cells provides an opportunity to understand the molecular underpinnings of germ cell development. Here, we established robust methods for induced pluripotent stem cell (iPSC) culture in the common marmoset (Callithrix jacchus [cj]), allowing stable propagation in an undifferentiated state. Notably, iPSCs cultured on a feeder layer in the presence of a WNT signaling inhibitor upregulated genes related to ubiquitin-dependent protein catabolic processes and enter a permissive state that enables differentiation into primordial germ cell-like cells (PGCLCs) bearing immunophenotypic and transcriptomic similarities to pre-migratory cjPGCs in vivo. Induction of cjPGCLCs is accompanied by transient upregulation of mesodermal genes, culminating in the establishment of a primate-specific germline transcriptional network. Moreover, cjPGCLCs can be expanded in monolayer while retaining the germline state. Upon co-culture with mouse testicular somatic cells, these cells acquire an early prospermatogonia-like phenotype. Our findings provide a framework for understanding and reconstituting marmoset germ cell development in vitro, thus providing a comparative tool and foundation for a preclinical modeling of human in vitro gametogenesis.
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Affiliation(s)
- Yasunari Seita
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary MedicinePhiladelphiaUnited States
- Institute for Regenerative Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Bell Research Center for Reproductive Health and CancerNagoyaJapan
| | - Keren Cheng
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary MedicinePhiladelphiaUnited States
- Institute for Regenerative Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - John R McCarrey
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
| | - Nomesh Yadu
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
| | - Ian H Cheeseman
- Texas Biomedical Research InstituteSan AntonioUnited States
- Southwest National Primate Research CenterSan AntonioUnited States
| | - Alec Bagwell
- Texas Biomedical Research InstituteSan AntonioUnited States
- Southwest National Primate Research CenterSan AntonioUnited States
| | - Corinna N Ross
- Texas Biomedical Research InstituteSan AntonioUnited States
- Southwest National Primate Research CenterSan AntonioUnited States
| | - Isamar Santana Toro
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
| | - Li-hua Yen
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
| | - Sean Vargas
- Genomics Core, The University of Texas at San AntonioSan AntonioUnited States
| | - Christopher S Navara
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
| | - Brian P Hermann
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San AntonioSan AntonioUnited States
- Genomics Core, The University of Texas at San AntonioSan AntonioUnited States
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary MedicinePhiladelphiaUnited States
- Institute for Regenerative Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Department of Pathology and Laboratory Medicine, University of PennsylvaniaPhiladelphiaUnited States
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12
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Kong S, Li R, Tian Y, Zhang Y, Lu Y, Ou Q, Gao P, Li K, Zhang Y. Single-cell omics: A new direction for functional genetic research in human diseases and animal models. Front Genet 2023; 13:1100016. [PMID: 36685871 PMCID: PMC9846559 DOI: 10.3389/fgene.2022.1100016] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Over the past decade, with the development of high-throughput single-cell sequencing technology, single-cell omics has been emerged as a powerful tool to understand the molecular basis of cellular mechanisms and refine our knowledge of diverse cell states. They can reveal the heterogeneity at different genetic layers and elucidate their associations by multiple omics analysis, providing a more comprehensive genetic map of biological regulatory networks. In the post-GWAS era, the molecular biological mechanisms influencing human diseases will be further elucidated by single-cell omics. This review mainly summarizes the development and trend of single-cell omics. This involves single-cell omics technologies, single-cell multi-omics technologies, multiple omics data integration methods, applications in various human organs and diseases, classic laboratory cell lines, and animal disease models. The review will reveal some perspectives for elucidating human diseases and constructing animal models.
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Affiliation(s)
- Siyuan Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,*Correspondence: Siyuan Kong, ; Yubo Zhang,
| | - Rongrong Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yunhan Tian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yaqiu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuhui Lu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiaoer Ou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peiwen Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,College of Life Science and Engineering, Foshan University, Foshan, China,*Correspondence: Siyuan Kong, ; Yubo Zhang,
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13
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Shu Z, Long Q, Zhang L, Yu Z, Wu XJ. Robust Graph Regularized NMF with Dissimilarity and Similarity Constraints for ScRNA-seq Data Clustering. J Chem Inf Model 2022; 62:6271-6286. [PMID: 36459053 DOI: 10.1021/acs.jcim.2c01305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The notable progress in single-cell RNA sequencing (ScRNA-seq) technology is beneficial to accurately discover the heterogeneity and diversity of cells. Clustering is an extremely important step during the ScRNA-seq data analysis. However, it cannot achieve satisfactory performances by directly clustering ScRNA-seq data due to its high dimensionality and noise. To address these issues, we propose a novel ScRNA-seq data representation model, termed Robust Graph regularized Non-Negative Matrix Factorization with Dissimilarity and Similarity constraints (RGNMF-DS), for ScRNA-seq data clustering. To accurately characterize the structure information of the labeled samples and the unlabeled samples, respectively, the proposed RGNMF-DS model adopts a couple of complementary regularizers (i.e., similarity and dissimilar regularizers) to guide matrix decomposition. In addition, we construct a graph regularizer to discover the local geometric structure hidden in ScRNA-seq data. Moreover, we adopt the l2,1-norm to measure the reconstruction error and thereby effectively improve the robustness of the proposed RGNMF-DS model to the noises. Experimental results on several ScRNA-seq datasets have demonstrated that our proposed RGNMF-DS model outperforms other state-of-the-art competitors in clustering.
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Affiliation(s)
- Zhenqiu Shu
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming 650093, China
| | - Qinghan Long
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming 650093, China
| | - Luping Zhang
- Library of Kunming Medical University, Kunming 650031, China
| | - Zhengtao Yu
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming 650093, China
| | - Xiao-Jun Wu
- Jiangsu Provincial Engineering Laboratory of Pattern Recognition and Computational Intelligence, Jiangnan University, Wuxi 214122, China
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14
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Sakata Y, Cheng K, Mayama M, Seita Y, Detlefsen AJ, Mesaros CA, Penning TM, Shishikura K, Yang W, Auchus RJ, Strauss JF, Sasaki K. Reconstitution of human adrenocortical specification and steroidogenesis using induced pluripotent stem cells. Dev Cell 2022; 57:2566-2583.e8. [PMID: 36413950 PMCID: PMC9927873 DOI: 10.1016/j.devcel.2022.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/18/2022] [Accepted: 10/25/2022] [Indexed: 11/23/2022]
Abstract
The mechanisms leading to adrenal cortex development and steroid synthesis in humans remain poorly understood due to the paucity of model systems. Herein, we recapitulate human fetal adrenal cortex specification processes through stepwise induction of human-induced pluripotent stem cells through posterior intermediate mesoderm-like and adrenocortical progenitor-like states to ultimately generate fetal zone adrenal-cortex-like cells (FZLCs), as evidenced by histomorphological, ultrastructural, and transcriptome features and adrenocorticotropic hormone (ACTH)-independent Δ5 steroid biosynthesis. Furthermore, FZLC generation is promoted by SHH and inhibited by NOTCH, ACTIVIN, and WNT signaling, and steroid synthesis is amplified by ACTH/PKA signaling and blocked by inhibitors of Δ5 steroid synthesis enzymes. Finally, NR5A1 promotes FZLC survival and steroidogenesis. Together, these findings provide a framework for understanding and reconstituting human adrenocortical development in vitro, paving the way for cell-based therapies of adrenal insufficiency.
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Affiliation(s)
- Yuka Sakata
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,These authors contributed equally to this work
| | - Keren Cheng
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,These authors contributed equally to this work
| | - Michinori Mayama
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,These authors contributed equally to this work
| | - Yasunari Seita
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Bell Research Center for Reproductive Health and Cancer, Nagoya 460-0003, Japan
| | - Andrea J. Detlefsen
- Department of Biochemistry and Biophysics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Clementina A. Mesaros
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Trevor M. Penning
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyosuke Shishikura
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenli Yang
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Richard J. Auchus
- Division of Metabolism, Endocrinology, and Diabetes, Departments of Internal Medicine and Pharmacology, University of Michigan, Ann Arbor, MI 48105, USA
| | - Jerome F. Strauss
- Department of Obstetrics and Gynecology, University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
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15
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Suzuki D, Sasaki K, Kumamoto S, Tanaka K, Ogawa H. Dynamic Changes of Gene Expression in Mouse Mural Trophectoderm Regulated by Cdx2 During Implantation. Front Cell Dev Biol 2022; 10:945241. [PMID: 36051443 PMCID: PMC9425295 DOI: 10.3389/fcell.2022.945241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/21/2022] [Indexed: 11/24/2022] Open
Abstract
Implantation of the blastocyst into the uterus is a specific and essential process for mammalian embryonic development. In mice, implantation is initiated from the mural trophectoderm of the blastocyst and the mTE controls implantation progression by acquiring the ability to attach and invade into the endometrium while differentiating into primary trophoblast giant cells. Nevertheless, it remains largely unclear when and how the mTE differentiates and acquires this ability during implantation. Here, by RNA sequencing analysis with the pre- and peri-implantation mTE, we show that the mTE undergoes stage-specific and dynamic changes of gene expression during implantation. We also reveal that the mTE begins down-regulating Cdx2 and up-regulating differentiation marker genes during the peri-implantation stage. In addition, using trophectoderm (TE) -specific lentiviral vector-mediated gene transduction, we demonstrate that TE-specific Cdx2 overexpression represses differentiation of the mTE into the primary trophoblast giant cells. Moreover, we reveal that TE-specific Cdx2 overexpression also represses the up-regulation of cell adhesion- and migration-related genes, including Slc6a14, Slc16a3, Itga7, Itgav and Itgb3, which are known to regulate migration of trophectoderm cells. In particular, the expression of Itgb3, an integrin subunit gene, exhibits high inverse correlation with that of Cdx2 in the TE. Reflecting the down-regulation of the genes for TE migration, TE-specific Cdx2 overexpression causes suppression of the blastocyst outgrowth in vitro and abnormal progression of implantation in vivo. Thus, our results specify the time-course changes of global gene expression in the mTE during implantation and uncover the significance of Cdx2 down-regulation for implantation progression.
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Affiliation(s)
- Daisuke Suzuki
- Department of Bioscience, Graduate School of Life Science, Tokyo University of Agriculture, Tokyo, Japan
| | - Keisuke Sasaki
- Bioresource Center, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Soichiro Kumamoto
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Hidehiko Ogawa
- Department of Bioscience, Graduate School of Life Science, Tokyo University of Agriculture, Tokyo, Japan
- *Correspondence: Hidehiko Ogawa,
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16
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Imoto Y, Nakamura T, Escolar EG, Yoshiwaki M, Kojima Y, Yabuta Y, Katou Y, Yamamoto T, Hiraoka Y, Saitou M. Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis. Life Sci Alliance 2022; 5:e202201591. [PMID: 35944930 PMCID: PMC9363502 DOI: 10.26508/lsa.202201591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 11/24/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) can determine gene expression in numerous individual cells simultaneously, promoting progress in the biomedical sciences. However, scRNA-seq data are high-dimensional with substantial technical noise, including dropouts. During analysis of scRNA-seq data, such noise engenders a statistical problem known as the curse of dimensionality (COD). Based on high-dimensional statistics, we herein formulate a noise reduction method, RECODE (resolution of the curse of dimensionality), for high-dimensional data with random sampling noise. We show that RECODE consistently resolves COD in relevant scRNA-seq data with unique molecular identifiers. RECODE does not involve dimension reduction and recovers expression values for all genes, including lowly expressed genes, realizing precise delineation of cell fate transitions and identification of rare cells with all gene information. Compared with representative imputation methods, RECODE employs different principles and exhibits superior overall performance in cell-clustering, expression value recovery, and single-cell-level analysis. The RECODE algorithm is parameter-free, data-driven, deterministic, and high-speed, and its applicability can be predicted based on the variance normalization performance. We propose RECODE as a powerful strategy for preprocessing noisy high-dimensional data.
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Affiliation(s)
- Yusuke Imoto
- Institute for the Advanced Study of Human Biology, Kyoto University Institute for Advanced Study, Kyoto University, Kyoto, Japan
| | - Tomonori Nakamura
- Institute for the Advanced Study of Human Biology, Kyoto University Institute for Advanced Study, Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Emerson G Escolar
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
- Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan
| | | | - Yoji Kojima
- Institute for the Advanced Study of Human Biology, Kyoto University Institute for Advanced Study, Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology, Kyoto University Institute for Advanced Study, Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshitaka Katou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology, Kyoto University Institute for Advanced Study, Kyoto University, Kyoto, Japan
- Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yasuaki Hiraoka
- Institute for the Advanced Study of Human Biology, Kyoto University Institute for Advanced Study, Kyoto University, Kyoto, Japan
- Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan
- Center for Advanced Study, Kyoto University Institute for Advanced Study, Kyoto University, Kyoto, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology, Kyoto University Institute for Advanced Study, Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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17
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The trophectoderm acts as a niche for the inner cell mass through C/EBPα-regulated IL-6 signaling. Stem Cell Reports 2022; 17:1991-2004. [PMID: 35961310 PMCID: PMC9481899 DOI: 10.1016/j.stemcr.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/14/2022] [Accepted: 07/14/2022] [Indexed: 11/26/2022] Open
Abstract
IL-6 has been shown to be required for somatic cell reprogramming into induced pluripotent stem cells (iPSCs). However, how Il6 expression is regulated and whether it plays a role during embryo development remains unknown. Here, we describe that IL-6 is necessary for C/EBPα-enhanced reprogramming of B cells into iPSCs but not for B cell to macrophage transdifferentiation. C/EBPα overexpression activates both Il6 and Il6ra genes in B cells and in PSCs. In embryo development, Cebpa is enriched in the trophectoderm of blastocysts together with Il6, while Il6ra is mostly expressed in the inner cell mass (ICM). In addition, Il6 expression in blastocysts requires Cebpa. Blastocysts secrete IL-6 and neutralization of the cytokine delays the morula to blastocyst transition. The observed requirement of C/EBPα-regulated IL-6 signaling for pluripotency during somatic cell reprogramming thus recapitulates a physiologic mechanism in which the trophectoderm acts as niche for the ICM through the secretion of IL-6. IL-6 is required for the C/EBPα-enhanced B cell to iPSC reprogramming C/EBPα regulates the IL-6 signaling pathway during pluripotency acquisition A Cebpa-Il6 expression axis is conserved in mouse and human trophectoderm IL-6 signals to the Il6ra-expressing ICM and facilitates blastocyst development
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18
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Mizuta K, Katou Y, Nakakita B, Kishine A, Nosaka Y, Saito S, Iwatani C, Tsuchiya H, Kawamoto I, Nakaya M, Tsukiyama T, Nagano M, Kojima Y, Nakamura T, Yabuta Y, Horie A, Mandai M, Ohta H, Saitou M. Ex vivo reconstitution of fetal oocyte development in humans and cynomolgus monkeys. EMBO J 2022; 41:e110815. [PMID: 35912849 PMCID: PMC9475534 DOI: 10.15252/embj.2022110815] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/14/2022] Open
Abstract
In vitro oogenesis is key to elucidating the mechanism of human female germ-cell development and its anomalies. Accordingly, pluripotent stem cells have been induced into primordial germ cell-like cells and into oogonia with epigenetic reprogramming, yet further reconstitutions remain a challenge. Here, we demonstrate ex vivo reconstitution of fetal oocyte development in both humans and cynomolgus monkeys (Macaca fascicularis). With an optimized culture of fetal ovary reaggregates over three months, human and monkey oogonia enter and complete the first meiotic prophase to differentiate into diplotene oocytes that form primordial follicles, the source for oogenesis in adults. The cytological and transcriptomic progressions of fetal oocyte development in vitro closely recapitulate those in vivo. A comparison of single-cell transcriptomes among humans, monkeys, and mice unravels primate-specific and conserved programs driving fetal oocyte development, the former including a distinct transcriptomic transformation upon oogonia-to-oocyte transition and the latter including two active X chromosomes with little X-chromosome upregulation. Our study provides a critical step forward for realizing human in vitro oogenesis and uncovers salient characteristics of fetal oocyte development in primates.
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Affiliation(s)
- Ken Mizuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshitaka Katou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Baku Nakakita
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Aoi Kishine
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshiaki Nosaka
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Saki Saito
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Chizuru Iwatani
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Hideaki Tsuchiya
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Ikuo Kawamoto
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Masataka Nakaya
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Tomoyuki Tsukiyama
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Masahiro Nagano
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoji Kojima
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomonori Nakamura
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akihito Horie
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Ohta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
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19
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Seong J, Frias-Aldeguer J, Holzmann V, Kagawa H, Sestini G, Heidari Khoei H, Scholte Op Reimer Y, Kip M, Pradhan SJ, Verwegen L, Vivié J, Li L, Alemany A, Korving J, Darmis F, van Oudenaarden A, Ten Berge D, Geijsen N, Rivron NC. Epiblast inducers capture mouse trophectoderm stem cells in vitro and pattern blastoids for implantation in utero. Cell Stem Cell 2022; 29:1102-1118.e8. [PMID: 35803228 DOI: 10.1016/j.stem.2022.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/21/2022] [Accepted: 06/02/2022] [Indexed: 11/03/2022]
Abstract
The embryo instructs the allocation of cell states to spatially regulate functions. In the blastocyst, patterning of trophoblast (TR) cells ensures successful implantation and placental development. Here, we defined an optimal set of molecules secreted by the epiblast (inducers) that captures in vitro stable, highly self-renewing mouse trophectoderm stem cells (TESCs) resembling the blastocyst stage. When exposed to suboptimal inducers, these stem cells fluctuate to form interconvertible subpopulations with reduced self-renewal and facilitated differentiation, resembling peri-implantation cells, known as TR stem cells (TSCs). TESCs have enhanced capacity to form blastoids that implant more efficiently in utero due to inducers maintaining not only local TR proliferation and self-renewal, but also WNT6/7B secretion that stimulates uterine decidualization. Overall, the epiblast maintains sustained growth and decidualization potential of abutting TR cells, while, as known, distancing imposed by the blastocyst cavity differentiates TR cells for uterus adhesion, thus patterning the essential functions of implantation.
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Affiliation(s)
- Jinwoo Seong
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Javier Frias-Aldeguer
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands; Maastricht University, Maastricht, the Netherlands
| | - Viktoria Holzmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Harunobu Kagawa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Giovanni Sestini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Heidar Heidari Khoei
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria; Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Yvonne Scholte Op Reimer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Maarten Kip
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Saurabh J Pradhan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Lucas Verwegen
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Judith Vivié
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Linfeng Li
- Maastricht University, Maastricht, the Netherlands
| | - Anna Alemany
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Jeroen Korving
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Frank Darmis
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | | | - Derk Ten Berge
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Niels Geijsen
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands; Department of Anatomy and Embryology, LUMC, Leiden University, Leiden, the Netherlands
| | - Nicolas C Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria; Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands; Maastricht University, Maastricht, the Netherlands.
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20
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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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21
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Naitou Y, Nagamatsu G, Hamazaki N, Shirane K, Hayashi M, Hayashi M, Kobayashi S, Hayashi K. Dual role of Ovol2 on the germ cell lineage segregation during gastrulation in mouse embryogenesis. Development 2022; 149:274415. [DOI: 10.1242/dev.200319] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022]
Abstract
ABSTRACT
In mammals, primordial germ cells (PGCs), the origin of the germ line, are specified from the epiblast at the posterior region where gastrulation simultaneously occurs, yet the functional relationship between PGC specification and gastrulation remains unclear. Here, we show that OVOL2, a transcription factor conserved across the animal kingdom, balances these major developmental processes by repressing the epithelial-to-mesenchymal transition (EMT) that drives gastrulation and the upregulation of genes associated with PGC specification. Ovol2a, a splice variant encoding a repressor domain, directly regulates EMT-related genes and, consequently, induces re-acquisition of potential pluripotency during PGC specification, whereas Ovol2b, another splice variant missing the repressor domain, directly upregulates genes associated with PGC specification. Taken together, these results elucidate the molecular mechanism underlying allocation of the germ line among epiblast cells differentiating into somatic cells through gastrulation.
This article has an associated ‘The people behind the papers’ interview.
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Affiliation(s)
- Yuki Naitou
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Go Nagamatsu
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Nobuhiko Hamazaki
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kenjiro Shirane
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masafumi Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Makoto Hayashi
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Satoru Kobayashi
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Germline Genetics, Graduate School of Medicine, Osaka University, Suita 565-0871, Osaka, Japan
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22
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Okamoto I, Nakamura T, Sasaki K, Yabuta Y, Iwatani C, Tsuchiya H, Nakamura SI, Ema M, Yamamoto T, Saitou M. The X chromosome dosage compensation program during the development of cynomolgus monkeys. Science 2021; 374:eabd8887. [PMID: 34793202 DOI: 10.1126/science.abd8887] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Ikuhiro Okamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomonori Nakamura
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Hakubi Center for Advanced Research, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kotaro Sasaki
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Chizuru Iwatani
- Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Hideaki Tsuchiya
- Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Shin-Ichiro Nakamura
- Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Masatsugu Ema
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan.,Medical-Risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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23
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Herrera-Delgado E, Maître JL. A theoretical understanding of mammalian preimplantation development. Cells Dev 2021; 168:203752. [PMID: 34634520 DOI: 10.1016/j.cdev.2021.203752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022]
Abstract
The blastocyst has long been a hallmark system of study in developmental biology due to its importance in mammalian development and clinical relevance for assisted reproductive technologies. In recent years, the blastocyst is emerging as a system of study for mathematical modelling. In this review, we compile, to our knowledge, all models describing preimplantation development. Coupled with experiments, these models have provided insight regarding the morphogenesis and cell-fate specification throughout preimplantation development. In the case of cell-fate specification, theoretical models have provided mechanisms explaining how proportion of cell types are established and maintained when confronted to perturbations. For cell-shape based models, they have described quantitatively how mechanical forces sculpt the blastocyst and even predicted how morphogenesis could be manipulated. As theoretical biology develops, we believe the next critical stage in modelling involves an integration of cell fate and mechanics to provide integrative models of development at distinct spatiotemporal scales. We discuss how, building on a balanced base of mechanical and chemical models, the preimplantation embryo will play a key role in integrating these two faces of the same coin.
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Affiliation(s)
| | - Jean-Léon Maître
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France.
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24
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In vitro reconstitution of the whole male germ-cell development from mouse pluripotent stem cells. Cell Stem Cell 2021; 28:2167-2179.e9. [PMID: 34496297 DOI: 10.1016/j.stem.2021.08.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/25/2021] [Accepted: 08/09/2021] [Indexed: 01/08/2023]
Abstract
Mammalian male germ-cell development consists of three distinct phases: primordial germ cell (PGC) development, male germ-cell specification for spermatogonium development, and ensuing spermatogenesis. Here, we show an in vitro reconstitution of whole male germ-cell development by pluripotent stem cells (PSCs). Mouse embryonic stem cells (mESCs) are induced into PGC-like cells (mPGCLCs), which are expanded for epigenetic reprogramming. In reconstituted testes under an optimized condition, such mPGCLCs differentiate into spermatogonium-like cells with proper developmental transitions, gene expression, and cell-cycle dynamics and are expanded robustly as germline stem cell-like cells (GSCLCs) with an appropriate androgenetic epigenome. Importantly, GSCLCs show vigorous spermatogenesis, not only upon transplantation into testes in vivo but also under an in vitro culture of testis transplants, and the resultant spermatids contribute to fertile offspring. By uniting faithful recapitulations of the three phases of male germ-cell development, our study creates a paradigm for the in vitro male gametogenesis by PSCs.
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25
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Aramaki S, Kagiwada S, Wu G, Obridge D, Adachi K, Kutejova E, Lickert H, Hübner K, Schöler HR. Residual pluripotency is required for inductive germ cell segregation. EMBO Rep 2021; 22:e52553. [PMID: 34156139 PMCID: PMC8344911 DOI: 10.15252/embr.202152553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/31/2022] Open
Abstract
Fine‐tuned dissolution of pluripotency is critical for proper cell differentiation. Here we show that the mesodermal transcription factor, T, globally affects the properties of pluripotency through binding to Oct4 and to the loci of other pluripotency regulators. Strikingly, lower T levels coordinately affect naïve pluripotency, thereby directly activating the germ cell differentiation program, in contrast to the induction of germ cell fate of primed models. Contrary to the effect of lower T levels, higher T levels more severely affect the pluripotency state, concomitantly enhancing the somatic differentiation program and repressing the germ cell differentiation program. Consistent with such in vitro findings, nascent germ cells in vivo are detected in the region of lower T levels at the posterior primitive streak. Furthermore, T and core pluripotency regulators co‐localize at the loci of multiple germ cell determinants responsible for germ cell development. In conclusion, our findings indicate that residual pluripotency establishes the earliest and fundamental regulatory mechanism for inductive germline segregation from somatic lineages.
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Affiliation(s)
- Shinya Aramaki
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Saya Kagiwada
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - David Obridge
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Kenjiro Adachi
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Eva Kutejova
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Heiko Lickert
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Karin Hübner
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Medical Faculty, University of Münster, Münster, Germany
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26
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Yang Y, He JP, Liu JL. Cell-Cell Communication at the Embryo Implantation Site of Mouse Uterus Revealed by Single-Cell Analysis. Int J Mol Sci 2021; 22:5177. [PMID: 34068395 PMCID: PMC8153605 DOI: 10.3390/ijms22105177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/09/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
As a crucial step for human reproduction, embryo implantation is a low-efficiency process. Despite rapid advances in recent years, the molecular mechanism underlying embryo implantation remains poorly understood. Here, we used the mouse as an animal model and generated a single-cell transcriptomic atlas of embryo implantation sites. By analyzing inter-implantation sites of the uterus as control, we were able to identify global gene expression changes associated with embryo implantation in each cell type. Additionally, we predicted signaling interactions between uterine luminal epithelial cells and mural trophectoderm of blastocysts, which represent the key mechanism of embryo implantation. We also predicted signaling interactions between uterine epithelial-stromal crosstalk at implantation sites, which are crucial for post-implantation development. Our data provide a valuable resource for deciphering the molecular mechanism underlying embryo implantation.
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Affiliation(s)
- Yi Yang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China;
| | - Jia-Peng He
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
| | - Ji-Long Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
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27
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Sasaki K, Oguchi A, Cheng K, Murakawa Y, Okamoto I, Ohta H, Yabuta Y, Iwatani C, Tsuchiya H, Yamamoto T, Seita Y, Saitou M. The embryonic ontogeny of the gonadal somatic cells in mice and monkeys. Cell Rep 2021; 35:109075. [PMID: 33951437 DOI: 10.1016/j.celrep.2021.109075] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/21/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
In the early fetal stage, the gonads are bipotent and only later become the ovary or testis, depending on the genetic sex. Despite many studies examining how sex determination occurs from biopotential gonads, the spatial and temporal organization of bipotential gonads and their progenitors is poorly understood. Here, using lineage tracing in mice, we find that the gonads originate from a T+ primitive streak through WT1+ posterior intermediate mesoderm and appear to share origins anteriorly with the adrenal glands and posteriorly with the metanephric mesenchyme. Comparative single-cell transcriptomic analyses in mouse and cynomolgus monkey embryos reveal the convergence of the lineage trajectory and genetic programs accompanying the specification of biopotential gonadal progenitor cells. This process involves sustained expression of epithelial genes and upregulation of mesenchymal genes, thereby conferring an epithelial-mesenchymal hybrid state. Our study provides key resources for understanding early gonadogenesis in mice and primates.
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Affiliation(s)
- Kotaro Sasaki
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Akiko Oguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Keren Cheng
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Ikuhiro Okamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroshi Ohta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Chizuru Iwatani
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan
| | - Hideaki Tsuchiya
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan; Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; AMED-CREST, AMED, Tokyo 100-0004, Japan; Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Yasunari Seita
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Bell Research Center for Reproductive Health and Cancer, Nagoya 460-0003, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
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28
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Io S, Kabata M, Iemura Y, Semi K, Morone N, Minagawa A, Wang B, Okamoto I, Nakamura T, Kojima Y, Iwatani C, Tsuchiya H, Kaswandy B, Kondoh E, Kaneko S, Woltjen K, Saitou M, Yamamoto T, Mandai M, Takashima Y. Capturing human trophoblast development with naive pluripotent stem cells in vitro. Cell Stem Cell 2021; 28:1023-1039.e13. [PMID: 33831365 DOI: 10.1016/j.stem.2021.03.013] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/05/2021] [Accepted: 03/15/2021] [Indexed: 01/06/2023]
Abstract
Trophoblasts are extraembryonic cells that are essential for maintaining pregnancy. Human trophoblasts arise from the morula as trophectoderm (TE), which, after implantation, differentiates into cytotrophoblasts (CTs), syncytiotrophoblasts (STs), and extravillous trophoblasts (EVTs), composing the placenta. Here we show that naïve, but not primed, human pluripotent stem cells (PSCs) recapitulate trophoblast development. Naive PSC-derived TE and CTs (nCTs) recreated human and monkey TE-to-CT transition. nCTs self-renewed as CT stem cells and had the characteristics of proliferating villous CTs and CTs in the cell column of the first trimester. Notably, although primed PSCs differentiated into trophoblast-like cells (BMP4, A83-01, and PD173074 [BAP]-treated primed PSCs [pBAPs]), pBAPs were distinct from nCTs and human placenta-derived CT stem cells, exhibiting properties consistent with the amnion. Our findings establish an authentic paradigm for human trophoblast development, demonstrating the invaluable properties of naive human PSCs. Our system provides a platform to study the molecular mechanisms underlying trophoblast development and related diseases.
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Affiliation(s)
- Shingo Io
- Department of Life Science Frontiers, CiRA, Kyoto University, Kyoto 606-8507, Japan; Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan; Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Mio Kabata
- Department of Life Science Frontiers, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshiki Iemura
- Department of Life Science Frontiers, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Katsunori Semi
- Department of Life Science Frontiers, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Nobuhiro Morone
- MRC Toxicology Unit, University of Cambridge, Cambridge CB2 1QR, UK
| | - Atsutaka Minagawa
- Department of Cell Growth and Differentiation, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Bo Wang
- Department of Cell Growth and Differentiation, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Ikuhiro Okamoto
- Department of Anatomy and Cell Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Tomonori Nakamura
- Department of Anatomy and Cell Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan; The HAKUBI Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan
| | - Yoji Kojima
- Department of Life Science Frontiers, CiRA, Kyoto University, Kyoto 606-8507, Japan; Department of Anatomy and Cell Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Chizuru Iwatani
- Research Center for Animal Life Science, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Hideaki Tsuchiya
- Research Center for Animal Life Science, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Belinda Kaswandy
- Department of Life Science Frontiers, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Eiji Kondoh
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Shin Kaneko
- Department of Cell Growth and Differentiation, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, CiRA, Kyoto University, Kyoto 606-8507, Japan
| | - Mitinori Saitou
- Department of Life Science Frontiers, CiRA, Kyoto University, Kyoto 606-8507, Japan; Department of Anatomy and Cell Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, CiRA, Kyoto University, Kyoto 606-8507, Japan; Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan; AMED-CREST, AMED, Tokyo 100-0004, Japan; Medical Risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Projects (AIP), Kyoto 606-8507, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Yasuhiro Takashima
- Department of Life Science Frontiers, CiRA, Kyoto University, Kyoto 606-8507, Japan.
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29
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Kojima Y, Yamashiro C, Murase Y, Yabuta Y, Okamoto I, Iwatani C, Tsuchiya H, Nakaya M, Tsukiyama T, Nakamura T, Yamamoto T, Saitou M. GATA transcription factors, SOX17 and TFAP2C, drive the human germ-cell specification program. Life Sci Alliance 2021; 4:4/5/e202000974. [PMID: 33608411 PMCID: PMC7918644 DOI: 10.26508/lsa.202000974] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/07/2021] [Accepted: 02/05/2021] [Indexed: 12/28/2022] Open
Abstract
This work shows that GATA transcription factors transduce the BMP signaling and, with SOX17 and TFAP2C, induce the human germ-cell fate, delineating the mechanism for human germ-cell specification. The in vitro reconstitution of human germ-cell development provides a robust framework for clarifying key underlying mechanisms. Here, we explored transcription factors (TFs) that engender the germ-cell fate in their pluripotent precursors. Unexpectedly, SOX17, TFAP2C, and BLIMP1, which act under the BMP signaling and are indispensable for human primordial germ-cell-like cell (hPGCLC) specification, failed to induce hPGCLCs. In contrast, GATA3 or GATA2, immediate BMP effectors, combined with SOX17 and TFAP2C, generated hPGCLCs. GATA3/GATA2 knockouts dose-dependently impaired BMP-induced hPGCLC specification, whereas GATA3/GATA2 expression remained unaffected in SOX17, TFAP2C, or BLIMP1 knockouts. In cynomolgus monkeys, a key model for human development, GATA3, SOX17, and TFAP2C were co-expressed exclusively in early PGCs. Crucially, the TF-induced hPGCLCs acquired a hallmark of bona fide hPGCs to undergo epigenetic reprogramming and mature into oogonia/gonocytes in xenogeneic reconstituted ovaries. By uncovering a TF circuitry driving the germ line program, our study provides a paradigm for TF-based human gametogenesis.
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Affiliation(s)
- Yoji Kojima
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan .,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin-Kawahara-cho, Kyoto, Japan
| | - Chika Yamashiro
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan
| | - Yusuke Murase
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan
| | - Ikuhiro Okamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan
| | - Chizuru Iwatani
- Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Japan
| | - Hideaki Tsuchiya
- Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Japan
| | - Masataka Nakaya
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan.,Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Japan
| | - Tomoyuki Tsukiyama
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan.,Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Japan
| | - Tomonori Nakamura
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan.,The Hakubi Center for Advanced Research, Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin-Kawahara-cho, Kyoto, Japan.,AMED-CREST, AMED, Tokyo, Japan.,Medical-Risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan .,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin-Kawahara-cho, Kyoto, Japan
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30
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Liu T, Li J, Yu L, Sun HX, Li J, Dong G, Hu Y, Li Y, Shen Y, Wu J, Gu Y. Cross-species single-cell transcriptomic analysis reveals pre-gastrulation developmental differences among pigs, monkeys, and humans. Cell Discov 2021; 7:8. [PMID: 33531465 PMCID: PMC7854681 DOI: 10.1038/s41421-020-00238-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Interspecies blastocyst complementation enables organ-specific enrichment of xenogeneic pluripotent stem cell (PSC) derivatives, which raises an intriguing possibility to generate functional human tissues/organs in an animal host. However, differences in embryo development between human and host species may constitute the barrier for efficient chimera formation. Here, to understand these differences we constructed a complete single-cell landscape of early embryonic development of pig, which is considered one of the best host species for human organ generation, and systematically compared its epiblast development with that of human and monkey. Our results identified a developmental coordinate of pluripotency spectrum among pigs, humans and monkeys, and revealed species-specific differences in: (1) pluripotency progression; (2) metabolic transition; (3) epigenetic and transcriptional regulations of pluripotency; (4) cell surface proteins; and (5) trophectoderm development. These differences may prevent proper recognition and communication between donor human cells and host pig embryos, resulting in low integration and survival of human cells. These results offer new insights into evolutionary conserved and divergent processes during mammalian development and may be helpful for developing effective strategies to overcome low human-pig chimerism, thereby enabling the generation of functional human organs in pigs in the future.
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Affiliation(s)
- Tianbin Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Jie Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Leqian Yu
- 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
| | - Hai-Xi Sun
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Jing Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Guoyi Dong
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Yingying Hu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Yong Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. .,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Ying Gu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China. .,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China. .,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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31
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Lieberman B, Kusi M, Hung CN, Chou CW, He N, Ho YY, Taverna JA, Huang THM, Chen CL. Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2021; 5:1-21. [PMID: 34322662 PMCID: PMC8315474 DOI: 10.20517/jtgg.2020.51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Among single-cell analysis technologies, single-cell RNA-seq (scRNA-seq) has been one of the front runners in technical inventions. Since its induction, scRNA-seq has been well received and undergone many fast-paced technical improvements in cDNA synthesis and amplification, processing and alignment of next generation sequencing reads, differentially expressed gene calling, cell clustering, subpopulation identification, and developmental trajectory prediction. scRNA-seq has been exponentially applied to study global transcriptional profiles in all cell types in humans and animal models, healthy or with diseases, including cancer. Accumulative novel subtypes and rare subpopulations have been discovered as potential underlying mechanisms of stochasticity, differentiation, proliferation, tumorigenesis, and aging. scRNA-seq has gradually revealed the uncharted territory of cellular heterogeneity in transcriptomes and developed novel therapeutic approaches for biomedical applications. This review of the advancement of scRNA-seq methods provides an exploratory guide of the quickly evolving technical landscape and insights of focused features and strengths in each prominent area of progress.
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Affiliation(s)
- Brandon Lieberman
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Meena Kusi
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Chia-Nung Hung
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Chih-Wei Chou
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Ning He
- Department of Nursing, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yen-Yi Ho
- Department of Statistics, University of South Carolina, Columbia, SC 29208, USA
| | - Josephine A. Taverna
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Tim H. M. Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Chun-Liang Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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32
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Ohta H, Yabuta Y, Kurimoto K, Nakamura T, Murase Y, Yamamoto T, Saitou M. Cyclosporin A and FGF signaling support the proliferation/survival of mouse primordial germ cell-like cells in vitro†. Biol Reprod 2020; 104:344-360. [PMID: 33079185 DOI: 10.1093/biolre/ioaa195] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/29/2020] [Accepted: 10/19/2020] [Indexed: 01/20/2023] Open
Abstract
Primordial germ cells (PGCs) are the founding population of the germ cell lineage that undergo a multistep process to generate spermatozoa or oocytes. Establishing an appropriate culture system for PGCs is a key challenge in reproductive biology. By a chemical screening using mouse PGC-like cells (mPGCLCs), which were induced from mouse embryonic stem cells, we reported previously that forskolin and rolipram synergistically enhanced the proliferation/survival of mPGCLCs with an average expansion rate of ~20-fold. In the present study, we evaluated other chemicals or cytokines to see whether they would improve the current mPGCLC culture system. Among the chemicals and cytokines examined, in the presence of forskolin and rolipram, cyclosporin A (CsA) and fibroblast growth factors (FGFs: FGF2 and FGF10) effectively enhanced the expansion of mPGCLCs in vitro (~50-fold on average). During the expansion by CsA or FGFs, mPGCLCs comprehensively erased their DNA methylation to acquire a profile equivalent to that of gonadal germ cells in vivo, while maintaining their highly motile phenotype as well as their transcriptional properties as sexually uncommitted PGCs. Importantly, these mPGCLCs robustly contributed to spermatogenesis and produced fertile offspring. Furthermore, mouse PGCs (mPGCs) cultured with CsA ex vivo showed transcriptomes and DNA methylomes similar to those of cultured mPGCLCs. The improved culture system for mPGCLCs/mPGCs would be instructive for addressing key questions in PGC biology, including the mechanisms for germ cell migration, epigenetic reprogramming, and sex determination of the germline.
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Affiliation(s)
- Hiroshi Ohta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuki Kurimoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Embryology, Nara Medical University, Nara, Japan
| | - Tomonori Nakamura
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Murase
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.,The Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology, Tokyo, Japan.,Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project, Kyoto, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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33
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Murase Y, Yabuta Y, Ohta H, Yamashiro C, Nakamura T, Yamamoto T, Saitou M. Long-term expansion with germline potential of human primordial germ cell-like cells in vitro. EMBO J 2020; 39:e104929. [PMID: 32954504 DOI: 10.15252/embj.2020104929] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/22/2022] Open
Abstract
Human germ cells perpetuate human genetic and epigenetic information. However, the underlying mechanism remains elusive, due to a lack of appropriate experimental systems. Here, we show that human primordial germ cell-like cells (hPGCLCs) derived from human-induced pluripotent stem cells (hiPSCs) can be propagated to at least ~106 -fold over a period of 4 months under a defined condition in vitro. During expansion, hPGCLCs maintain an early hPGC-like transcriptome and preserve their genome-wide DNA methylation profiles, most likely due to retention of maintenance DNA methyltransferase activity. These characteristics contrast starkly with those of mouse PGCLCs, which, under an analogous condition, show a limited propagation (up to ~50-fold) and persist only around 1 week, yet undergo cell-autonomous genome-wide DNA demethylation. Importantly, upon aggregation culture with mouse embryonic ovarian somatic cells in xenogeneic-reconstituted ovaries, expanded hPGCLCs initiate genome-wide DNA demethylation and differentiate into oogonia/gonocyte-like cells, demonstrating their germline potential. By creating a paradigm for hPGCLC expansion, our study uncovers critical divergences in expansion potential and the mechanism for epigenetic reprogramming between the human and mouse germ cell lineage.
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Affiliation(s)
- Yusuke Murase
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Ohta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Chika Yamashiro
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomonori Nakamura
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,AMED-CREST, AMED, Tokyo, Japan.,Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
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34
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Mahadevaiah SK, Sangrithi MN, Hirota T, Turner JMA. A single-cell transcriptome atlas of marsupial embryogenesis and X inactivation. Nature 2020; 586:612-617. [PMID: 32814901 DOI: 10.1038/s41586-020-2629-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/20/2020] [Indexed: 11/09/2022]
Abstract
Single-cell RNA sequencing of embryos can resolve the transcriptional landscape of development at unprecedented resolution. To date, single-cell RNA-sequencing studies of mammalian embryos have focused exclusively on eutherian species. Analysis of mammalian outgroups has the potential to identify deeply conserved lineage specification and pluripotency factors, and can extend our understanding of X dosage compensation. Metatherian (marsupial) mammals diverged from eutherians around 160 million years ago. They exhibit distinctive developmental features, including late implantation1 and imprinted X chromosome inactivation2, which is associated with expression of the XIST-like noncoding RNA RSX3. Here we perform a single-cell RNA-sequencing analysis of embryogenesis and X chromosome inactivation in a marsupial, the grey short-tailed opossum (Monodelphis domestica). We resolve the developmental trajectory and transcriptional signatures of the epiblast, primitive endoderm and trophectoderm, and identify deeply conserved lineage-specific markers that pre-date the eutherian-marsupial divergence. RSX coating and inactivation of the X chromosome occurs early and rapidly. This observation supports the hypothesis that-in organisms with early X chromosome inactivation-imprinted X chromosome inactivation prevents biallelic X silencing. We identify XSR, an RSX antisense transcript expressed from the active X chromosome, as a candidate for the regulator of imprinted X chromosome inactivation. Our datasets provide insights into the evolution of mammalian embryogenesis and X dosage compensation.
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Affiliation(s)
| | - Mahesh N Sangrithi
- Division of Obstetrics and Gynaecology, KK Women's and Children's Hospital, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Takayuki Hirota
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK.
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35
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Sozen B, Cox AL, De Jonghe J, Bao M, Hollfelder F, Glover DM, Zernicka-Goetz M. Self-Organization of Mouse Stem Cells into an Extended Potential Blastoid. Dev Cell 2020; 51:698-712.e8. [PMID: 31846649 DOI: 10.1016/j.devcel.2019.11.014] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/10/2019] [Accepted: 11/19/2019] [Indexed: 11/18/2022]
Abstract
Mammalian blastocysts comprise three distinct cell lineages essential for development beyond implantation: the pluripotent epiblast, which generates the future embryo, and surrounding it the extra-embryonic primitive endoderm and the trophectoderm tissues. Embryonic stem cells can reintegrate into embryogenesis but contribute primarily to epiblast lineages. Here, we show that mouse embryonic stem cells cultured under extended pluripotent conditions (EPSCs) can be partnered with trophoblast stem cells to self-organize into blastocyst-like structures with all three embryonic and extra-embryonic lineages. Morphogenetic and transcriptome profiling analyses reveal that these blastocyst-like structures show distinct embryonic-abembryonic axes and primitive endoderm differentiation and can initiate the transition from the pre- to post-implantation egg cylinder morphology in vitro.
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Affiliation(s)
- Berna Sozen
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Andy L Cox
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Joachim De Jonghe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Min Bao
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - David M Glover
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Magdalena Zernicka-Goetz
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
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36
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Yang F, Liu Z, Zhao M, Mu Q, Che T, Xie Y, Ma L, Mi L, Li J, Zhao Y. Skin transcriptome reveals the periodic changes in genes underlying cashmere (ground hair) follicle transition in cashmere goats. BMC Genomics 2020; 21:392. [PMID: 32503427 PMCID: PMC7275469 DOI: 10.1186/s12864-020-06779-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
Background Cashmere goats make an outstanding contribution to the livestock textile industry and their cashmere is famous for its slenderness and softness and has been extensively studied. However, there are few reports on the molecular regulatory mechanisms of the secondary hair follicle growth cycle in cashmere goats. In order to explore the regular transition through the follicle cycle and the role of key genes in this cycle, we used a transcriptome sequencing technique to sequence the skin of Inner Mongolian cashmere goats during different months. We analyzed the variation and difference in genes throughout the whole hair follicle cycle. We then verified the regulatory mechanism of the cashmere goat secondary hair follicle growth cycle using fluorescence quantitative PCR. Results The growth cycle of cashmere hair could be divided into three distinct periods: a growth period (March–September), a regression period (September–December), and a resting period (December–March). The results of differential gene analyses showed that March was the most significant month. Cluster analysis of gene expression throughout the whole growth cycle further supported the key nodes of the three periods of cashmere growth, and the differential gene expression of keratin corresponding to the ground haircashmere growth cycle further supported the results from tissue slices. Quantitative fluorescence analysis showed that KAP3–1, KRTAP 8–1, and KRTAP 24–1 genes had close positive correlation with the cashmere growth cycle, and their regulation was consistent with the growth cycle of cashmere. Conclusion The growth cycle of cashmere cashmere could be divided into three distinct periods: a growth period (March–September), a regression period (September–December) and a resting period (December–March). March was considered to be the beginning of the cycle. KAP and KRTAP showed close positive correlation with the growth cycle of secondary hair follicle cashmere growth, and their regulation was consistent with the cashmere growth cycle. But hair follicle development-related genes are expressed earlier than cashmere growth, indicating that cycle regulation could alter the temporal growth of cashmere. This study laid a theoretical foundation for the study of the cashmere development cycle and provided evidence for key genes during transition through the cashmere cycle. Our study provides a theoretical basis for cashmere goat breeding.
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Affiliation(s)
- Feng Yang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Meng Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Qing Mu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Tianyu Che
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yuchun Xie
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lina Ma
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lu Mi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
| | - Yanhong Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
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37
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Chakraborty C, Bhattacharya M, Agoramoorthy G. Single-cell sequencing of miRNAs: A modified technology. Cell Biol Int 2020; 44:1773-1780. [PMID: 32379363 DOI: 10.1002/cbin.11376] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 03/07/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022]
Abstract
The recent development of next-generation sequencing technologies has offered valuable insights into individual cells. This technology is centered on the characterization of single cells for epigenomics, genomics, and transcriptomics. Ever since the first report appeared in 2009, the single-cell RNA-sequencing saga started to explore deeper into the mechanics intrigued within a single cell. microRNA (miRNA) has been increasingly recognized as an essential molecule triggering an additional layer for gene regulation. Therefore, single-cell sequencing of miRNAs is crucial to explore the logical riddles surrounding the epigenomics, genomics, and transcriptomics of an individual cell. Scientists from the Vienna Biocenter Campus have lately performed single-cell sequencing of miRNAs in the fly, Drosophila, and nematode, Caenorhabditis elegans. In this review, we present the latest scientific explorations supported by all-inclusive data on this novel subject matter of next-generation sequencing.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, Odisha, India
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38
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Lau KX, Mason EA, Kie J, De Souza DP, Kloehn J, Tull D, McConville MJ, Keniry A, Beck T, Blewitt ME, Ritchie ME, Naik SH, Zalcenstein D, Korn O, Su S, Romero IG, Spruce C, Baker CL, McGarr TC, Wells CA, Pera MF. Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal. Nat Commun 2020; 11:2420. [PMID: 32415101 PMCID: PMC7229198 DOI: 10.1038/s41467-020-16214-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/16/2020] [Indexed: 01/06/2023] Open
Abstract
Archetypal human pluripotent stem cells (hPSC) are widely considered to be equivalent in developmental status to mouse epiblast stem cells, which correspond to pluripotent cells at a late post-implantation stage of embryogenesis. Heterogeneity within hPSC cultures complicates this interspecies comparison. Here we show that a subpopulation of archetypal hPSC enriched for high self-renewal capacity (ESR) has distinct properties relative to the bulk of the population, including a cell cycle with a very low G1 fraction and a metabolomic profile that reflects a combination of oxidative phosphorylation and glycolysis. ESR cells are pluripotent and capable of differentiation into primordial germ cell-like cells. Global DNA methylation levels in the ESR subpopulation are lower than those in mouse epiblast stem cells. Chromatin accessibility analysis revealed a unique set of open chromatin sites in ESR cells. RNA-seq at the subpopulation and single cell levels shows that, unlike mouse epiblast stem cells, the ESR subset of hPSC displays no lineage priming, and that it can be clearly distinguished from gastrulating and extraembryonic cell populations in the primate embryo. ESR hPSC correspond to an earlier stage of post-implantation development than mouse epiblast stem cells. Human pluripotent cells (hPSCs) in standard culture are similar to mouse epiblast cells, but heterogeneity within hPSC cultures complicates comparisons. Here the authors show that a subpopulation of hPSCs enriched for self-renewal capacity have distinct cell cycle, metabolic, DNA methylation, and ATAC-seq profiles.
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Affiliation(s)
- Kevin X Lau
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Elizabeth A Mason
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Joshua Kie
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - David P De Souza
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Joachim Kloehn
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Dedreia Tull
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Malcolm J McConville
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Andrew Keniry
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Tamara Beck
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Marnie E Blewitt
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Matthew E Ritchie
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Shalin H Naik
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Daniela Zalcenstein
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Othmar Korn
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Shian Su
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Irene Gallego Romero
- Melbourne Integrative Genomics, School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | | | | | | | - Christine A Wells
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Divisions of Cancer and Hematology and Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Martin F Pera
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia. .,Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia. .,The Jackson Laboratory, Bar Harbor, ME, 04609, USA. .,The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, Parkville, Victoria, 3052, Australia.
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O'Neill K, Brocks D, Hammell MG. Mobile genomics: tools and techniques for tackling transposons. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190345. [PMID: 32075565 PMCID: PMC7061981 DOI: 10.1098/rstb.2019.0345] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2019] [Indexed: 12/22/2022] Open
Abstract
Next-generation sequencing approaches have fundamentally changed the types of questions that can be asked about gene function and regulation. With the goal of approaching truly genome-wide quantifications of all the interaction partners and downstream effects of particular genes, these quantitative assays have allowed for an unprecedented level of detail in exploring biological interactions. However, many challenges remain in our ability to accurately describe and quantify the interactions that take place in those hard to reach and extremely repetitive regions of our genome comprised mostly of transposable elements (TEs). Tools dedicated to TE-derived sequences have lagged behind, making the inclusion of these sequences in genome-wide analyses difficult. Recent improvements, both computational and experimental, allow for the better inclusion of TE sequences in genomic assays and a renewed appreciation for the importance of TE biology. This review will discuss the recent improvements that have been made in the computational analysis of TE-derived sequences as well as the areas where such analysis still proves difficult. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Kathryn O'Neill
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David Brocks
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
| | - Molly Gale Hammell
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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40
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Kobayashi T, Kobayashi H, Goto T, Takashima T, Oikawa M, Ikeda H, Terada R, Yoshida F, Sanbo M, Nakauchi H, Kurimoto K, Hirabayashi M. Germline development in rat revealed by visualization and deletion of Prdm14. Development 2020; 147:dev.183798. [PMID: 32001439 DOI: 10.1242/dev.183798] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/15/2020] [Indexed: 12/22/2022]
Abstract
Primordial germ cells (PGCs), the founder cells of the germline, are specified in pre-gastrulating embryos in mammals, and subsequently migrate towards gonads to mature into functional gametes. Here, we investigated PGC development in rats, by genetically modifying Prdm14, a unique marker and an essential PGC transcriptional regulator. We trace PGC development in rats, for the first time, from specification until the sex determination stage in fetal gonads using Prdm14 H2BVenus knock-in rats. We uncover that the crucial role of Prdm14 in PGC specification is conserved between rat and mice, by analyzing Prdm14-deficient rat embryos. Notably, loss of Prdm14 completely abrogates the PGC program, as demonstrated by failure of the maintenance and/or activation of germ cell markers and pluripotency genes. Finally, we profile the transcriptome of the post-implantation epiblast and all PGC stages in rat to reveal enrichment of distinct gene sets at each transition point, thereby providing an accurate transcriptional timeline for rat PGC development. Thus, the novel genetically modified rats and data sets obtained in this study will advance our knowledge on conserved versus species-specific features for germline development in mammals.
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Affiliation(s)
- Toshihiro Kobayashi
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan.,Department of Physiological Sciences, The Graduate University of Advanced Studies, Okazaki, 444-8787 Aichi, Japan
| | - Hisato Kobayashi
- Department of Embryology, Nara Medical University, Kashihara, 634-0813 Nara, Japan
| | - Teppei Goto
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Tomoya Takashima
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, 156-8502 Tokyo, Japan
| | - Mami Oikawa
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Hiroki Ikeda
- Department of Embryology, Nara Medical University, Kashihara, 634-0813 Nara, Japan
| | - Reiko Terada
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Fumika Yoshida
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Makoto Sanbo
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Institute of Medical Science, The University of Tokyo, Minato-ku, 108-8639 Tokyo, Japan.,Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Kashihara, 634-0813 Nara, Japan
| | - Masumi Hirabayashi
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan .,Department of Physiological Sciences, The Graduate University of Advanced Studies, Okazaki, 444-8787 Aichi, Japan
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41
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Abstract
Cells, the basic units of life, have striking differences at transcriptomic, proteomic and epigenomic levels across tissues, organs, organ systems and organisms. The coordination of individual immune cells is essential for the generation of effective immune responses to pathogens while immune tolerance is maintained to protect the host. In rheumatic diseases, when immune responses are dysregulated, pathologically important cells might represent only a small fraction of the immune system. Interrogation of the contributions of individual immune cells to pathogenesis and disease progression should therefore reveal important insights into the complicated aetiology of rheumatic diseases. Technological advances are enabling the high-dimensional dissection of single cells at multiple omics levels, which could facilitate the identification of dysregulated molecular mechanisms in patients with rheumatic diseases and the discovery of new therapeutic targets and biomarkers. The single-cell technologies that have been developed over the past decade and the experimental platforms that enable multi-omics integrative analyses have already made inroads into immunology-related fields of study and have potential for use in rheumatology. Layers of omics data derived from single cells are likely to fundamentally change our understanding of the molecular pathways that underpin the pathogenesis of rheumatic diseases.
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Nagaoka SI, Nakaki F, Miyauchi H, Nosaka Y, Ohta H, Yabuta Y, Kurimoto K, Hayashi K, Nakamura T, Yamamoto T, Saitou M. ZGLP1 is a determinant for the oogenic fate in mice. Science 2020; 367:science.aaw4115. [PMID: 32054698 DOI: 10.1126/science.aaw4115] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 10/17/2019] [Accepted: 01/31/2020] [Indexed: 11/03/2022]
Abstract
Sex determination of germ cells is vital to creating the sexual dichotomy of germ cell development, thereby ensuring sexual reproduction. However, the underlying mechanisms remain unclear. Here, we show that ZGLP1, a conserved transcriptional regulator with GATA-like zinc fingers, determines the oogenic fate in mice. ZGLP1 acts downstream of bone morphogenetic protein, but not retinoic acid (RA), and is essential for the oogenic program and meiotic entry. ZGLP1 overexpression induces differentiation of in vitro primordial germ cell-like cells (PGCLCs) into fetal oocytes by activating the oogenic programs repressed by Polycomb activities, whereas RA signaling contributes to oogenic program maturation and PGC program repression. Our findings elucidate the mechanism for mammalian oogenic fate determination, providing a foundation for promoting in vitro gametogenesis and reproductive medicine.
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Affiliation(s)
- So I Nagaoka
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fumio Nakaki
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hidetaka Miyauchi
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshiaki Nosaka
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Ohta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuki Kurimoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Katsuhiko Hayashi
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomonori Nakamura
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.,Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, 606-8507, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan. .,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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43
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Kang K, Wang X, Meng C, He L, Sang X, Zheng Y, Xu H. The application of single-cell sequencing technology in the diagnosis and treatment of hepatocellular carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:790. [PMID: 32042806 DOI: 10.21037/atm.2019.11.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-cell sequencing technology refers to the sequencing of the genome, transcriptome and epigenome in one single cell. Comparing to traditional histology, single-cell sequencing can reveal the genetic heterogeneity among different cells. Due to the complex pathogenesis and various pathological types of hepatocellular carcinoma (HCC), studies on the heterogeneity of tumor cells confer improvement for its clinical diagnosis, treatment and prognosis. This article summarizes the principal basis and development of single-cell sequencing technology, as well as its increasing application in the field of HCC.
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Affiliation(s)
- Kai Kang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xuezhu Wang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Chan Meng
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Li He
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xinting Sang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yongchang Zheng
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Haifeng Xu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Matuła K, Rivello F, Huck WTS. Single-Cell Analysis Using Droplet Microfluidics. ACTA ACUST UNITED AC 2019; 4:e1900188. [PMID: 32293129 DOI: 10.1002/adbi.201900188] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/30/2019] [Indexed: 12/12/2022]
Abstract
Droplet microfluidics has revolutionized the study of single cells. The ability to compartmentalize cells within picoliter droplets in microfluidic devices has opened up a wide range of strategies to extract information at the genomic, transcriptomic, proteomic, or metabolomic level from large numbers of individual cells. Studying the different molecular landscapes at single-cell resolution has provided the authors with a detailed picture of intracellular heterogeneity and the resulting changes in cellular phenotypes. In addition, these technologies have aided in the discovery of rare cells in tumors or in the immune system, and left the authors with a deeper understanding of the fundamental biological processes that determine cell fate. This review aims to provide a detailed overview of the various droplet microfluidic strategies reported in the literature, taking into account the sometimes subtle differences in workflow or reagents that enable or improve certain protocols. Specifically, approaches to targeted- and whole-genome analysis, as well as whole-transcriptome profiling techniques, are reviewed. In addition, an up-to-date overview of new methods to characterize and quantify single-cell protein levels, and of developments to screen secreted molecules such as antibodies, cytokines, or metabolites at the single-cell level, is provided.
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Affiliation(s)
- Kinga Matuła
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Francesca Rivello
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
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Induction of the germ cell fate from pluripotent stem cells in cynomolgus monkeys†. Biol Reprod 2019; 102:620-638. [DOI: 10.1093/biolre/ioz205] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/30/2019] [Accepted: 10/19/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract
In vitro reconstitution of germ-cell development from pluripotent stem cells (PSCs) has created key opportunities to explore the fundamental mechanisms underlying germ-cell development, particularly in mice and humans. Importantly, such investigations have clarified critical species differences in the mechanisms regulating mouse and human germ-cell development, highlighting the necessity of establishing an in vitro germ-cell development system in other mammals, such as non-human primates. Here, we show that multiple lines of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) in cynomolgus monkeys (Macaca fascicularis; cy) can be maintained stably in an undifferentiated state under a defined condition with an inhibitor for WNT signaling, and such PSCs are induced efficiently into primordial germ cell-like cells (PGCLCs) bearing a transcriptome similar to early cyPGCs. Interestingly, the induction kinetics of cyPGCLCs from cyPSCs is faster than that of human (h) PGCLCs from hPSCs, and while the transcriptome dynamics during cyPGCLC induction is relatively similar to that during hPGCLC induction, it is substantially divergent from that during mouse (m) PGCLC induction. Our findings delineate common as well as species-specific traits for PGC specification, creating a foundation for parallel investigations into the mechanism for germ-cell development in mice, monkeys, and humans.
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Targeted transcript quantification in single disseminated cancer cells after whole transcriptome amplification. PLoS One 2019; 14:e0216442. [PMID: 31430289 PMCID: PMC6701776 DOI: 10.1371/journal.pone.0216442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022] Open
Abstract
Gene expression analysis of rare or heterogeneous cell populations such as disseminated cancer cells (DCCs) requires a sensitive method allowing reliable analysis of single cells. Therefore, we developed and explored the feasibility of a quantitative PCR (qPCR) assay to analyze single-cell cDNA pre-amplified using a previously established whole transcriptome amplification (WTA) protocol. We carefully selected and optimized multiple steps of the protocol, e.g. re-amplification of WTA products, quantification of amplified cDNA yields and final qPCR quantification, to identify the most reliable and accurate workflow for quantitation of gene expression of the ERBB2 gene in DCCs. We found that absolute quantification outperforms relative quantification. We then validated the performance of our method on single cells of established breast cancer cell lines displaying distinct levels of HER2 protein. The different protein levels were faithfully reflected by transcript expression across the tested cell lines thereby proving the accuracy of our approach. Finally, we applied our method to breast cancer DCCs of a patient undergoing anti-HER2-directed therapy. Here, we were able to measure ERBB2 expression levels in all HER2-protein-positive DCCs. In summary, we developed a reliable single-cell qPCR assay applicable to measure distinct levels of ERBB2 in DCCs.
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Hashimoto M, Sasaki H. Epiblast Formation by TEAD-YAP-Dependent Expression of Pluripotency Factors and Competitive Elimination of Unspecified Cells. Dev Cell 2019; 50:139-154.e5. [PMID: 31204175 DOI: 10.1016/j.devcel.2019.05.024] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/29/2019] [Accepted: 05/10/2019] [Indexed: 01/15/2023]
Abstract
The epiblast is a pluripotent cell population first formed in preimplantation embryos, and its quality is important for proper development. Here, we examined the mechanisms of epiblast formation and found that the Hippo pathway transcription factor TEAD and its coactivator YAP regulate expression of pluripotency factors. After specification of the inner cell mass, YAP accumulates in the nuclei and activates TEAD. TEAD activity is required for strong expression of pluripotency factors and is variable in the forming epiblast. Cells showing low TEAD activity are eliminated from the epiblast through cell competition. Pluripotency factor expression and MYC control cell competition downstream of TEAD activity. Cell competition eliminates unspecified cells and is required for proper organization of the epiblast. These results suggest that induction of pluripotency factors by TEAD activity and elimination of unspecified cells via cell competition ensure the production of an epiblast with naive pluripotency.
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Affiliation(s)
- Masakazu Hashimoto
- Laboratory for Embryogenesis, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroshi Sasaki
- Laboratory for Embryogenesis, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.
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Abstract
Germ cells undergo epigenome reprogramming for proper development of the next generation. The achievement of in vitro germ cell derivation from human and mouse pluripotent stem cells and further differentiation in a plane culture and in aggregation with gonadal somatic cells offers unprecedented opportunities for investigation of the germ cell development. Moreover, advances in low-input/single-cell genomics have enabled detailed investigation of epigenome dynamics during germ cell development. These technologies have advanced our knowledge of epigenome reprogramming during the specification and development of primordial germ cells, their sex differentiation, and gametogenesis. Key findings include details of chromatin remodeling and transcriptional regulation, progressive and comprehensive DNA demethylation, and tight links between DNA demethylation and histone marks during the development of primordial germ cells, acquisition of unique totipotent epigenome during oogenesis (e.g., broad H3K4me3 domains and low-level three-dimensional genomic organization), and unexpected organization of the sperm genome. Moreover, these studies suggest the importance of epigenome analyses for in-depth evaluations of in vitro gametogenesis.
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Affiliation(s)
- Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan.
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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Sasagawa Y, Hayashi T, Nikaido I. Strategies for Converting RNA to Amplifiable cDNA for Single-Cell RNA Sequencing Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1129:1-17. [PMID: 30968357 DOI: 10.1007/978-981-13-6037-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This review describes the features of molecular biology techniques for single-cell RNA sequencing (scRNA-seq), including methods developed in our laboratory. Existing scRNA-seq methods require the conversion of first-strand cDNA to amplifiable cDNA followed by whole-transcript amplification. There are three primary strategies for this conversion: poly-A tagging, template switching, and RNase H-DNA polymerase I-mediated second-strand cDNA synthesis for in vitro transcription. We discuss the merits and limitations of these strategies and describe our Reverse Transcription with Random Displacement Amplification technology that allows for direct first-strand cDNA amplification from RNA without the need for conversion to an amplifiable cDNA. We believe that this review provides all users of single-cell transcriptome technologies with an understanding of the relationship between the quantitative performance of various methods and their molecular features.
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Affiliation(s)
- Yohei Sasagawa
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan
| | - Tetsutaro Hayashi
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan
| | - Itoshi Nikaido
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan.
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Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:149-158. [PMID: 29943302 DOI: 10.1007/978-981-13-0502-3_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The advent of single-cell omics technology has promoted our understanding of the genomic, epigenomic, and transcriptomic heterogeneity in individual cells. Compared to traditional sequencing studies using bulk cells, single-cell transcriptome technology is naturally more dynamic for in depth analysis of genomic variation resulting from cell division and is useful in unraveling the regulatory mechanisms of gene networks in many diseases. However, there are still some limitations of current single-cell RNA sequencing (scRNA-seq) protocols. Biases that arise during the RNA reverse transcription and cDNA pre-amplification steps are the most common problems and play pivotal roles in limiting the quantitative accuracy of scRNA-seq. In this review, we will describe how these biases emerge and impact scRNA-seq protocols. Moreover, we will introduce several current and convenient modified scRNA-seq methods that allow for bias to be decreased and estimated.
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