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Cloutier M, Kumar S, Buttigieg E, Keller L, Lee B, Williams A, Mojica-Perez S, Erliandri I, Rocha AMD, Cadigan K, Smith GD, Kalantry S. Preventing erosion of X-chromosome inactivation in human embryonic stem cells. Nat Commun 2022; 13:2516. [PMID: 35523820 PMCID: PMC9076865 DOI: 10.1038/s41467-022-30259-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/11/2022] [Indexed: 12/12/2022] Open
Abstract
X-chromosome inactivation is a paradigm of epigenetic transcriptional regulation. Female human embryonic stem cells (hESCs) often undergo erosion of X-inactivation upon prolonged culture. Here, we investigate the sources of X-inactivation instability by deriving new primed pluripotent hESC lines. We find that culture media composition dramatically influenced the expression of XIST lncRNA, a key regulator of X-inactivation. hESCs cultured in a defined xenofree medium stably maintained XIST RNA expression and coating, whereas hESCs cultured in the widely used mTeSR1 medium lost XIST RNA expression. We pinpointed lithium chloride in mTeSR1 as a cause of XIST RNA loss. The addition of lithium chloride or inhibitors of GSK-3 proteins that are targeted by lithium to the defined hESC culture medium impeded XIST RNA expression. GSK-3 inhibition in differentiating female mouse embryonic stem cells and epiblast stem cells also resulted in a loss of XIST RNA expression. Together, these data may reconcile observed variations in X-inactivation in hESCs and inform the faithful culture of pluripotent stem cells.
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Affiliation(s)
- Marissa Cloutier
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Surinder Kumar
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Emily Buttigieg
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Laura Keller
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Brandon Lee
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Aaron Williams
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sandra Mojica-Perez
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Indri Erliandri
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Andre Monteiro Da Rocha
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine & Cardiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kenneth Cadigan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Gary D Smith
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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2
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Weldemariam MM, Han CL, Shekari F, Kitata RB, Chuang CY, Hsu WT, Kuo HC, Choong WK, Sung TY, He FC, Chung MCM, Salekdeh GH, Chen YJ. Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins. J Proteome Res 2018; 17:4138-4151. [DOI: 10.1021/acs.jproteome.8b00407] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mehari Muuz Weldemariam
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 112, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
| | - Faezeh Shekari
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Ching-Yu Chuang
- Genomics Research Center, Academia Sinica, Taiepei 115, Taiwan
| | | | | | | | | | - Fu-Chu He
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, 102206 China
| | - Maxey Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, 14 Science Drive 4, singapore, 117543 Singpore
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 112, Taiwan
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Sahakyan A, Plath K, Rougeulle C. Regulation of X-chromosome dosage compensation in human: mechanisms and model systems. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0363. [PMID: 28947660 DOI: 10.1098/rstb.2016.0363] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2017] [Indexed: 01/01/2023] Open
Abstract
The human blastocyst forms 5 days after one of the smallest human cells (the sperm) fertilizes one of the largest human cells (the egg). Depending on the sex-chromosome contribution from the sperm, the resulting embryo will either be female, with two X chromosomes (XX), or male, with an X and a Y chromosome (XY). In early development, one of the major differences between XX female and XY male embryos is the conserved process of X-chromosome inactivation (XCI), which compensates gene expression of the two female X chromosomes to match the dosage of the single X chromosome of males. Most of our understanding of the pre-XCI state and XCI establishment is based on mouse studies, but recent evidence from human pre-implantation embryo research suggests that many of the molecular steps defined in the mouse are not conserved in human. Here, we will discuss recent advances in understanding the control of X-chromosome dosage compensation in early human embryonic development and compare it to that of the mouse.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- Anna Sahakyan
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Claire Rougeulle
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, Université Paris Diderot, Paris, France
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4
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Tofoli FA, Dasso M, Morato-Marques M, Nunes K, Pereira LA, da Silva GS, Fonseca SAS, Costas RM, Santos HC, da Costa Pereira A, Lotufo PA, Bensenor IM, Meyer D, Pereira LV. Increasing The Genetic Admixture of Available Lines of Human Pluripotent Stem Cells. Sci Rep 2016; 6:34699. [PMID: 27708369 PMCID: PMC5052616 DOI: 10.1038/srep34699] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/19/2016] [Indexed: 01/06/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) may significantly improve drug development pipeline, serving as an in vitro system for the identification of novel leads, and for testing drug toxicity. Furthermore, these cells may be used to address the issue of differential drug response, a phenomenon greatly influenced by genetic factors. This application depends on the availability of hPSC lines from populations with diverse ancestries. So far, it has been reported that most lines of hPSCs derived worldwide are of European or East Asian ancestries. We have established 23 lines of hPSCs from Brazilian individuals, and we report the analysis of their genomic ancestry. We show that embryo-derived PSCs are mostly of European descent, while induced PSCs derived from participants of a national-wide Brazilian cohort study present high levels of admixed European, African and Native American genomic ancestry. Additionally, we use high density SNP data and estimate local ancestries, particularly those of CYP genes loci. Such information will be of key importance when interpreting variation among cell lines with respect to cellular phenotypes of interest. The availability of genetically admixed lines of hPSCs will be of relevance when setting up future in vitro studies of drug response.
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Affiliation(s)
- Fabiano A Tofoli
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Maximiliano Dasso
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Mariana Morato-Marques
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Kelly Nunes
- Laboratory of Evolutionary Genetics, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Lucas Assis Pereira
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Giselle Siqueira da Silva
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Simone A S Fonseca
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Roberta Montero Costas
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Hadassa Campos Santos
- Instituto do Coração, Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo. Av. Dr. Enéas de Carvalho Aguiar, 44, São Paulo, SP 05403-900, Brazil
| | - Alexandre da Costa Pereira
- Instituto do Coração, Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo. Av. Dr. Enéas de Carvalho Aguiar, 44, São Paulo, SP 05403-900, Brazil
| | - Paulo A Lotufo
- Center of Clinical and Epidemiologic Research, University Hospital, University of São Paulo, SP 05508-000. Brazil
| | - Isabela M Bensenor
- Center of Clinical and Epidemiologic Research, University Hospital, University of São Paulo, SP 05508-000. Brazil
| | - Diogo Meyer
- Laboratory of Evolutionary Genetics, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Lygia Veiga Pereira
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
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5
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Debowski K, Drummer C, Lentes J, Cors M, Dressel R, Lingner T, Salinas-Riester G, Fuchs S, Sasaki E, Behr R. The transcriptomes of novel marmoset monkey embryonic stem cell lines reflect distinct genomic features. Sci Rep 2016; 6:29122. [PMID: 27385131 PMCID: PMC4935898 DOI: 10.1038/srep29122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 06/13/2016] [Indexed: 12/21/2022] Open
Abstract
Embryonic stem cells (ESCs) are useful for the study of embryonic development. However, since research on naturally conceived human embryos is limited, non-human primate (NHP) embryos and NHP ESCs represent an excellent alternative to the corresponding human entities. Though, ESC lines derived from naturally conceived NHP embryos are still very rare. Here, we report the generation and characterization of four novel ESC lines derived from natural preimplantation embryos of the common marmoset monkey (Callithrix jacchus). For the first time we document derivation of NHP ESCs derived from morula stages. We show that quantitative chromosome-wise transcriptome analyses precisely reflect trisomies present in both morula-derived ESC lines. We also demonstrate that the female ESC lines exhibit different states of X-inactivation which is impressively reflected by the abundance of the lncRNA X inactive-specific transcript (XIST). The novel marmoset ESC lines will promote basic primate embryo and ESC studies as well as preclinical testing of ESC-based regenerative approaches in NHP.
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Affiliation(s)
- Katharina Debowski
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Charis Drummer
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jana Lentes
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Maren Cors
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Ralf Dressel
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen (UMG), Humboldtallee 34, 37073 Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Germany
| | - Thomas Lingner
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen (UMG), Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Gabriela Salinas-Riester
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen (UMG), Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Sigrid Fuchs
- Department of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Erika Sasaki
- Department of Applied Developmental Biology, Central Institute for Experimental Animals, 3-25-12 Tonomachi Kawasaki-ku, Kawasaki, 210-0821 Japan.,Keio Advanced Research Center, Keio University, Shinjuku-ku, Tokyo, Japan
| | - Rüdiger Behr
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Germany
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6
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Fonseca SAS, Costas RM, Morato-Marques M, Costa S, Alegretti JR, Rosenberg C, da Motta ELA, Serafini PC, Pereira LV. A Euploid Line of Human Embryonic Stem Cells Derived from a 43,XX,dup(9q),+12,-14,-15,-18,-21 Embryo. PLoS One 2015; 10:e0140999. [PMID: 26540511 PMCID: PMC4634922 DOI: 10.1371/journal.pone.0140999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/02/2015] [Indexed: 11/18/2022] Open
Abstract
Aneuploid embryos diagnosed by FISH-based preimplantation genetic screening (PGS) have been shown to yield euploid lines of human embryonic stem cells (hESCs) with a relatively high frequency. Given that the diagnostic procedure is usually based on the analysis of 1–2 blastomeres of 5 to 10-cell cleavage-stage embryos, mosaicism has been a likely explanation for the phenomena. However, FISH-based PGS can have a significant rate of misdiagnosis, and therefore some of those lines may have been derived from euploid embryos misdiagnosed as aneuploid. More recently, coupling of trophectoderm (TE) biopsy at the blastocyst stage and array-CGH lead to a more informative form of PGS. Here we describe the establishment of a new line of hESCs from an embryo with a 43,XX,dup(9q),+12,-14,-15,-18,-21 chromosomal content based on array-CGH of TE biopsy. We show that, despite the complex chromosomal abnormality, the corresponding hESC line BR-6 is euploid (46,XX). Single nucleotide polymorphism analysis showed that the embryo´s missing chromosomes were not duplicated in BR-6, suggesting the existence of extensive mosaicism in the TE lineage.
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Affiliation(s)
- Simone Aparecida Siqueira Fonseca
- National Laboratory of Embryonic Stem Cell (LaNCE), University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Roberta Montero Costas
- National Laboratory of Embryonic Stem Cell (LaNCE), University of São Paulo, São Paulo, Brazil
| | - Mariana Morato-Marques
- National Laboratory of Embryonic Stem Cell (LaNCE), University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Silvia Costa
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | | | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | | | | | - Lygia V. Pereira
- National Laboratory of Embryonic Stem Cell (LaNCE), University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
- * E-mail:
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Pranke P, Chagastelles P, Sperling LE. The Current State of Research with Human Pluripotent Stem Cells in Brazil. Stem Cells Dev 2014; 23 Suppl 1:20-3. [DOI: 10.1089/scd.2014.0320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Patricia Pranke
- Hematology and Stem Cell Laboratory, Faculty of Pharmacy, and Stem Cell Laboratory, Fundamental Health Science Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Stem Cell Research Institute, Porto Alegre, Brazil
| | - Pedro Chagastelles
- Hematology and Stem Cell Laboratory, Faculty of Pharmacy, and Stem Cell Laboratory, Fundamental Health Science Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Laura E. Sperling
- Hematology and Stem Cell Laboratory, Faculty of Pharmacy, and Stem Cell Laboratory, Fundamental Health Science Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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