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Monteagudo-Sánchez A, Richard Albert J, Scarpa M, Noordermeer D, Greenberg MC. The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation. Nucleic Acids Res 2024; 52:10934-10950. [PMID: 39180406 PMCID: PMC11472158 DOI: 10.1093/nar/gkae724] [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: 11/20/2023] [Revised: 07/23/2024] [Accepted: 08/21/2024] [Indexed: 08/26/2024] Open
Abstract
During mammalian embryogenesis, both the 5-cytosine DNA methylation (5meC) landscape and three dimensional (3D) chromatin architecture are profoundly remodeled during a process known as 'epigenetic reprogramming.' An understudied aspect of epigenetic reprogramming is how the 5meC flux, per se, affects the 3D genome. This is pertinent given the 5meC-sensitivity of DNA binding for a key regulator of chromosome folding: CTCF. We profiled the CTCF binding landscape using a mouse embryonic stem cell (ESC) differentiation protocol that models embryonic 5meC dynamics. Mouse ESCs lacking DNA methylation machinery are able to exit naive pluripotency, thus allowing for dissection of subtle effects of CTCF on gene expression. We performed CTCF HiChIP in both wild-type and mutant conditions to assess gained CTCF-CTCF contacts in the absence of 5meC. We performed H3K27ac HiChIP to determine the impact that ectopic CTCF binding has on cis-regulatory contacts. Using 5meC epigenome editing, we demonstrated that the methyl-mark is able to impair CTCF binding at select loci. Finally, a detailed dissection of the imprinted Zdbf2 locus showed how 5meC-antagonism of CTCF allows for proper gene regulation during differentiation. This work provides a comprehensive overview of how 5meC impacts the 3D genome in a relevant model for early embryonic events.
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Affiliation(s)
| | | | - Margherita Scarpa
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91998 Gif-sur-Yvette, France
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2
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Clancy CE, Santana LF. Advances in induced pluripotent stem cell-derived cardiac myocytes: technological breakthroughs, key discoveries and new applications. J Physiol 2024; 602:3871-3892. [PMID: 39032073 PMCID: PMC11326976 DOI: 10.1113/jp282562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 07/02/2024] [Indexed: 07/22/2024] Open
Abstract
A transformation is underway in precision and patient-specific medicine. Rapid progress has been enabled by multiple new technologies including induced pluripotent stem cell-derived cardiac myocytes (iPSC-CMs). Here, we delve into these advancements and their future promise, focusing on the efficiency of reprogramming techniques, the fidelity of differentiation into the cardiac lineage, the functional characterization of the resulting cardiac myocytes, and the many applications of in silico models to understand general and patient-specific mechanisms controlling excitation-contraction coupling in health and disease. Furthermore, we explore the current and potential applications of iPSC-CMs in both research and clinical settings, underscoring the far-reaching implications of this rapidly evolving field.
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Affiliation(s)
- Colleen E Clancy
- Department of Physiology & Membrane Biology, School of Medicine, University of California Davis, Davis, CA, USA
- Center for Precision Medicine and Data Sciences, University of California Davis, School of Medicine, Sacramento, CA, USA
| | - L Fernando Santana
- Department of Physiology & Membrane Biology, School of Medicine, University of California Davis, Davis, CA, USA
- Center for Precision Medicine and Data Sciences, University of California Davis, School of Medicine, Sacramento, CA, USA
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3
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Magaña-López G, Calzone L, Zinovyev A, Paulevé L. scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics. PLoS Comput Biol 2024; 20:e1011620. [PMID: 38976751 PMCID: PMC11257695 DOI: 10.1371/journal.pcbi.1011620] [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: 10/22/2023] [Revised: 07/18/2024] [Accepted: 06/24/2024] [Indexed: 07/10/2024] Open
Abstract
Boolean networks are largely employed to model the qualitative dynamics of cell fate processes by describing the change of binary activation states of genes and transcription factors with time. Being able to bridge such qualitative states with quantitative measurements of gene expression in cells, as scRNA-seq, is a cornerstone for data-driven model construction and validation. On one hand, scRNA-seq binarisation is a key step for inferring and validating Boolean models. On the other hand, the generation of synthetic scRNA-seq data from baseline Boolean models provides an important asset to benchmark inference methods. However, linking characteristics of scRNA-seq datasets, including dropout events, with Boolean states is a challenging task. We present scBoolSeq, a method for the bidirectional linking of scRNA-seq data and Boolean activation state of genes. Given a reference scRNA-seq dataset, scBoolSeq computes statistical criteria to classify the empirical gene pseudocount distributions as either unimodal, bimodal, or zero-inflated, and fit a probabilistic model of dropouts, with gene-dependent parameters. From these learnt distributions, scBoolSeq can perform both binarisation of scRNA-seq datasets, and generate synthetic scRNA-seq datasets from Boolean traces, as issued from Boolean networks, using biased sampling and dropout simulation. We present a case study demonstrating the application of scBoolSeq's binarisation scheme in data-driven model inference. Furthermore, we compare synthetic scRNA-seq data generated by scBoolSeq with BoolODE's, data for the same Boolean Network model. The comparison shows that our method better reproduces the statistics of real scRNA-seq datasets, such as the mean-variance and mean-dropout relationships while exhibiting clearly defined trajectories in two-dimensional projections of the data.
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Affiliation(s)
| | - Laurence Calzone
- Institut Curie, Université PSL, Paris, France
- INSERM, U900, Paris, France
- Mines ParisTech, Université PSL, Paris, France
| | | | - Loïc Paulevé
- Univ. Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800, Talence, France
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4
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Gaudet A, Zheng X, Kambham N, Bhalla V. Esm-1 mediates transcriptional polarization associated with diabetic kidney disease. Am J Physiol Renal Physiol 2024; 326:F1016-F1031. [PMID: 38601985 PMCID: PMC11386982 DOI: 10.1152/ajprenal.00419.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/20/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024] Open
Abstract
Esm-1, endothelial cell-specific molecule-1, is a susceptibility gene for diabetic kidney disease (DKD) and is a secreted proteoglycan, with notable expression in kidney, which attenuates inflammation and albuminuria. However, little is known about Esm1 expression in mature tissues in the presence or absence of diabetes. We utilized publicly available single-cell RNA sequencing data to characterize Esm1 expression in 27,786 renal endothelial cells (RECs) obtained from three mouse and four human databases. We validated our findings using bulk transcriptome data from 20 healthy subjects and 41 patients with DKD and using RNAscope. In both mice and humans, Esm1 is expressed in a subset of all REC types and represents a minority of glomerular RECs. In patients, Esm1(+) cells exhibit conserved enrichment for blood vessel development genes. With diabetes, these cells are fewer in number and shift expression toward chemotaxis pathways. Esm1 correlates with a majority of genes within these pathways, delineating a glomerular transcriptional polarization reflected by the magnitude of Esm1 deficiency. Diabetes correlates with lower Esm1 expression and with changes in the functional characterization of Esm1(+) cells. Thus, Esm1 appears to be a marker for glomerular transcriptional polarization in DKD.NEW & NOTEWORTHY Esm-1 is primarily expressed in glomerular endothelium in humans. Cells expressing Esm1 exhibit a high degree of conservation in the enrichment of genes related to blood vessel development. In the context of diabetes, these cells are reduced in number and show a significant transcriptional shift toward the chemotaxis pathway. In diabetes, there is a transcriptional polarization in the glomerulus that is reflected by the degree of Esm1 deficiency.
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Affiliation(s)
- Alexandre Gaudet
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Xiaoyi Zheng
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States
| | - Neeraja Kambham
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Vivek Bhalla
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States
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5
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Hu X, van Sluijs B, García-Blay Ó, Stepanov Y, Rietrae K, Huck WTS, Hansen MMK. ARTseq-FISH reveals position-dependent differences in gene expression of micropatterned mESCs. Nat Commun 2024; 15:3918. [PMID: 38724524 PMCID: PMC11082235 DOI: 10.1038/s41467-024-48107-5] [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: 02/17/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
Differences in gene-expression profiles between individual cells can give rise to distinct cell fate decisions. Yet how localisation on a micropattern impacts initial changes in mRNA, protein, and phosphoprotein abundance remains unclear. To identify the effect of cellular position on gene expression, we developed a scalable antibody and mRNA targeting sequential fluorescence in situ hybridisation (ARTseq-FISH) method capable of simultaneously profiling mRNAs, proteins, and phosphoproteins in single cells. We studied 67 (phospho-)protein and mRNA targets in individual mouse embryonic stem cells (mESCs) cultured on circular micropatterns. ARTseq-FISH reveals relative changes in both abundance and localisation of mRNAs and (phospho-)proteins during the first 48 hours of exit from pluripotency. We confirm these changes by conventional immunofluorescence and time-lapse microscopy. Chemical labelling, immunofluorescence, and single-cell time-lapse microscopy further show that cells closer to the edge of the micropattern exhibit increased proliferation compared to cells at the centre. Together these data suggest that while gene expression is still highly heterogeneous position-dependent differences in mRNA and protein levels emerge as early as 12 hours after LIF withdrawal.
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Affiliation(s)
- Xinyu Hu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Oncode Institute, Nijmegen, The Netherlands
| | - Bob van Sluijs
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Óscar García-Blay
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Oncode Institute, Nijmegen, The Netherlands
| | - Yury Stepanov
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Koen Rietrae
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
- Oncode Institute, Nijmegen, The Netherlands.
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6
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Valverde-Lopez JA, Li-Bao L, Sierra R, Santos E, Giovinazzo G, Díaz-Díaz C, Torres M. P53 and BCL-2 family proteins PUMA and NOXA define competitive fitness in pluripotent cell competition. PLoS Genet 2024; 20:e1011193. [PMID: 38489392 PMCID: PMC10971546 DOI: 10.1371/journal.pgen.1011193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 03/27/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024] Open
Abstract
Cell Competition is a process by which neighboring cells compare their fitness. As a result, viable but suboptimal cells are selectively eliminated in the presence of fitter cells. In the early mammalian embryo, epiblast pluripotent cells undergo extensive Cell Competition, which prevents suboptimal cells from contributing to the newly forming organism. While competitive ability is regulated by MYC in the epiblast, the mechanisms that contribute to competitive fitness in this context are largely unknown. Here, we report that P53 and its pro-apoptotic targets PUMA and NOXA regulate apoptosis susceptibility and competitive fitness in pluripotent cells. PUMA is widely expressed specifically in pluripotent cells in vitro and in vivo. We found that P53 regulates MYC levels in pluripotent cells, which connects these two Cell Competition pathways, however, MYC and PUMA/NOXA levels are independently regulated by P53. We propose a model that integrates a bifurcated P53 pathway regulating both MYC and PUMA/NOXA levels and determines competitive fitness.
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Affiliation(s)
- Jose A Valverde-Lopez
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Lin Li-Bao
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Rocío Sierra
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Elisa Santos
- Pluripotent Cell Technology Unit, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Giovanna Giovinazzo
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Pluripotent Cell Technology Unit, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Covadonga Díaz-Díaz
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Miguel Torres
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
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7
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Rapöhn M, Cyganek L, Voigt N, Hasenfuß G, Lehnart SE, Wegener JW. Noninvasive analysis of contractility during identical maturations revealed two phenotypes in ventricular but not in atrial iPSC-CM. Am J Physiol Heart Circ Physiol 2024; 326:H599-H611. [PMID: 38180453 PMCID: PMC11221812 DOI: 10.1152/ajpheart.00527.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/06/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
Patient-derived induced pluripotent stem cells (iPSCs) can be differentiated into atrial and ventricular cardiomyocytes to allow for personalized drug screening. A hallmark of differentiation is the manifestation of spontaneous beating in a two-dimensional (2-D) cell culture. However, an outstanding observation is the high variability in this maturation process. We valued that contractile parameters change during differentiation serving as an indicator of maturation. Consequently, we recorded noninvasively spontaneous motion activity during the differentiation of male iPSC toward iPSC cardiomyocytes (iPSC-CMs) to further analyze similar maturated iPSC-CMs. Surprisingly, our results show that identical differentiations into ventricular iPSC-CMs are variable with respect to contractile parameters resulting in two distinct subpopulations of ventricular-like cells. In contrast, differentiation into atrial iPSC-CMs resulted in only one phenotype. We propose that the noninvasive and cost-effective recording of contractile activity during maturation using a smartphone device may help to reduce the variability in results frequently reported in studies on ventricular iPSC-CMs.NEW & NOTEWORTHY Differentiation of induced pluripotent stem cells (iPSCs) into iPSC-derived cardiomyocytes (iPSC-CMs) exhibits a high variability in mature parameters. Here, we monitored noninvasively contractile parameters of iPSC-CM during full-time differentiation using a smartphone device. Our results show that parallel maturations of iPSCs into ventricular iPSC-CMs, but not into atrial iPSC-CMs, resulted in two distinct subpopulations of iPSC-CMs. These findings suggest that our cost-effective method may help to compare iPSC-CMs at the same maturation level.
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Affiliation(s)
- Marcel Rapöhn
- Department of Cardiology and Pulmonology, University Medical Center of Göttingen, Göttingen, Germany
| | - Lukas Cyganek
- Department of Cardiology and Pulmonology, University Medical Center of Göttingen, Göttingen, Germany
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung), Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells," University of Göttingen, Göttingen, Germany
| | - Niels Voigt
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung), Göttingen, Germany
- Department of Pharmacology and Toxicology, University Medical Center of Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells," University of Göttingen, Göttingen, Germany
| | - Gerd Hasenfuß
- Department of Cardiology and Pulmonology, University Medical Center of Göttingen, Göttingen, Germany
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung), Göttingen, Germany
| | - Stephan E Lehnart
- Department of Cardiology and Pulmonology, University Medical Center of Göttingen, Göttingen, Germany
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung), Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells," University of Göttingen, Göttingen, Germany
| | - Jörg W Wegener
- Department of Cardiology and Pulmonology, University Medical Center of Göttingen, Göttingen, Germany
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung), Göttingen, Germany
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Aranda S, Alcaine-Colet A, Ballaré C, Blanco E, Mocavini I, Sparavier A, Vizán P, Borràs E, Sabidó E, Di Croce L. Thymine DNA glycosylase regulates cell-cycle-driven p53 transcriptional control in pluripotent cells. Mol Cell 2023:S1097-2765(23)00517-8. [PMID: 37506700 DOI: 10.1016/j.molcel.2023.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/11/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Cell cycle progression is linked to transcriptome dynamics and variations in the response of pluripotent cells to differentiation cues, mostly through unknown determinants. Here, we characterized the cell-cycle-associated transcriptome and proteome of mouse embryonic stem cells (mESCs) in naive ground state. We found that the thymine DNA glycosylase (TDG) is a cell-cycle-regulated co-factor of the tumor suppressor p53. Furthermore, TDG and p53 co-bind ESC-specific cis-regulatory elements and thereby control transcription of p53-dependent genes during self-renewal. We determined that the dynamic expression of TDG is required to promote the cell-cycle-associated transcriptional heterogeneity. Moreover, we demonstrated that transient depletion of TDG influences cell fate decisions during the early differentiation of mESCs. Our findings reveal an unanticipated role of TDG in promoting molecular heterogeneity during the cell cycle and highlight the central role of protein dynamics for the temporal control of cell fate during development.
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Anna Alcaine-Colet
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Ivano Mocavini
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | | | - Pedro Vizán
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Blanquerna School of Health Science, Universitat Ramon Llull, Barcelona 08025, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain.
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9
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Poggio F, Brofiga M, Callegari F, Tedesco M, Massobrio P. Developmental conditions and culture medium influence the neuromodulated response of in vitro cortical networks. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-4. [PMID: 38083479 DOI: 10.1109/embc40787.2023.10340933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Goal of this work is to show how the developmental conditions of in vitro neuronal networks influence the effect of drug delivery. The proposed experimental neuronal model consists of dissociated cortical neurons plated to Micro-Electrode Arrays (MEAs) and grown according to different conditions (i.e., by varying both the adopted culture medium and the number of days needed to let the network grow before performing the chemical modulation). We delivered rising amount of bicuculline (BIC), a competitive antagonist of GABAA receptors, and we computed the firing rate dose-response curve for each culture. We found that networks matured in BrainPhys for 18 days in vitro exhibited a decreasing firing trend as a function of the BIC concentration, quantified by an average IC50 (i.e., half maximal inhibitory concentration) of 4.64 ± 4.02 µM. On the other hand, both cultures grown in the same medium for 11 days, and ones matured in Neurobasal for 18 days displayed an increasing firing rate when rising amounts of BIC were delivered, characterized by average EC50 values (i.e., half maximal excitatory concentration) of 0.24 ± 0.05 µM and 0.59 ± 0.46 µM, respectively.Clinical Relevance- This research proves the relevance of the experimental factors that can influence the network development as key variables when developing a neuronal model to conduct drug delivery in vitro, simulating the in vivo environment. Our findings suggest that not considering the consequences of the chosen growing conditions when performing in vitro pharmacological studies could lead to incomplete predictions of the chemically induced alterations.
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10
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Gil N, Perry RBT, Mukamel Z, Tuck A, Bühler M, Ulitsky I. Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus. Cell Rep 2023; 42:112569. [PMID: 37256750 PMCID: PMC10320833 DOI: 10.1016/j.celrep.2023.112569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are implicated in a plethora of cellular processes, but an in-depth understanding of their functional features or their mechanisms of action is currently lacking. Here we study Meteor, a lncRNA transcribed near the gene encoding EOMES, a pleiotropic transcription factor implicated in various processes throughout development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in mouse embryonic stem cells, with Meteor repression linked to a change in the subpopulation primed to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus-namely, the underlying DNA element-is required for suppressing Eomes expression following neuronal differentiation. Our results demonstrate the complex regulation that can be conferred by a single locus and emphasize the importance of careful selection of perturbation techniques when studying lncRNA loci.
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Affiliation(s)
- Noa Gil
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Ben-Tov Perry
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zohar Mukamel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alex Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
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11
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Gaudet A, Zheng X, Kambham N, Bhalla V. Esm-1 mediates transcriptional polarization associated with diabetic kidney disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530562. [PMID: 36993439 PMCID: PMC10054923 DOI: 10.1101/2023.03.01.530562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background Esm-1, endothelial cell-specific molecule-1, is a susceptibility gene for diabetic kidney disease (DKD) and is a cytokine- and glucose-regulated, secreted proteoglycan, that is notably expressed in kidney and attenuates inflammation and albuminuria. Esm1 has restricted expression at the vascular tip during development but little is known about its expression pattern in mature tissues, and its precise effects in diabetes. Methods We utilized publicly available single-cell RNA sequencing data to explore the characteristics of Esm1 expression in 27,786 renal endothelial cells obtained from four adult human and three mouse databases. We validated our findings using bulk transcriptome data from an additional 20 healthy subjects and 41 patients with DKD and using RNAscope. Using correlation matrices, we relate Esm1 expression to the glomerular transcriptome and evaluated these matrices with systemic over-expression of Esm-1. Results In both mice and humans, Esm1 is expressed in a subset of all renal endothelial cell types and represents a minority of glomerular endothelial cells. In patients, Esm1 (+) cells exhibit a highly conserved enrichment for blood vessel development genes. With diabetes, these cells are fewer in number and profoundly shift expression to reflect chemotaxis pathways. Analysis of these gene sets highlight candidate genes such as Igfbp5 for cross talk between cell types. We also find that diabetes induces correlations in the expression of large clusters of genes, within cell type-enriched transcripts. Esm1 significantly correlates with a majority genes within these clusters, delineating a glomerular transcriptional polarization reflected by the magnitude of Esm1 deficiency. In diabetic mice, these gene clusters link Esm1 expression to albuminuria, and over-expression of Esm-1 reverses the expression pattern in many of these genes. Conclusions A comprehensive analysis of single cell and bulk transcriptomes demonstrates that diabetes correlates with lower Esm1 expression and with changes in the functional characterization of Esm1 (+) cells. Esm1 is both a marker for glomerular transcriptional polarization, and a mediator that re-orients the transcriptional program in DKD.
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12
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Baral I, Shirude MB, Jothi DL, Mukherjee A, Dutta D. Characterization of a Distinct State in the Continuum of Pluripotency Facilitated by Inhibition of PKCζ in Mouse Embryonic Stem Cells. Stem Cell Rev Rep 2023; 19:1098-1115. [PMID: 36781773 DOI: 10.1007/s12015-023-10513-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2023] [Indexed: 02/15/2023]
Abstract
Inhibition of PKC (PKCi) signaling maintains pluripotency of embryonic stem cells (ESCs) across different mammalian species. However, the position of PKCi maintained ESCs in the pluripotency continuum is largely unknown. Here we demonstrate that mouse ESCs when cultured continuously, with PKCi, for 75 days are retained in naïve state of pluripotency. Gene expression analysis and proteomics studies demonstrated enhanced naïve character of PKCi maintained ESCs in comparison to classical serum/LIF (S/L) supported ESCs. Molecular analysis revealed that activation of PKCζ isoform associate with primed state of pluripotency, present in epiblast-like stem cells generated in vitro while inhibition of PKCζ phosphorylation associated with naïve state of pluripotency in vitro and in vivo. Phosphoproteomics and chromatin modification enzyme array based studies showed loss in DNA methyl transferase 3B (DNMT3B) and its phosphorylation level upon functional inhibition of PKCζ as one of the crucial components of this regulatory pathway. Unlike ground state of pluripotency maintained by MEK/GSK3 inhibitor in addition to LIF (2i/LIF), loss in DNMT3B is a reversible phenomenon in PKCi maintained ESCs. Absence of phosphorylation of c-MYC, RAF1, SPRY4 while presence of ERF, DUSP6, CIC and YAP1 phosphorylation underlined the phosphoproteomics signature of PKCi mediated maintenance of naïve pluripotency. States of pluripotency represent the developmental continuum and the existence of PKCi mediated mouse ESCs in a distinct state in the continuum of pluripotency (DiSCo) might contribute to the establishment of stages of murine embryonic development that were non-permissible till date.
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Affiliation(s)
- Ishita Baral
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.,Manipal Academy of Higher Education, Karnataka State, Manipal, 576104, India
| | - Mayur Balkrishna Shirude
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.,Manipal Academy of Higher Education, Karnataka State, Manipal, 576104, India
| | - Dhana Lakshmi Jothi
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India
| | - Ananda Mukherjee
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India
| | - Debasree Dutta
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.
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13
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Brofiga M, Poggio F, Callegari F, Tedesco M, Massobrio P. Modularity and neuronal heterogeneity: Two properties that influence in vitro neuropharmacological experiments. Front Cell Neurosci 2023; 17:1147381. [PMID: 37020847 PMCID: PMC10067731 DOI: 10.3389/fncel.2023.1147381] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/02/2023] [Indexed: 04/07/2023] Open
Abstract
Introduction The goal of this work is to prove the relevance of the experimental model (in vitro neuronal networks in this study) when drug-delivery testing is performed. Methods We used dissociated cortical and hippocampal neurons coupled to Micro-Electrode Arrays (MEAs) arranged in different configurations characterized by modularity (i.e., the presence of interconnected sub-networks) and heterogeneity (i.e., the co-existence of neurons coming from brain districts). We delivered increasing concentrations of bicuculline (BIC), a neuromodulator acting on the GABAergic system, and we extracted the IC50 values (i.e., the effective concentration yielding a reduction in the response by 50%) of the mean firing rate for each configuration. Results We found significant lower values of the IC50 computed for modular cortical-hippocampal ensembles than isolated cortical or hippocampal ones. Discussion Although tested with a specific neuromodulator, this work aims at proving the relevance of ad hoc experimental models to perform neuropharmacological experiments to avoid errors of overestimation/underestimation leading to biased information in the characterization of the effects of a drug on neuronal networks.
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Affiliation(s)
- Martina Brofiga
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genova, Genova, Italy
- ScreenNeuroPharm S.r.l., Sanremo, Italy
| | - Fabio Poggio
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genova, Genova, Italy
| | - Francesca Callegari
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genova, Genova, Italy
| | | | - Paolo Massobrio
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genova, Genova, Italy
- National Institute for Nuclear Physics (INFN), Genova, Italy
- MNESYS Extended Partnership Neuroscience and Neuropharmacology, Genova, Italy
- *Correspondence: Paolo Massobrio,
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14
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Epigenetics as "conductor" in "orchestra" of pluripotent states. Cell Tissue Res 2022; 390:141-172. [PMID: 35838826 DOI: 10.1007/s00441-022-03667-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
Pluripotent character is described as the potency of cells to differentiate into all three germ layers. The best example to reinstate the term lies in the context of embryonic stem cells (ESCs). Pluripotent ESC describes the in vitro status of those cells that originate during the complex process of embryogenesis. Pre-implantation to post-implantation development of embryo embrace cells with different levels of stemness. Currently, four states of pluripotency have been recognized, in the progressing order of "naïve," "poised," "formative," and "primed." Epigenetics act as the "conductor" in this "orchestra" of transition in pluripotent states. With a distinguishable gene expression profile, these four states associate with different epigenetic signatures, sometimes distinct while otherwise overlapping. The present review focuses on how epigenetic factors, including DNA methylation, bivalent chromatin, chromatin remodelers, chromatin/nuclear architecture, and microRNA, could dictate pluripotent states and their transition among themselves.
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15
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Ando Y, Okeyo KO, Adachi T. Pluripotency state of mouse ES cells determines their contribution to self-organized layer formation by mesh closure on microstructured adhesion-limiting substrates. Biochem Biophys Res Commun 2022; 590:97-102. [PMID: 34973536 DOI: 10.1016/j.bbrc.2021.12.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/18/2021] [Indexed: 11/02/2022]
Abstract
Assembly of pluripotent stem cells to initiate self-organized tissue formation on engineered scaffolds is an important process in stem cell engineering. Pluripotent stem cells are known to exist in diverse pluripotency states, with heterogeneous subpopulations exhibiting differential gene expression levels, but how such diverse pluripotency states orchestrate tissue formation is still an unrevealed question. In this study, using microstructured adhesion-limiting substrates, we aimed to clarify the contribution to self-organized layer formation by mouse embryonic stem cells in different pluripotency states: ground and naïve state. We found that while ground state cells as well as sorted REX1-high expression cells formed discontinuous cell layers with limited lateral spread, naïve state cells could successfully self-organize to form a continuous layer by progressive mesh closure within 3 days. Using sequential immunofluorescence microscopy to examine the mesh closure process, we found that KRT8+ cells were particularly localized around unfilled holes, occasionally bridging the holes in a manner suggestive of their role in the closure process. These results highlight that compared with ground state cells, naïve state cells possess a higher capability to contribute to self-organized layer formation by mesh closure. Thus, this study provides insights with implications for the application of stem cells in scaffold-based tissue engineering.
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Affiliation(s)
- Yuta Ando
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto Daigaku-katsura, Nishikyo-ku, Kyoto, 615-8530, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Kennedy Omondi Okeyo
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto Daigaku-katsura, Nishikyo-ku, Kyoto, 615-8530, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan; Division of Systemic Life Science, Graduate School of Biostudies, Kyoto University, Yoshida-Konoecho, Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Taiji Adachi
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto Daigaku-katsura, Nishikyo-ku, Kyoto, 615-8530, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan; Division of Systemic Life Science, Graduate School of Biostudies, Kyoto University, Yoshida-Konoecho, Sakyo-ku, Kyoto, 606-8501, Japan
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16
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Jang M, Scheffold J, Røst LM, Cheon H, Bruheim P. Serum-free cultures of C2C12 cells show different muscle phenotypes which can be estimated by metabolic profiling. Sci Rep 2022; 12:827. [PMID: 35039582 PMCID: PMC8764040 DOI: 10.1038/s41598-022-04804-z] [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: 08/10/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022] Open
Abstract
In vitro skeletal muscle cell production is emerging in the field of artificial lab-grown meat as alternative future food. Currently, there is an urgent paradigm shift towards a serum replacement culture system. Surprisingly, little is known about the impact of serum-free culture on skeletal muscle cells to date. Therefore, we performed metabolic profiling of the C2C12 myoblasts and myotubes in serum-free mediums (B27, AIM-V) and compared it with conventional serum supplementation culture. Furthermore, cell morphology, viability, and myogenic differentiation were observed for 7 days of cultivation. Intriguingly, the metabolic difference is more dominant between the cell status than medium effects. In addition, proliferative myoblast showed more distinct metabolic differences than differentiated myotubes in different culture conditions. The intracellular levels of GL3P and UDP-GlcNAc were significantly increased in myotubes versus myoblast. Non-essential amino acids and pyruvate reduction and transamination showed significant differences among serum, B27, and AIM-V cultures. Intracellular metabolite profiles indicated that C2C12 myotubes cultured in serum and B27 had predominant glycolytic and oxidative metabolism, respectively, indicating fast and slow types of muscle confirmed by MHC immunostaining. This work might be helpful to understand the altered metabolism of skeletal muscle cells in serum-free culture and contribute to future artificial meat research work.
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Affiliation(s)
- Mi Jang
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway
| | - Jana Scheffold
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway
| | - Hyejeong Cheon
- PoreLab, Department of Physics, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Hogskoleringen 1, 7491, Trondheim, Norway.
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17
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Gordeev MN, Bakhmet EI, Tomilin AN. Pluripotency Dynamics during Embryogenesis and in Cell Culture. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421060059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Morales JS, Raspopovic J, Marcon L. From embryos to embryoids: How external signals and self-organization drive embryonic development. Stem Cell Reports 2021; 16:1039-1050. [PMID: 33979592 PMCID: PMC8185431 DOI: 10.1016/j.stemcr.2021.03.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/15/2022] Open
Abstract
Embryonic development has been traditionally seen as an inductive process directed by exogenous maternal inputs and extra-embryonic signals. Increasing evidence, however, is showing that, in addition to exogenous signals, the development of the embryo involves endogenous self-organization. Recently, this self-organizing potential has been highlighted by a number of stem cell models known as embryoids that can recapitulate different aspects of embryogenesis in vitro. Here, we review the self-organizing behaviors observed in different embryoid models and seek to reconcile this new evidence with classical knowledge of developmental biology. This analysis leads to reexamine embryonic development as a guided self-organizing process, where patterning and morphogenesis are controlled by a combination of exogenous signals and endogenous self-organization. Finally, we discuss the multidisciplinary approach required to investigate the genetic and cellular basis of self-organization.
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Affiliation(s)
- J Serrano Morales
- Andalusian Center for Developmental Biology (CABD), CSIC - UPO - JA, Seville, Spain
| | - Jelena Raspopovic
- Andalusian Center for Developmental Biology (CABD), CSIC - UPO - JA, Seville, Spain.
| | - Luciano Marcon
- Andalusian Center for Developmental Biology (CABD), CSIC - UPO - JA, Seville, Spain.
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19
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Koldobskiy MA, Jenkinson G, Abante J, Rodriguez DiBlasi VA, Zhou W, Pujadas E, Idrizi A, Tryggvadottir R, Callahan C, Bonifant CL, Rabin KR, Brown PA, Ji H, Goutsias J, Feinberg AP. Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis. Nat Biomed Eng 2021; 5:360-376. [PMID: 33859388 PMCID: PMC8370714 DOI: 10.1038/s41551-021-00703-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/18/2021] [Indexed: 02/02/2023]
Abstract
In cancer, linking epigenetic alterations to drivers of transformation has been difficult, in part because DNA methylation analyses must capture epigenetic variability, which is central to tumour heterogeneity and tumour plasticity. Here, by conducting a comprehensive analysis, based on information theory, of differences in methylation stochasticity in samples from patients with paediatric acute lymphoblastic leukaemia (ALL), we show that ALL epigenomes are stochastic and marked by increased methylation entropy at specific regulatory regions and genes. By integrating DNA methylation and single-cell gene-expression data, we arrived at a relationship between methylation entropy and gene-expression variability, and found that epigenetic changes in ALL converge on a shared set of genes that overlap with genetic drivers involved in chromosomal translocations across the disease spectrum. Our findings suggest that an epigenetically driven gene-regulation network, with UHRF1 (ubiquitin-like with PHD and RING finger domains 1) as a central node, links genetic drivers and epigenetic mediators in ALL.
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Affiliation(s)
- Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Garrett Jenkinson
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Varenka A Rodriguez DiBlasi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Cancer Immunology and Immune Modulation, Boehringer Ingelheim, Ridgefield, CT, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Elisabet Pujadas
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Colin Callahan
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Challice L Bonifant
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen R Rabin
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Patrick A Brown
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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20
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Wang X, Ping C, Tan P, Sun C, Liu G, Liu T, Yang S, Si Y, Zhao L, Hu Y, Jia Y, Wang X, Zhang M, Wang F, Wang D, Yu J, Ma Y, Huang Y. hnRNPLL controls pluripotency exit of embryonic stem cells by modulating alternative splicing of Tbx3 and Bptf. EMBO J 2021; 40:e104729. [PMID: 33349972 PMCID: PMC7883296 DOI: 10.15252/embj.2020104729] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/09/2022] Open
Abstract
The regulatory circuitry underlying embryonic stem (ES) cell self-renewal is well defined, but how this circuitry is disintegrated to enable lineage specification is unclear. RNA-binding proteins (RBPs) have essential roles in RNA-mediated gene regulation, and preliminary data suggest that they might regulate ES cell fate. By combining bioinformatic analyses with functional screening, we identified seven RBPs played important roles for the exit from pluripotency of ES cells. We characterized hnRNPLL, which mainly functions as a global regulator of alternative splicing in ES cells. Specifically, hnRNPLL promotes multiple ES cell-preferred exon skipping events during the onset of ES cell differentiation. hnRNPLL depletion thus leads to sustained expression of ES cell-preferred isoforms, resulting in a differentiation deficiency that causes developmental defects and growth impairment in hnRNPLL-KO mice. In particular, hnRNPLL-mediated alternative splicing of two transcription factors, Bptf and Tbx3, is important for pluripotency exit. These data uncover the critical role of RBPs in pluripotency exit and suggest the application of targeting RBPs in controlling ES cell fate.
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Affiliation(s)
- Xue Wang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Changyun Ping
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Present address:
Department of PathologyHenan Provincial People's HospitalPeople's Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Puwen Tan
- Department of BioinformaticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Chenguang Sun
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Guang Liu
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Tao Liu
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical University (General Hospital)ChongqingChina
| | - Shuchun Yang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Yanmin Si
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Lijun Zhao
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Yongfei Hu
- Department of BioinformaticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Yuyan Jia
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Xiaoshuang Wang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Meili Zhang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Fang Wang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Dong Wang
- Department of BioinformaticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
- Dermatology HospitalSouthern Medical UniversityGuangzhouChina
- Center for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Jia Yu
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Yanni Ma
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Yue Huang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
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Abstract
In the past several decades, the establishment of in vitro models of pluripotency has ushered in a golden era for developmental and stem cell biology. Research in this arena has led to profound insights into the regulatory features that shape early embryonic development. Nevertheless, an integrative theory of the epigenetic principles that govern the pluripotent nucleus remains elusive. Here, we summarize the epigenetic characteristics that define the pluripotent state. We cover what is currently known about the epigenome of pluripotent stem cells and reflect on the use of embryonic stem cells as an experimental system. In addition, we highlight insights from super-resolution microscopy, which have advanced our understanding of the form and function of chromatin, particularly its role in establishing the characteristically "open chromatin" of pluripotent nuclei. Further, we discuss the rapid improvements in 3C-based methods, which have given us a means to investigate the 3D spatial organization of the pluripotent genome. This has aided the adaptation of prior notions of a "pluripotent molecular circuitry" into a more holistic model, where hotspots of co-interacting domains correspond with the accumulation of pluripotency-associated factors. Finally, we relate these earlier hypotheses to an emerging model of phase separation, which posits that a biophysical mechanism may presuppose the formation of a pluripotent-state-defining transcriptional program.
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Affiliation(s)
| | - Eran Meshorer
- Department of Genetics, the Institute of Life Sciences
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel 9190400
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22
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Aljazi MB, Gao Y, Wu Y, Mias GI, He J. Cell Signaling Coordinates Global PRC2 Recruitment and Developmental Gene Expression in Murine Embryonic Stem Cells. iScience 2020; 23:101646. [PMID: 33103084 PMCID: PMC7578752 DOI: 10.1016/j.isci.2020.101646] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/16/2020] [Accepted: 10/01/2020] [Indexed: 01/12/2023] Open
Abstract
The recruitment of Polycomb repressive complex 2 (PRC2) to gene promoters is critical for its function in repressing gene expression in murine embryonic stem cells (mESCs). However, previous studies have demonstrated that although the expression of early lineage-specific genes is largely repressed, the genome-wide PRC2 occupancy is unexpectedly reduced in naive mESCs. In this study, we provide evidence that fibroblast growth factor/extracellular signal-regulated kinase signaling determines the global PRC2 occupancy through regulating the expression of PRC2-recruiting factor JARID2 in naive mESCs. At the transcriptional level, the de-repression of bivalent genes is predominantly determined by the presence of cell signaling-associated transcription factors but not the status of PRC2 occupancy at gene promoters. Hence, this study not only reveals a key molecular mechanism by which cell signaling regulates the PRC2 occupancy in mESCs but also elucidates the functional roles of transcription factors and Polycomb-mediated epigenetic mechanisms in transcriptional regulation. FGF/ERK signaling positively regulates Jarid2 expression in mESCs Reduced JARID2 causes global reduction of PRC2 occupancy in naive mESCs Reduced PRC2 occupancy alone is insufficient to induce transcriptional activation Cell signaling-associated transcription factors drive bivalent gene expression
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Affiliation(s)
- Mohammad B Aljazi
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI 48824, USA
| | - Yuen Gao
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI 48824, USA
| | - Yan Wu
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI 48824, USA
| | - George I Mias
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI 48824, USA.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jin He
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI 48824, USA
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23
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Lafontaine S, Labrecque R, Palomino JM, Blondin P, Sirard MA. Specific imprinted genes demethylation in association with oocyte donor's age and culture conditions in bovine embryos assessed at day 7 and 12 post insemination. Theriogenology 2020; 158:321-330. [PMID: 33010654 DOI: 10.1016/j.theriogenology.2020.09.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/24/2020] [Accepted: 09/23/2020] [Indexed: 12/30/2022]
Abstract
The production of bovine embryos through in vitro maturation and fertilization is an important tool of the genomic revolution in dairy cattle. Gene expression analysis of these embryos revealed differences according to the culture conditions or oocyte donor's pubertal status compared to in vivo derived embryos. We hypothesized that some of the methylation patterns in oocytes are acquired in the last step of folliculogenesis and could be influenced by the environment created in the follicles containing these oocytes. These altered patterns may not be erased during the first week of embryonic development in culture or may be sensitive to the conditions during that time. To quantify the changes related to culture conditions, an in vivo control group consisting of embryos (Day 12 post fertilization for all groups) obtained from superovulated and artificially inseminated cows was compared to in vitro produced (IVP) embryos cultured with or without Fetal Bovine Serum (FBS). To measure the effect of the oocytes donor's age, we also compared a fourth group consisting of IVP embryos produced with oocytes collected following ovarian stimulation of pre-pubertal animals. Embryonic disk and trophoblast cells were processed separately and the methylation status of ten imprinted genes (H19, MEST, KCNQ1, SNRPN, PEG3, NNAT, GNASXL, IGF2R, PEG10, and PLAGL1) was assessed by pyrosequencing. Next, ten Day 7 blastocysts were produced following the same methodology as for the D12 embryos (four groups) to observe the most interesting genes (KCNQ1, SNRPN, IGF2R and PLAGL1) at an earlier developmental stage. For all samples, we observed overall lower methylation levels and greater variability in the three in vitro groups compared to the in vivo group. The individual embryo analysis indicated that some embryos were deviant from the others and some were not affected. We concluded that IGF2R, SNRPN, and PEG10 were particularly sensitive to culture conditions and the presence of FBS, while KCNQ1 and PLAGL1 were more affected in embryos derived from pre-pubertal donors. This work provides markers at the single imprinted control region (ICR) resolution to assess the culture environment required to minimize epigenetic perturbations in bovine embryos generated by assisted reproduction techniques, thus laying the groundwork for a better comprehension of the complex interplay between in vitro conditions and imprinted genes.
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Affiliation(s)
- Simon Lafontaine
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animals, Faculté des Sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Canada
| | - Rémi Labrecque
- SEMEX Boviteq, 3450 Rue Sicotte, Saint-Hyacinthe, QC J2S, Canada
| | | | - Patrick Blondin
- SEMEX Boviteq, 3450 Rue Sicotte, Saint-Hyacinthe, QC J2S, Canada
| | - Marc-André Sirard
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animals, Faculté des Sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Canada.
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24
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Capp JP, Thomas F. A Similar Speciation Process Relying on Cellular Stochasticity in Microbial and Cancer Cell Populations. iScience 2020; 23:101531. [PMID: 33083761 PMCID: PMC7502340 DOI: 10.1016/j.isci.2020.101531] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Similarities between microbial and cancer cells were noticed in recent years and serve as a basis for an atavism theory of cancer. Cancer cells would rely on the reactivation of an ancestral "genetic program" that would have been repressed in metazoan cells. Here we argue that cancer cells resemble unicellular organisms mainly in their similar way to exploit cellular stochasticity to produce cell specialization and maximize proliferation. Indeed, the relationship between low stochasticity, specialization, and quiescence found in normal differentiated metazoan cells is lost in cancer. On the contrary, low stochasticity and specialization are associated with high proliferation among cancer cells, as it is observed for the "specialist" cells in microbial populations that fully exploit nutritional resources to maximize proliferation. Thus, we propose a model where the appearance of cancer phenotypes can be solely due to an adaptation and a speciation process based on initial increase in cellular stochasticity.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, 31077 Toulouse, France
| | - Frédéric Thomas
- CREEC, UMR IRD 224, CNRS 5290, University of Montpellier, 34394 Montpellier, France
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25
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Okamoto S, Negishi K, Toyama Y, Ushijima T, Morohashi K. Leaf Trichome Distribution Pattern in Arabidopsis Reveals Gene Expression Variation Associated with Environmental Adaptation. PLANTS 2020; 9:plants9070909. [PMID: 32709158 PMCID: PMC7412270 DOI: 10.3390/plants9070909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/12/2020] [Accepted: 07/15/2020] [Indexed: 01/28/2023]
Abstract
Gene expression varies stochastically even in both heterogenous and homogeneous cell populations. This variation is not simply useless noise; rather, it is important for many biological processes. Unicellular organisms or cultured cell lines are useful for analyzing the variation in gene expression between cells; however, owing to technical challenges, the biological relevance of this variation in multicellular organisms such as higher plants remain unclear. Here, we addressed the biological relevance of this variation between cells by examining the genetic basis of trichome distribution patterns in Arabidopsis thaliana. The distribution pattern of a trichome on a leaf is stochastic and can be mathematically represented using Turing’s reaction-diffusion (RD) model. We analyzed simulations based on the RD model and found that the variability in the trichome distribution pattern increased with the increase in stochastic variation in a particular gene expression. Moreover, differences in heat-dependent variability of the trichome distribution pattern between the accessions showed a strong correlation with environmental factors to which each accession was adapted. Taken together, we successfully visualized variations in gene expression by quantifying the variability in the Arabidopsis trichome distribution pattern. Thus, our data provide evidence for the biological importance of variations in gene expression for environmental adaptation.
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Affiliation(s)
- Shotaro Okamoto
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan; (S.O.); (K.N.); (Y.T.)
| | - Kohei Negishi
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan; (S.O.); (K.N.); (Y.T.)
| | - Yuko Toyama
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan; (S.O.); (K.N.); (Y.T.)
| | - Takeo Ushijima
- Department of Mathematics, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan;
| | - Kengo Morohashi
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan; (S.O.); (K.N.); (Y.T.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: or ; Tel.: +1-614-407-6676
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26
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Ochiai H, Hayashi T, Umeda M, Yoshimura M, Harada A, Shimizu Y, Nakano K, Saitoh N, Liu Z, Yamamoto T, Okamura T, Ohkawa Y, Kimura H, Nikaido I. Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells. SCIENCE ADVANCES 2020; 6:eaaz6699. [PMID: 32596448 PMCID: PMC7299619 DOI: 10.1126/sciadv.aaz6699] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/25/2020] [Indexed: 05/03/2023]
Abstract
Transcriptional bursting is the stochastic activation and inactivation of promoters, contributing to cell-to-cell heterogeneity in gene expression. However, the mechanism underlying the regulation of transcriptional bursting kinetics (burst size and frequency) in mammalian cells remains elusive. In this study, we performed single-cell RNA sequencing to analyze the intrinsic noise and mRNA levels for elucidating the transcriptional bursting kinetics in mouse embryonic stem cells. Informatics analyses and functional assays revealed that transcriptional bursting kinetics was regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 and transcription elongation factors. Furthermore, large-scale CRISPR-Cas9-based screening identified that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncovered the key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.
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Affiliation(s)
- Hiroshi Ochiai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Tetsutaro Hayashi
- Laboratory for Bioinformatics Research, RIKEN BDR, Wako, Saitama 351-0198, Japan
| | - Mana Umeda
- Laboratory for Bioinformatics Research, RIKEN BDR, Wako, Saitama 351-0198, Japan
| | - Mika Yoshimura
- Laboratory for Bioinformatics Research, RIKEN BDR, Wako, Saitama 351-0198, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-0054, Japan
| | - Yukiko Shimizu
- Department of Animal Medicine, National Center for Global Health and Medicine (NCGM), Tokyo 812-0054, Japan
| | - Kenta Nakano
- Department of Animal Medicine, National Center for Global Health and Medicine (NCGM), Tokyo 812-0054, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo 135-8550, Japan
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Tadashi Okamura
- Department of Animal Medicine, National Center for Global Health and Medicine (NCGM), Tokyo 812-0054, Japan
- Section of Animal Models, Department of Infectious Diseases, National Center for Global Health and Medicine (NCGM), Tokyo 812-0054, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-0054, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Itoshi Nikaido
- Laboratory for Bioinformatics Research, RIKEN BDR, Wako, Saitama 351-0198, Japan
- Bioinformatics Course, Master’s/Doctoral Program in Life Science Innovation (T-LSI), School of Integrative and Global Majors (SIGMA), University of Tsukuba, Wako 351-0198, Japan
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27
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Huyghe A, Furlan G, Ozmadenci D, Galonska C, Charlton J, Gaume X, Combémorel N, Riemenschneider C, Allègre N, Zhang J, Wajda P, Rama N, Vieugué P, Durand I, Brevet M, Gadot N, Imhof T, Merrill BJ, Koch M, Mehlen P, Chazaud C, Meissner A, Lavial F. Netrin-1 promotes naive pluripotency through Neo1 and Unc5b co-regulation of Wnt and MAPK signalling. Nat Cell Biol 2020; 22:389-400. [PMID: 32231305 DOI: 10.1038/s41556-020-0483-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/13/2020] [Indexed: 12/20/2022]
Abstract
In mouse embryonic stem cells (mESCs), chemical blockade of Gsk3α/β and Mek1/2 (2i) instructs a self-renewing ground state whose endogenous inducers are unknown. Here we show that the axon guidance cue Netrin-1 promotes naive pluripotency by triggering profound signalling, transcriptomic and epigenetic changes in mESCs. Furthermore, we demonstrate that Netrin-1 can substitute for blockade of Gsk3α/β and Mek1/2 to sustain self-renewal of mESCs in combination with leukaemia inhibitory factor and regulates the formation of the mouse pluripotent blastocyst. Mechanistically, we reveal how Netrin-1 and the balance of its receptors Neo1 and Unc5B co-regulate Wnt and MAPK pathways in both mouse and human ESCs. Netrin-1 induces Fak kinase to inactivate Gsk3α/β and stabilize β-catenin while increasing the phosphatase activity of a Ppp2r2c-containing Pp2a complex to reduce Erk1/2 activity. Collectively, this work identifies Netrin-1 as a regulator of pluripotency and reveals that it mediates different effects in mESCs depending on its receptor dosage, opening perspectives for balancing self-renewal and lineage commitment.
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Affiliation(s)
- Aurélia Huyghe
- Cellular Reprogramming and Oncogenesis Laboratory, Equipe labellisée la Ligue contre le cancer, Labex DEVweCAN, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France
| | - Giacomo Furlan
- Cellular Reprogramming and Oncogenesis Laboratory, Equipe labellisée la Ligue contre le cancer, Labex DEVweCAN, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France
| | - Duygu Ozmadenci
- Cellular Reprogramming and Oncogenesis Laboratory, Equipe labellisée la Ligue contre le cancer, Labex DEVweCAN, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France
| | - Christina Galonska
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jocelyn Charlton
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Xavier Gaume
- Cellular Reprogramming and Oncogenesis Laboratory, Equipe labellisée la Ligue contre le cancer, Labex DEVweCAN, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France
| | - Noémie Combémorel
- Cellular Reprogramming and Oncogenesis Laboratory, Equipe labellisée la Ligue contre le cancer, Labex DEVweCAN, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France
| | | | - Nicolas Allègre
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP38, Clermont-Ferrand, France
| | - Jenny Zhang
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Pauline Wajda
- Cellular Reprogramming and Oncogenesis Laboratory, Equipe labellisée la Ligue contre le cancer, Labex DEVweCAN, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France
| | - Nicolas Rama
- Apoptosis, Cancer and Development Laboratory, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France
| | - Pauline Vieugué
- Apoptosis, Cancer and Development Laboratory, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France
| | - Isabelle Durand
- Cytometry Facility, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, INSERM 1052, CNRS 5286, Lyon, France
| | - Marie Brevet
- Research Pathology platform, Department of translational research and innovation, Centre Léon Bérard, Lyon, France
| | - Nicolas Gadot
- Research Pathology platform, Department of translational research and innovation, Centre Léon Bérard, Lyon, France
| | - Thomas Imhof
- Institute for Dental Research and Oral Musculoskeletal Research, Center for Biochemistry, University of Cologne, Cologne, Germany
| | - Bradley J Merrill
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Research, Center for Biochemistry, University of Cologne, Cologne, Germany
| | - Patrick Mehlen
- Apoptosis, Cancer and Development Laboratory, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France.,Department of Translational Research and Innovation, Centre Léon Bérard, Lyon, France
| | - Claire Chazaud
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP38, Clermont-Ferrand, France
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Fabrice Lavial
- Cellular Reprogramming and Oncogenesis Laboratory, Equipe labellisée la Ligue contre le cancer, Labex DEVweCAN, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France.
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28
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Xiong C, Wang M, Ling W, Xie D, Chu X, Li Y, Huang Y, Li T, Otieno E, Qiu X, Xiao X. Advances in Isolation and Culture of Chicken Embryonic Stem Cells In Vitro. Cell Reprogram 2020; 22:43-54. [PMID: 32150690 DOI: 10.1089/cell.2019.0080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Chicken embryonic stem cells (cESCs) isolated from the egg at the stage X hold great promise for cell therapy, tissue engineering, pharmaceutical, and biotechnological applications. They are considered to be pluripotent cells with the capacity to self-renewal and differentiate into specialized cells. However, long-term maintenance of cESCs cannot be realized now, which impedes the establishment of cESC line and limits their applications. Therefore, the separation locations, isolation methods, and culture conditions especially the supplements and action mechanisms of cytokines, including leukemia inhibitory factor, fibroblast growth factor, transforming growth factor beta, bone morphogenic protein, and activin for cESCs in vitro, have been reviewed here. These defined strategies will contribute to identify the key mechanism on the self-renewal of cESCs, facilitate to optimize system that supports the derivation and longtime maintenance of cESCs, establish the cESC line, and develop the biobank of genetic resources in chicken.
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Affiliation(s)
- Chunxia Xiong
- Department of Veterinary Medicine, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Mingyu Wang
- Department of Veterinary Medicine, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Wenhui Ling
- Department of Veterinary Medicine, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Dengfeng Xie
- Department of Veterinary Medicine, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xinyue Chu
- Department of Veterinary Medicine, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yunxin Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yun Huang
- Department of Veterinary Medicine, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Tong Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Edward Otieno
- Department of Veterinary Medicine, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xiaoyan Qiu
- Department of Veterinary Medicine, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xiong Xiao
- Department of Veterinary Medicine, College of Animal Science and Technology, Southwest University, Chongqing, China
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29
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Albergante L, Mirkes E, Bac J, Chen H, Martin A, Faure L, Barillot E, Pinello L, Gorban A, Zinovyev A. Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph. ENTROPY (BASEL, SWITZERLAND) 2020; 22:E296. [PMID: 33286070 PMCID: PMC7516753 DOI: 10.3390/e22030296] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 12/19/2022]
Abstract
Multidimensional datapoint clouds representing large datasets are frequently characterized by non-trivial low-dimensional geometry and topology which can be recovered by unsupervised machine learning approaches, in particular, by principal graphs. Principal graphs approximate the multivariate data by a graph injected into the data space with some constraints imposed on the node mapping. Here we present ElPiGraph, a scalable and robust method for constructing principal graphs. ElPiGraph exploits and further develops the concept of elastic energy, the topological graph grammar approach, and a gradient descent-like optimization of the graph topology. The method is able to withstand high levels of noise and is capable of approximating data point clouds via principal graph ensembles. This strategy can be used to estimate the statistical significance of complex data features and to summarize them into a single consensus principal graph. ElPiGraph deals efficiently with large datasets in various fields such as biology, where it can be used for example with single-cell transcriptomic or epigenomic datasets to infer gene expression dynamics and recover differentiation landscapes.
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Affiliation(s)
- Luca Albergante
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
- Sensyne Health, Oxford OX4 4GE, UK
| | - Evgeny Mirkes
- Center for Mathematical Modeling, University of Leicester, Leicester LE1 7RH, UK; (E.M.); (A.G.)
- Lobachevsky University, 603000 Nizhny Novgorod, Russia
| | - Jonathan Bac
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
- Centre de Recherches Interdisciplinaires, Université de Paris, F-75000 Paris, France
| | - Huidong Chen
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA; (H.C.); (L.P.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexis Martin
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
- ECE Paris, F-75015 Paris, France
| | - Louis Faure
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
- Center for Brain Research, Medical University of Vienna, 22180 Vienna, Austria
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
| | - Luca Pinello
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA; (H.C.); (L.P.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Gorban
- Center for Mathematical Modeling, University of Leicester, Leicester LE1 7RH, UK; (E.M.); (A.G.)
- Lobachevsky University, 603000 Nizhny Novgorod, Russia
| | - Andrei Zinovyev
- Institut Curie, PSL Research University, 75005 Paris, France; (J.B.); (A.M.); (L.F.); (E.B.)
- INSERM U900, 75248 Paris, France
- CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, 75006 Paris, France
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30
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Kainov YA, Makeyev EV. A transcriptome-wide antitermination mechanism sustaining identity of embryonic stem cells. Nat Commun 2020; 11:361. [PMID: 31953406 PMCID: PMC6969169 DOI: 10.1038/s41467-019-14204-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/11/2019] [Indexed: 11/29/2022] Open
Abstract
Eukaryotic gene expression relies on extensive crosstalk between transcription and RNA processing. Changes in this composite regulation network may provide an important means for shaping cell type-specific transcriptomes. Here we show that the RNA-associated protein Srrt/Ars2 sustains embryonic stem cell (ESC) identity by preventing premature termination of numerous transcripts at cryptic cleavage/polyadenylation sites in first introns. Srrt interacts with the nuclear cap-binding complex and facilitates recruitment of the spliceosome component U1 snRNP to cognate intronic positions. At least in some cases, U1 recruited in this manner inhibits downstream cleavage/polyadenylation events through a splicing-independent mechanism called telescripting. We further provide evidence that the naturally high expression of Srrt in ESCs offsets deleterious effects of retrotransposable sequences accumulating in its targets. Our work identifies Srrt as a molecular guardian of the pluripotent cell state. Besides its role in splicing, U1 snRNP can suppress pre-mRNA cleavage and polyadenylation. The authors show that the nuclear cap-binding complex component Srrt/Ars2 maintains embryonic stem cell identity by promoting U1 recruitment to first introns and preventing premature termination of multiple transcripts.
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Affiliation(s)
- Yaroslav A Kainov
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
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31
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Lv B, An Q, Zeng Q, Zhang X, Lu P, Wang Y, Zhu X, Ji Y, Fan G, Xue Z. Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses. PLoS Biol 2019; 17:e3000187. [PMID: 31596842 PMCID: PMC6802852 DOI: 10.1371/journal.pbio.3000187] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/21/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022] Open
Abstract
Multipotent trophoblasts undergo dynamic morphological movement and cellular differentiation after conceptus implantation to generate placenta. However, the mechanism controlling trophoblast development and differentiation during peri-implantation development in human remains elusive. In this study, we modeled human conceptus peri-implantation development from blastocyst to early postimplantation stages by using an in vitro coculture system and profiled the transcriptome of 476 individual trophoblast cells from these conceptuses. We revealed the genetic networks regulating peri-implantation trophoblast development. While determining when trophoblast differentiation happens, our bioinformatic analysis identified T-box transcription factor 3 (TBX3) as a key regulator for the differentiation of cytotrophoblast (CT) into syncytiotrophoblast (ST). The function of TBX3 in trophoblast differentiation is then validated by a loss-of-function experiment. In conclusion, our results provided a valuable resource to study the regulation of trophoblasts development and differentiation during human peri-implantation development.
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Affiliation(s)
- Bo Lv
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Qin An
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, State of California, United States of America
| | - Qiao Zeng
- Center of Reproductive Medicine of Ji’an Maternal and Child Health Hospital, Ji’an, Jiangxi, China
| | - Xunyi Zhang
- Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, China
| | - Ping Lu
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Yanqiu Wang
- Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, China
| | - Xianmin Zhu
- Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yazhong Ji
- Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, China
- * E-mail: (ZX); (GF); (YJ)
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, State of California, United States of America
- * E-mail: (ZX); (GF); (YJ)
| | - Zhigang Xue
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, China
- Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, China
- * E-mail: (ZX); (GF); (YJ)
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32
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Gökbuget D, Blelloch R. Epigenetic control of transcriptional regulation in pluripotency and early differentiation. Development 2019; 146:dev164772. [PMID: 31554624 PMCID: PMC6803368 DOI: 10.1242/dev.164772] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pluripotent stem cells give rise to all cells of the adult organism, making them an invaluable tool in regenerative medicine. In response to differentiation cues, they can activate markedly distinct lineage-specific gene networks while turning off or rewiring pluripotency networks. Recent innovations in chromatin and nuclear structure analyses combined with classical genetics have led to novel insights into the transcriptional and epigenetic mechanisms underlying these networks. Here, we review these findings in relation to their impact on the maintenance of and exit from pluripotency and highlight the many factors that drive these processes, including histone modifying enzymes, DNA methylation and demethylation, nucleosome remodeling complexes and transcription factor-mediated enhancer switching.
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Affiliation(s)
- Deniz Gökbuget
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94143, USA
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33
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Choi KH, Lee DK, Kim SW, Woo SH, Kim DY, Lee CK. Chemically Defined Media Can Maintain Pig Pluripotency Network In Vitro. Stem Cell Reports 2019; 13:221-234. [PMID: 31257130 PMCID: PMC6626979 DOI: 10.1016/j.stemcr.2019.05.028] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022] Open
Abstract
Pig embryonic stem cells (pESCs) have been considered an important candidate for preclinical research on human therapies. However, the lack of understanding of pig pluripotent networks has hampered establishment of authentic pESCs. Here, we report that FGF2, ACTVIN, and WNT signaling are essential to sustain pig pluripotency in vitro. Newly derived pESCs were stably maintained over an extended period, and capable of forming teratomas that contained three germ layers. Transcriptome analysis showed that pESCs were developmentally similar to late epiblasts of preimplantation embryos and in terms of biological functions resembled human rather than mouse pluripotent stem cells. However, the pESCs had distinct features such as coexpression of SSEA1 and SSEA4, two active X chromosomes, and a unique transcriptional pattern. Our findings will facilitate both the development of large animal models for human stem cell therapy and the generation of pluripotent stem cells from other domestic animals for agricultural use.
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Affiliation(s)
- Kwang-Hwan Choi
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea
| | - Dong-Kyung Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea
| | - Sung Woo Kim
- Animal Genetic Resources Research Center, National Institute of Animal Science, RDA, Namwon, Jeollabuk-do 55717, Korea
| | - Sang-Ho Woo
- Department of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Dae-Yong Kim
- Department of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea; Institute of Green Bio Science and Technology, Seoul National University, Pyeong Chang, Kangwon-do 25354, Korea.
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34
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van Mierlo G, Veenstra GJC, Vermeulen M, Marks H. The Complexity of PRC2 Subcomplexes. Trends Cell Biol 2019; 29:660-671. [PMID: 31178244 DOI: 10.1016/j.tcb.2019.05.004] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is a multisubunit protein complex essential for the development of multicellular organisms. Recruitment of PRC2 to target genes, followed by deposition and propagation of its catalytic product histone H3 lysine 27 trimethylation (H3K27me3), are key to the spatiotemporal control of developmental gene expression. Recent breakthrough studies have uncovered unexpected roles for substoichiometric PRC2 subunits in these processes. Here, we elaborate on how the facultative PRC2 subunits regulate catalytic activity, locus-specific PRC2 binding, and propagation of H3K27me3, and how this affects chromatin structure, gene expression, and cell fate.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen 6525GA, The Netherlands; Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen 6525GA, The Netherlands
| | - Gert Jan C Veenstra
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen 6500HB, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen 6525GA, The Netherlands; Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen 6525GA, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen 6525GA, The Netherlands.
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35
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Waisman A, Sevlever F, Elías Costa M, Cosentino MS, Miriuka SG, Ventura AC, Guberman AS. Cell cycle dynamics of mouse embryonic stem cells in the ground state and during transition to formative pluripotency. Sci Rep 2019; 9:8051. [PMID: 31142785 PMCID: PMC6541595 DOI: 10.1038/s41598-019-44537-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Mouse embryonic stem cells (mESCs) can be maintained as homogeneous populations in the ground state of pluripotency. Release from this state in minimal conditions allows to obtain cells that resemble those of the early post-implantation epiblast, providing an important developmental model to study cell identity transitions. However, the cell cycle dynamics of mESCs in the ground state and during its dissolution have not been extensively studied. By performing live imaging experiments of mESCs bearing cell cycle reporters, we show here that cells in the pluripotent ground state display a cell cycle structure comparable to the reported for mESCs in serum-based media. Upon release from self-renewal, the cell cycle is rapidly accelerated by a reduction in the length of the G1 phase and of the S/G2/M phases, causing an increased proliferation rate. Analysis of cell lineages indicates that cell cycle variables of sister cells are highly correlated, suggesting the existence of inherited cell cycle regulators from the parental cell. Together with a major morphological reconfiguration upon differentiation, our findings support a correlation between this in vitro model and early embryonic events.
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Affiliation(s)
- Ariel Waisman
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica (IQUIBICEN), Laboratorio de Regulación Génica en Células Madre, Buenos Aires, Argentina
- CONICET - Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Laboratorio de Investigación de Aplicación a Neurociencias (LIAN), Buenos Aires, Argentina
| | - Federico Sevlever
- CONICET - Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | | | - María Soledad Cosentino
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica (IQUIBICEN), Laboratorio de Regulación Génica en Células Madre, Buenos Aires, Argentina
| | - Santiago G Miriuka
- CONICET - Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Laboratorio de Investigación de Aplicación a Neurociencias (LIAN), Buenos Aires, Argentina
| | - Alejandra C Ventura
- CONICET - Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Alejandra S Guberman
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica (IQUIBICEN), Laboratorio de Regulación Génica en Células Madre, Buenos Aires, Argentina.
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Buenos Aires, Buenos Aires, Argentina.
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36
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Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan GC, Pinello L. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nat Commun 2019; 10:1903. [PMID: 31015418 PMCID: PMC6478907 DOI: 10.1038/s41467-019-09670-4] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. We have tested STREAM on several synthetic and real datasets generated with different single-cell technologies. We further demonstrate its utility for understanding myoblast differentiation and disentangling known heterogeneity in hematopoiesis for different organisms. STREAM is an open-source software package.
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Affiliation(s)
- Huidong Chen
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Department of Computer Science and Technology, Tongji University, 201804, Shanghai, China
| | - Luca Albergante
- Institut Curie, PSL Research University, F-75005, Paris, France
- INSERM, U900, F-75005, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006, Paris, France
| | - Jonathan Y Hsu
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caleb A Lareau
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Giosuè Lo Bosco
- Department of Mathematics and Computer Science, University of Palermo, 90123, Palermo, Italy
- Department of Sciences for technological innovation, Euro-Mediterranean Institute of Science and Technology, 90139, Palermo, Italy
| | - Jihong Guan
- Department of Computer Science and Technology, Tongji University, 201804, Shanghai, China
| | - Shuigeng Zhou
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 200433, Shanghai, China
| | - Alexander N Gorban
- Department of Mathematics, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Lobachevsky University, Nizhni Novgorod, 603022, Russia
| | - Daniel E Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02215, USA
| | - Martin J Aryee
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David M Langenau
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Andrei Zinovyev
- Institut Curie, PSL Research University, F-75005, Paris, France
- INSERM, U900, F-75005, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006, Paris, France
- Lobachevsky University, Nizhni Novgorod, 603022, Russia
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Society of Fellows, Harvard University, Cambridge, MA, 02138, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
| | - Luca Pinello
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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37
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Waisman A, La Greca A, Möbbs AM, Scarafía MA, Santín Velazque NL, Neiman G, Moro LN, Luzzani C, Sevlever GE, Guberman AS, Miriuka SG. Deep Learning Neural Networks Highly Predict Very Early Onset of Pluripotent Stem Cell Differentiation. Stem Cell Reports 2019; 12:845-859. [PMID: 30880077 PMCID: PMC6449871 DOI: 10.1016/j.stemcr.2019.02.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 01/23/2023] Open
Abstract
Deep learning is a significant step forward for developing autonomous tasks. One of its branches, computer vision, allows image recognition with high accuracy thanks to the use of convolutional neural networks (CNNs). Our goal was to train a CNN with transmitted light microscopy images to distinguish pluripotent stem cells from early differentiating cells. We induced differentiation of mouse embryonic stem cells to epiblast-like cells and took images at several time points from the initial stimulus. We found that the networks can be trained to recognize undifferentiated cells from differentiating cells with an accuracy higher than 99%. Successful prediction started just 20 min after the onset of differentiation. Furthermore, CNNs displayed great performance in several similar pluripotent stem cell (PSC) settings, including mesoderm differentiation in human induced PSCs. Accurate cellular morphology recognition in a simple microscopic set up may have a significant impact on how cell assays are performed in the near future.
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Affiliation(s)
- Ariel Waisman
- LIAN-CONICET, FLENI, Ruta 9 Km 52.2 (B1625XAF), Belén de Escobar, Argentina
| | - Alejandro La Greca
- LIAN-CONICET, FLENI, Ruta 9 Km 52.2 (B1625XAF), Belén de Escobar, Argentina
| | - Alan M Möbbs
- LIAN-CONICET, FLENI, Ruta 9 Km 52.2 (B1625XAF), Belén de Escobar, Argentina
| | | | | | - Gabriel Neiman
- LIAN-CONICET, FLENI, Ruta 9 Km 52.2 (B1625XAF), Belén de Escobar, Argentina
| | - Lucía N Moro
- LIAN-CONICET, FLENI, Ruta 9 Km 52.2 (B1625XAF), Belén de Escobar, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carlos Luzzani
- LIAN-CONICET, FLENI, Ruta 9 Km 52.2 (B1625XAF), Belén de Escobar, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gustavo E Sevlever
- LIAN-CONICET, FLENI, Ruta 9 Km 52.2 (B1625XAF), Belén de Escobar, Argentina
| | - Alejandra S Guberman
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Regulación Génica en Células Madre, Departamento de Química Biológica y Departamento de Fisiología, Biología Molecular y Celular, FCEN, Universidad de Buenos Aires, Argentina, Intendente Guiraldes 2160 (C1428EGA), Buenos Aires, Argentina; IQUIBICEN, UBA/CONICET, Buenos Aires, Argentina
| | - Santiago G Miriuka
- LIAN-CONICET, FLENI, Ruta 9 Km 52.2 (B1625XAF), Belén de Escobar, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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38
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Roger M, Fullard N, Costello L, Bradbury S, Markiewicz E, O'Reilly S, Darling N, Ritchie P, Määttä A, Karakesisoglou I, Nelson G, von Zglinicki T, Dicolandrea T, Isfort R, Bascom C, Przyborski S. Bioengineering the microanatomy of human skin. J Anat 2019; 234:438-455. [PMID: 30740672 PMCID: PMC6422806 DOI: 10.1111/joa.12942] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2019] [Indexed: 12/12/2022] Open
Abstract
Recreating the structure of human tissues in the laboratory is valuable for fundamental research, testing interventions, and reducing the use of animals. Critical to the use of such technology is the ability to produce tissue models that accurately reproduce the microanatomy of the native tissue. Current artificial cell-based skin systems lack thorough characterisation, are not representative of human skin, and can show variation. In this study, we have developed a novel full thickness model of human skin comprised of epidermal and dermal compartments. Using an inert porous scaffold, we created a dermal construct using human fibroblasts that secrete their own extracellular matrix proteins, which avoids the use of animal-derived materials. The dermal construct acts as a foundation upon which epidermal keratinocytes were seeded and differentiated into a stratified keratinised epithelium. In-depth morphological analyses of the model demonstrated very close similarities with native human skin. Extensive immunostaining and electron microscopy analysis revealed ultrastructural details such as keratohyalin granules and lamellar bodies within the stratum granulosum, specialised junctional complexes, and the presence of a basal lamina. These features reflect the functional characteristics and barrier properties of the skin equivalent. Robustness and reproducibility of in vitro models are important attributes in experimental practice, and we demonstrate the consistency of the skin construct between different users. In summary, a new model of full thickness human skin has been developed that possesses microanatomical features reminiscent of native tissue. This skin model platform will be of significant interest to scientists researching the structure and function of human skin.
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Affiliation(s)
| | | | | | | | | | - Steven O'Reilly
- Department of Health and Life SciencesNorthumbria UniversityNewcastleUK
| | | | | | - Arto Määttä
- Department of BiosciencesDurham UniversityDurhamUK
| | | | - Glyn Nelson
- Institute for Ageing and HealthUniversity of NewcastleNewcastleUK
| | | | | | - Robert Isfort
- Mason Business Centre, Procter & GambleMason, CincinnatiOHUSA
| | - Charles Bascom
- Mason Business Centre, Procter & GambleMason, CincinnatiOHUSA
| | - Stefan Przyborski
- Department of BiosciencesDurham UniversityDurhamUK
- Reprocell EuropeSedgefieldUK
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39
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Addressing Variability and Heterogeneity of Induced Pluripotent Stem Cell-Derived Cardiomyocytes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1212:1-29. [DOI: 10.1007/5584_2019_350] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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40
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Oosterhoff LA, Kruitwagen HS, van Wolferen ME, van Balkom BWM, Mokry M, Lansu N, van den Dungen NAM, Penning LC, Spanjersberg TCF, de Graaf JW, Veenendaal T, Zomerdijk F, Fledderus JO, Spee B, van Steenbeek FG. Characterization of Endothelial and Smooth Muscle Cells From Different Canine Vessels. Front Physiol 2019; 10:101. [PMID: 30809157 PMCID: PMC6379353 DOI: 10.3389/fphys.2019.00101] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/28/2019] [Indexed: 12/12/2022] Open
Abstract
Vasculature performs a critical function in tissue homeostasis, supply of oxygen and nutrients, and the removal of metabolic waste products. Vascular problems are implicated in a large variety of pathologies and accurate in vitro models resembling native vasculature are of great importance. Unfortunately, existing in vitro models do not sufficiently reflect their in vivo counterpart. The complexity of vasculature requires the examination of multiple cell types including endothelial cells (ECs) and vascular smooth muscle cells (VSMCs), as well as vessel location in the body from which they originate. The use of canine blood vessels provides a way to study vasculature with similar vessel size and physiology compared to human vasculature. We report an isolation procedure that provides the possibility to isolate both the endothelial and smooth muscle cells from the same vessels simultaneously, enabling new opportunities in investigating vasculature behavior. Canine primary ECs and VSMCs were isolated from the vena cava, vena porta and aorta. All tissue sources were derived from three donors for accurate comparison and to reduce inter-animal variation. The isolation and purification of the two distinct cell types was confirmed by morphology, gene- and protein-expression and function. As both cell types can be derived from the same vessel, this approach allows accurate modeling of vascular diseases and can also be used more widely, for example, in vascular bioreactors and tissue engineering designs. Additionally, we identified several new genes that were highly expressed in canine ECs, which may become candidate genes for novel EC markers. In addition, we observed transcriptional and functional differences between arterial- and venous-derived endothelium. Further exploration of the transcriptome and physiology of arteriovenous differentiation of primary cells may have important implications for a better understanding of the fundamental behavior of the vasculature and pathogenesis of vascular disease.
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Affiliation(s)
- Loes A Oosterhoff
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Hedwig S Kruitwagen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Monique E van Wolferen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Bas W M van Balkom
- Nephrology and Hypertension, Division of Internal Medicine and Dermatology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Michal Mokry
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands.,Epigenomics Facility, University Medical Center Utrecht, Utrecht, Netherlands
| | - Nico Lansu
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands.,Epigenomics Facility, University Medical Center Utrecht, Utrecht, Netherlands
| | - Noortje A M van den Dungen
- Epigenomics Facility, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
| | - Louis C Penning
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Talitha C F Spanjersberg
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Johannes W de Graaf
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Tomas Veenendaal
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Flin Zomerdijk
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Joost O Fledderus
- Nephrology and Hypertension, Division of Internal Medicine and Dermatology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Bart Spee
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Frank G van Steenbeek
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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41
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Wnt/β-catenin signaling pathway safeguards epigenetic stability and homeostasis of mouse embryonic stem cells. Sci Rep 2019; 9:948. [PMID: 30700782 PMCID: PMC6353868 DOI: 10.1038/s41598-018-37442-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 12/03/2018] [Indexed: 12/22/2022] Open
Abstract
Mouse embryonic stem cells (mESCs) are pluripotent and can differentiate into cells belonging to the three germ layers of the embryo. However, mESC pluripotency and genome stability can be compromised in prolonged in vitro culture conditions. Several factors control mESC pluripotency, including Wnt/β-catenin signaling pathway, which is essential for mESC differentiation and proliferation. Here we show that the activity of the Wnt/β-catenin signaling pathway safeguards normal DNA methylation of mESCs. The activity of the pathway is progressively silenced during passages in culture and this results into a loss of the DNA methylation at many imprinting control regions (ICRs), loss of recruitment of chromatin repressors, and activation of retrotransposons, resulting into impaired mESC differentiation. Accordingly, sustained Wnt/β-catenin signaling maintains normal ICR methylation and mESC homeostasis and is a key regulator of genome stability.
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42
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Zhang S, Chen T, Chen N, Gao D, Shi B, Kong S, West RC, Yuan Y, Zhi M, Wei Q, Xiang J, Mu H, Yue L, Lei X, Wang X, Zhong L, Liang H, Cao S, Belmonte JCI, Wang H, Han J. Implantation initiation of self-assembled embryo-like structures generated using three types of mouse blastocyst-derived stem cells. Nat Commun 2019; 10:496. [PMID: 30700702 PMCID: PMC6353907 DOI: 10.1038/s41467-019-08378-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/04/2019] [Indexed: 11/09/2022] Open
Abstract
Spatially ordered embryo-like structures self-assembled from blastocyst-derived stem cells can be generated to mimic embryogenesis in vitro. However, the assembly system and developmental potential of such structures needs to be further studied. Here, we devise a nonadherent-suspension-shaking system to generate self-assembled embryo-like structures (ETX-embryoids) using mouse embryonic, trophoblast and extra-embryonic endoderm stem cells. When cultured together, the three cell types aggregate and sort into lineage-specific compartments. Signaling among these compartments results in molecular and morphogenic events that closely mimic those observed in wild-type embryos. These ETX-embryoids exhibit lumenogenesis, asymmetric patterns of gene expression for markers of mesoderm and primordial germ cell precursors, and formation of anterior visceral endoderm-like tissues. After transplantation into the pseudopregnant mouse uterus, ETX-embryoids efficiently initiate implantation and trigger the formation of decidual tissues. The ability of the three cell types to self-assemble into an embryo-like structure in vitro provides a powerful model system for studying embryogenesis.
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Affiliation(s)
- Shaopeng Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China
| | - Tianzhi Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China
| | - Naixin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China
| | - Dengfeng Gao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China
| | - Bingbo Shi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China
| | - Shuangbo Kong
- Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, Xiamen, Fujian, 361102, China
| | | | - Ye Yuan
- Colorado Center for Reproductive Medicine, Lone Tree, CO, 80124, USA
| | - Minglei Zhi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China
| | - Qingqing Wei
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China
| | - Jinzhu Xiang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China
| | - Haiyuan Mu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China
| | - Liang Yue
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China
| | - Xiaohua Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuepeng Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liang Zhong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui Liang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China
| | - Suying Cao
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | | | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, Xiamen, Fujian, 361102, China
| | - Jianyong Han
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 10094, China. .,Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100083, China.
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43
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Stumpf PS, MacArthur BD. Machine Learning of Stem Cell Identities From Single-Cell Expression Data via Regulatory Network Archetypes. Front Genet 2019; 10:2. [PMID: 30723489 PMCID: PMC6349820 DOI: 10.3389/fgene.2019.00002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/07/2019] [Indexed: 01/04/2023] Open
Abstract
The molecular regulatory network underlying stem cell pluripotency has been intensively studied, and we now have a reliable ensemble model for the "average" pluripotent cell. However, evidence of significant cell-to-cell variability suggests that the activity of this network varies within individual stem cells, leading to differential processing of environmental signals and variability in cell fates. Here, we adapt a method originally designed for face recognition to infer regulatory network patterns within individual cells from single-cell expression data. Using this method we identify three distinct network configurations in cultured mouse embryonic stem cells-corresponding to naïve and formative pluripotent states and an early primitive endoderm state-and associate these configurations with particular combinations of regulatory network activity archetypes that govern different aspects of the cell's response to environmental stimuli, cell cycle status and core information processing circuitry. These results show how variability in cell identities arise naturally from alterations in underlying regulatory network dynamics and demonstrate how methods from machine learning may be used to better understand single cell biology, and the collective dynamics of cell communities.
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Affiliation(s)
- Patrick S. Stumpf
- Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Ben D. MacArthur
- Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- Mathematical Sciences, University of Southampton, Southampton, United Kingdom
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44
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Sanada CD, Ooi AT. Single-Cell Dosing and mRNA Sequencing of Suspension and Adherent Cells Using the Polaris TM System. Methods Mol Biol 2019; 1979:185-195. [PMID: 31028639 DOI: 10.1007/978-1-4939-9240-9_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Single-cell functional analysis provides a natural next step in the now widely adopted single-cell mRNA sequencing studies. Functional studies can be designed to study cellular context by using single-cell culture, perturbation, manipulation, or treatment. Here we present a method for a functional study of 48 single cells by single-cell isolation, dosing, and mRNA sequencing with an integrated fluidic circuit (IFC) on the Fluidigm® Polaris™ system. The major procedures required to execute this protocol are (1) cell preparation and staining; (2) priming, single-cell selection, cell dosing, cell staining, and cDNA generation on the Polaris IFC; and (3) preparation and sequencing of single-cell mRNA-seq libraries. The cell preparation and staining steps employ the use of a universal tracking dye to trace all cells that enter the IFC, while additional fluorescence dyes chosen by the user can be used to differentiate cell types in the overall mix. The steps on the Polaris IFC follow standard protocols, which are also described in the Fluidigm user documentation. The library preparation step adds Illumina® Nextera® XT indexes to the cDNA generated on the Polaris IFC. The resulting sequencing libraries can be sequenced on any Illumina sequencing platform.
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Affiliation(s)
| | - Aik T Ooi
- Fluidigm Corporation, South San Francisco, CA, USA
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45
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46
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Liu D, Wang X, He D, Sun C, He X, Yan L, Li Y, Han JDJ, Zheng P. Single-cell RNA-sequencing reveals the existence of naive and primed pluripotency in pre-implantation rhesus monkey embryos. Genome Res 2018; 28:1481-1493. [PMID: 30154223 PMCID: PMC6169889 DOI: 10.1101/gr.233437.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 08/27/2018] [Indexed: 01/23/2023]
Abstract
Naive pluripotency exists in epiblast cells of mouse pre-implantation embryos. However, whether the naive pluripotency is transient or nonexistent in primate embryos remains unclear. Using RNA-seq in single blastomeres from 16-cell embryos through to hatched blastocysts of rhesus monkey, we constructed the lineage segregation roadmap in which the specification of trophectoderm, epiblast, and primitive endoderm is initiated simultaneously at the early blastocyst stage. Importantly, we uncovered the existence of distinct pluripotent states in monkey pre-implantation embryos. At the early- and middle-blastocyst stages, the epiblast cells have the transcriptome features of naive pluripotency, whereas they display a continuum of primed pluripotency characteristics at the late and hatched blastocyst stages. Moreover, we identified potential regulators that might play roles in the transition from naive to primed pluripotency. Thus, our study suggests the transient existence of naive pluripotency in primates and proposes an ideal time window for derivation of primate embryonic stem cells with naive pluripotency.
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Affiliation(s)
- Denghui Liu
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xinyi Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Dajian He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chunli Sun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xiechao He
- Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Lanzhen Yan
- Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yizhou Li
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing-Dong J Han
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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47
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Feeders facilitate telomere maintenance and chromosomal stability of embryonic stem cells. Nat Commun 2018; 9:2620. [PMID: 29976922 PMCID: PMC6033898 DOI: 10.1038/s41467-018-05038-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 06/12/2018] [Indexed: 12/20/2022] Open
Abstract
Feeder cells like mouse embryonic fibroblasts (MEFs) have been widely applied for culture of pluripotent stem cells, but their roles remain elusive. Noticeably, ESCs cultured on the feeders display transcriptional heterogeneity. We investigated roles of feeder cells by examining the telomere maintenance. Here we show that telomere is longer in mESCs cultured with than without the feeders. mESC cultures without MEF feeders exhibit telomere loss, chromosomal fusion, and aneuploidy with increasing passages. Notably, feeders facilitate heterogeneous transcription of 2-cell genes including Zscan4 and telomere elongation. Moreover, feeders produce Fstl1 that together with BMP4 periodically activate Zscan4. Interestingly, Zscan4 is repressed in mESCs cultured in 2i (inhibitors of Mek and Gsk3β signaling) media, associated with shorter telomeres and increased chromosome instability. These data suggest the important role of feeders in maintaining telomeres for long-term stable self-renewal and developmental pluripotency of mESCs. Feeder cells are widely used for the culture of embryonic stem cells (ESCs), but their specific effects are not well known. Here, the authors demonstrate that mouse ESCs exhibit telomere loss and chromosomal aberrations associated with reduced Zscan4 with increasing passages in the absence of feeders
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48
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Pijuan-Sala B, Guibentif C, Göttgens B. Single-cell transcriptional profiling: a window into embryonic cell-type specification. Nat Rev Mol Cell Biol 2018; 19:399-412. [DOI: 10.1038/s41580-018-0002-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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49
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Han X, Chen H, Huang D, Chen H, Fei L, Cheng C, Huang H, Yuan GC, Guo G. Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. Genome Biol 2018; 19:47. [PMID: 29622030 PMCID: PMC5887227 DOI: 10.1186/s13059-018-1426-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/21/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Human pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differentiation roadmap for hPSCs has not been achieved. RESULTS We use high throughput single-cell RNA-sequencing (scRNA-seq), based on optimized microfluidic circuits, to profile early differentiation lineages in the human embryoid body system. We present a cellular-state landscape for hPSC early differentiation that covers multiple cellular lineages, including neural, muscle, endothelial, stromal, liver, and epithelial cells. Through pseudotime analysis, we construct the developmental trajectories of these progenitor cells and reveal the gene expression dynamics in the process of cell differentiation. We further reprogram primed H9 cells into naïve-like H9 cells to study the cellular-state transition process. We find that genes related to hemogenic endothelium development are enriched in naïve-like H9. Functionally, naïve-like H9 show higher potency for differentiation into hematopoietic lineages than primed cells. CONCLUSIONS Our single-cell analysis reveals the cellular-state landscape of hPSC early differentiation, offering new insights that can be harnessed for optimization of differentiation protocols.
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Affiliation(s)
- Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Institute of Hematology, The 1st Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Hangzhou, 310058, China. .,College of Animal Science, Zhejiang University, Hangzhou, 310058, China.
| | - Daosheng Huang
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Huidong Chen
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Chan School of Public Health, Boston, MA, 02115, USA.,Department of Computer Science and Technology, Tongji University, Shanghai, 201804, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Chen Cheng
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - He Huang
- Institute of Hematology, The 1st Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Chan School of Public Health, Boston, MA, 02115, USA.
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Institute of Hematology, The 1st Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Hangzhou, 310058, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China.
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50
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The Pleiotropic Effects of the Canonical Wnt Pathway in Early Development and Pluripotency. Genes (Basel) 2018; 9:genes9020093. [PMID: 29443926 PMCID: PMC5852589 DOI: 10.3390/genes9020093] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 12/20/2022] Open
Abstract
The technology to derive embryonic and induced pluripotent stem cells from early embryonic stages and adult somatic cells, respectively, emerged as a powerful resource to enable the establishment of new in vitro models, which recapitulate early developmental processes and disease. Additionally, pluripotent stem cells (PSCs) represent an invaluable source of relevant differentiated cell types with immense potential for regenerative medicine and cell replacement therapies. Pluripotent stem cells support self-renewal, potency and proliferation for extensive periods of culture in vitro. However, the core pathways that rule each of these cellular features specific to PSCs only recently began to be clarified. The Wnt signaling pathway is pivotal during early embryogenesis and is central for the induction and maintenance of the pluripotency of PSCs. Signaling by the Wnt family of ligands is conveyed intracellularly by the stabilization of β-catenin in the cytoplasm and in the nucleus, where it elicits the transcriptional activity of T-cell factor (TCF)/lymphoid enhancer factor (LEF) family of transcription factors. Interestingly, in PSCs, the Wnt/β-catenin–TCF/LEF axis has several unrelated and sometimes opposite cellular functions such as self-renewal, stemness, lineage commitment and cell cycle regulation. In addition, tight control of the Wnt signaling pathway enhances reprogramming of somatic cells to induced pluripotency. Several recent research efforts emphasize the pleiotropic functions of the Wnt signaling pathway in the pluripotent state. Nonetheless, conflicting results and unanswered questions still linger. In this review, we will focus on the diverse functions of the canonical Wnt signaling pathway on the developmental processes preceding embryo implantation, as well as on its roles in pluripotent stem cell biology such as self-renewal and cell cycle regulation and somatic cell reprogramming.
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