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      Rat post-implantation epiblast-derived pluripotent stem cells produce functional germ cells

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          Summary

          In mammals, pluripotent cells transit through a continuum of distinct molecular and functional states en route to initiating lineage specification. Capturing pluripotent stem cells (PSCs) mirroring in vivo pluripotent states provides accessible in vitro models to study the pluripotency program and mechanisms underlying lineage restriction. Here, we develop optimal culture conditions to derive and propagate post-implantation epiblast-derived PSCs (EpiSCs) in rats, a valuable model for biomedical research. We show that rat EpiSCs (rEpiSCs) can be reset toward the naive pluripotent state with exogenous Klf4, albeit not with the other five candidate genes ( Nanog, Klf2, Esrrb, Tfcp2l1, and Tbx3) effective in mice. Finally, we demonstrate that rat EpiSCs retain competency to produce authentic primordial germ cell-like cells that undergo functional gametogenesis leading to the birth of viable offspring. Our findings in the rat model uncover principles underpinning pluripotency and germline competency across species.

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          Highlights

          • Inhibition of WNT and ROCK is required for uniform and robust expansion of rEpiSCs

          • Exogenous Klf4 can reset rEpiSCs into rESC-like cells displaying naive pluripotency

          • rEpiSCs can generate rPGCLCs capable of spermatogenesis and giving birth to offspring

          Motivation

          Pluripotent stem cells (PSCs) that mirror the pluripotent state in the pre-gastrulation epiblast allow us to examine the molecular mechanisms underlying pluripotent transitions and the differentiation of germ line and soma. Despite rats being a prominent animal model for biomedical research, alongside mice, there has been limited investigation into the derivation and characterization of rat PSCs derived from the post-implantation epiblast (rEpiSCs). This study explores the optimal culture conditions for successfully deriving and expanding rEpiSCs. Additionally, we investigate the molecular characteristics of established rEpiSCs, their ability to reset to a naive pluripotent state, and their competence in producing functional germ cells.

          Abstract

          Iwatsuki et al. develop optimal culture conditions for rat epiblast-derived pluripotent stem cells (EpiSCs). These rEpiSCs exhibit molecular similarities to pre-gastrulating pluripotent epiblasts and demonstrate the ability to generate functional germ cells. Therefore, the approach provides valuable tools for studying pluripotency and in vitro gametogenesis.

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          Most cited references56

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          STAR: ultrafast universal RNA-seq aligner.

          Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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            Comprehensive Integration of Single-Cell Data

            Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.
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              Naive and primed pluripotent states.

              After maternal predetermination gives way to zygotic regulation, a ground state is established within the mammalian embryo. This tabula rasa for embryogenesis is present only transiently in the preimplantation epiblast. Here, we consider how unrestricted cells are first generated and then prepared for lineage commitment. We propose that two phases of pluripotency can be defined: naive and primed. This distinction extends to pluripotent stem cells derived from embryos or by molecular reprogramming ex vivo.
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                Author and article information

                Contributors
                Journal
                Cell Rep Methods
                Cell Rep Methods
                Cell Reports Methods
                Elsevier
                2667-2375
                27 July 2023
                28 August 2023
                27 July 2023
                : 3
                : 8
                : 100542
                Affiliations
                [1 ]Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
                [2 ]Graduate School of Medicine, Science and Technology, Shinshu University, Nagano 386-8567, Japan
                [3 ]Laboratory of Regenerative Medicine, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
                [4 ]Department of Embryology, Nara Medical University, Nara 634-0813, Japan
                [5 ]Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK
                [6 ]Centre for Trophoblast Research, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK
                [7 ]Wellcome Trust – Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
                [8 ]Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Aichi 444-8787, Japan
                [9 ]Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
                [10 ]Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
                [11 ]Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project, Kyoto 606-8501, Japan
                [12 ]Faculty of Textile Science and Technology, Shinshu University, Nagano 386-8567, Japan
                [13 ]The Graduate University of Advanced Studies, Aichi 444-8787, Japan
                Author notes
                []Corresponding author tkoba@ 123456g.ecc.u-tokyo.ac.jp
                [14]

                Lead contact

                Article
                S2667-2375(23)00179-0 100542
                10.1016/j.crmeth.2023.100542
                10475792
                37671016
                c31f192a-e7ad-4246-a2c2-f38e1f3aab5b
                © 2023 The Authors

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 11 January 2023
                : 10 May 2023
                : 3 July 2023
                Categories
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                pluripotency,epiblast stem cell,rat,klf4,reprogramming,germline competency,primordial germ cell-like cell

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