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Pavlinek A, Adhya D, Tsompanidis A, Warrier V, Vernon AC, Lancaster M, Mill J, Srivastava DP, Baron-Cohen S. Using Organoids to Model Sex Differences in the Human Brain. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:100343. [PMID: 39092139 PMCID: PMC11292257 DOI: 10.1016/j.bpsgos.2024.100343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 08/04/2024] Open
Abstract
Sex differences are widespread during neurodevelopment and play a role in neuropsychiatric conditions such as autism, which is more prevalent in males than females. In humans, males have been shown to have larger brain volumes than females with development of the hippocampus and amygdala showing prominent sex differences. Mechanistically, sex steroids and sex chromosomes drive these differences in brain development, which seem to peak during prenatal and pubertal stages. Animal models have played a crucial role in understanding sex differences, but the study of human sex differences requires an experimental model that can recapitulate complex genetic traits. To fill this gap, human induced pluripotent stem cell-derived brain organoids are now being used to study how complex genetic traits influence prenatal brain development. For example, brain organoids from individuals with autism and individuals with X chromosome-linked Rett syndrome and fragile X syndrome have revealed prenatal differences in cell proliferation, a measure of brain volume differences, and excitatory-inhibitory imbalances. Brain organoids have also revealed increased neurogenesis of excitatory neurons due to androgens. However, despite growing interest in using brain organoids, several key challenges remain that affect its validity as a model system. In this review, we discuss how sex steroids and the sex chromosomes each contribute to sex differences in brain development. Then, we examine the role of X chromosome inactivation as a factor that drives sex differences. Finally, we discuss the combined challenges of modeling X chromosome inactivation and limitations of brain organoids that need to be taken into consideration when studying sex differences.
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Affiliation(s)
- Adam Pavlinek
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | - Dwaipayan Adhya
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Alex Tsompanidis
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Anthony C. Vernon
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | | | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Deepak P. Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
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Barrero M, Lazarenkov A, Blanco E, Palma LG, López-Rubio AV, Bauer M, Bigas A, Di Croce L, Sardina JL, Payer B. The interferon γ pathway enhances pluripotency and X-chromosome reactivation in iPSC reprogramming. SCIENCE ADVANCES 2024; 10:eadj8862. [PMID: 39110794 PMCID: PMC11305397 DOI: 10.1126/sciadv.adj8862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) requires activation of the pluripotency network and resetting of the epigenome by erasing the epigenetic memory of the somatic state. In female mouse cells, a critical epigenetic reprogramming step is the reactivation of the inactive X chromosome. Despite its importance, a systematic understanding of the regulatory networks linking pluripotency and X-reactivation is missing. Here, we reveal important pathways for pluripotency acquisition and X-reactivation using a genome-wide CRISPR screen during neural precursor to iPSC reprogramming. In particular, we discover that activation of the interferon γ (IFNγ) pathway early during reprogramming accelerates pluripotency acquisition and X-reactivation. IFNγ stimulates STAT3 signaling and the pluripotency network and leads to enhanced TET-mediated DNA demethylation, which consequently boosts X-reactivation. We therefore gain a mechanistic understanding of the role of IFNγ in reprogramming and X-reactivation and provide a comprehensive resource of the molecular networks involved in these processes.
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Affiliation(s)
- Mercedes Barrero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | | | - Enrique Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luis G. Palma
- Josep Carreras Leukemia Research Institute (IJC), Badalona 08916, Spain
- Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona 08003, Spain
| | | | - Moritz Bauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Anna Bigas
- Josep Carreras Leukemia Research Institute (IJC), Badalona 08916, Spain
- Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona 08003, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- ICREA, Passeig Lluís Companys 23, Barcelona 08010, Spain
| | - José Luis Sardina
- Josep Carreras Leukemia Research Institute (IJC), Badalona 08916, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
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3
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Topa H, Benoit-Pilven C, Tukiainen T, Pietiläinen O. X-chromosome inactivation in human iPSCs provides insight into X-regulated gene expression in autosomes. Genome Biol 2024; 25:144. [PMID: 38822397 PMCID: PMC11143737 DOI: 10.1186/s13059-024-03286-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/17/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Variation in X chromosome inactivation (XCI) in human-induced pluripotent stem cells (hiPSCs) can impact their ability to model biological sex biases. The gene-wise landscape of X chromosome gene dosage remains unresolved in female hiPSCs. To characterize patterns of de-repression and escape from inactivation, we performed a systematic survey of allele specific expression in 165 female hiPSC lines. RESULTS XCI erosion is non-random and primarily affects genes that escape XCI in human tissues. Individual genes and cell lines vary in the frequency and degree of de-repression. Bi-allelic expression increases gradually after modest decrease of XIST in cultures, whose loss is commonly used to mark lines with eroded XCI. We identify three clusters of female lines at different stages of XCI. Increased XCI erosion amplifies female-biased expression at hypomethylated sites and regions normally occupied by repressive histone marks, lowering male-biased differences in the X chromosome. In autosomes, erosion modifies sex differences in a dose-dependent way. Male-biased genes are enriched for hypermethylated regions, and de-repression of XIST-bound autosomal genes in female lines attenuates normal male-biased gene expression in eroded lines. XCI erosion can compensate for a dominant loss of function effect in several disease genes. CONCLUSIONS We present a comprehensive view of X chromosome gene dosage in hiPSCs and implicate a direct mechanism for XCI erosion in regulating autosomal gene expression in trans. The uncommon and variable reactivation of X chromosome genes in female hiPSCs can provide insight into X chromosome's role in regulating gene expression and sex differences in humans.
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Affiliation(s)
- Hande Topa
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Clara Benoit-Pilven
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Olli Pietiläinen
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
- The Stanley Center for Psychiatric Research at the Broad Institute, of MIT and Harvard, Cambridge, MA, USA.
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4
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Mattimoe T, Payer B. The compleX balancing act of controlling X-chromosome dosage and how it impacts mammalian germline development. Biochem J 2023; 480:521-537. [PMID: 37096944 DOI: 10.1042/bcj20220450] [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: 08/24/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 04/26/2023]
Abstract
In female mammals, the two X chromosomes are subject to epigenetic gene regulation in order to balance X-linked gene dosage with autosomes and in relation to males, which have one X and one Y chromosome. This is achieved by an intricate interplay of several processes; X-chromosome inactivation and reactivation elicit global epigenetic regulation of expression from one X chromosome in a stage-specific manner, whilst the process of X-chromosome upregulation responds to this by fine-tuning transcription levels of the second X. The germline is unique in its function of transmitting both the genetic and epigenetic information from one generation to the next, and remodelling of the X chromosome is one of the key steps in setting the stage for successful development. Here, we provide an overview of the complex dynamics of X-chromosome dosage control during embryonic and germ cell development, and aim to decipher its potential role for normal germline competency.
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Affiliation(s)
- Tom Mattimoe
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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5
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Workman MJ, Lim RG, Wu J, Frank A, Ornelas L, Panther L, Galvez E, Perez D, Meepe I, Lei S, Valencia V, Gomez E, Liu C, Moran R, Pinedo L, Tsitkov S, Ho R, Kaye JA, Thompson T, Rothstein JD, Finkbeiner S, Fraenkel E, Sareen D, Thompson LM, Svendsen CN. Large-scale differentiation of iPSC-derived motor neurons from ALS and control subjects. Neuron 2023; 111:1191-1204.e5. [PMID: 36764301 PMCID: PMC10557526 DOI: 10.1016/j.neuron.2023.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/29/2022] [Accepted: 01/17/2023] [Indexed: 02/11/2023]
Abstract
Using induced pluripotent stem cells (iPSCs) to understand the mechanisms of neurological disease holds great promise; however, there is a lack of well-curated lines from a large array of participants. Answer ALS has generated over 1,000 iPSC lines from control and amyotrophic lateral sclerosis (ALS) patients along with clinical and whole-genome sequencing data. The current report summarizes cell marker and gene expression in motor neuron cultures derived from 92 healthy control and 341 ALS participants using a 32-day differentiation protocol. This is the largest set of iPSCs to be differentiated into motor neurons, and characterization suggests that cell composition and sex are significant sources of variability that need to be carefully controlled for in future studies. These data are reported as a resource for the scientific community that will utilize Answer ALS data for disease modeling using a wider array of omics being made available for these samples.
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Affiliation(s)
- Michael J Workman
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ryan G Lim
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Aaron Frank
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Loren Ornelas
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lindsay Panther
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Erick Galvez
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Daniel Perez
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Imara Meepe
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Susan Lei
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Viviana Valencia
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Emilda Gomez
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Chunyan Liu
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ruby Moran
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Louis Pinedo
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stanislav Tsitkov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ritchie Ho
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Neural Science and Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Julia A Kaye
- Center for Systems and Therapeutics, Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA; Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA; Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA; Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA; Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dhruv Sareen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Leslie M Thompson
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA; Department of Biological Chemistry, University of California, Irvine, CA, USA; Department of Neurobiology and Behavior, University of California, Irvine, CA, USA; Department of Psychiatry and Human Behavior and Sue and Bill Gross Stem Cell Center, University of California, Irvine, CA, USA.
| | - Clive N Svendsen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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6
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Cohesin controls X chromosome structure remodeling and X-reactivation during mouse iPSC-reprogramming. Proc Natl Acad Sci U S A 2023; 120:e2213810120. [PMID: 36669113 PMCID: PMC9942853 DOI: 10.1073/pnas.2213810120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Reactivation of the inactive X chromosome is a hallmark epigenetic event during reprogramming of mouse female somatic cells to induced pluripotent stem cells (iPSCs). This involves global structural remodeling from a condensed, heterochromatic into an open, euchromatic state, thereby changing a transcriptionally inactive into an active chromosome. Despite recent advances, very little is currently known about the molecular players mediating this process and how this relates to iPSC-reprogramming in general. To gain more insight, here we perform a RNAi-based knockdown screen during iPSC-reprogramming of mouse fibroblasts. We discover factors important for X chromosome reactivation (XCR) and iPSC-reprogramming. Among those, we identify the cohesin complex member SMC1a as a key molecule with a specific function in XCR, as its knockdown greatly affects XCR without interfering with iPSC-reprogramming. Using super-resolution microscopy, we find SMC1a to be preferentially enriched on the active compared with the inactive X chromosome and that SMC1a is critical for the decompacted state of the active X. Specifically, depletion of SMC1a leads to contraction of the active X both in differentiated and in pluripotent cells, where it normally is in its most open state. In summary, we reveal cohesin as a key factor for remodeling of the X chromosome from an inactive to an active structure and that this is a critical step for XCR during iPSC-reprogramming.
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7
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Sevinç K, Sevinç GG, Cavga AD, Philpott M, Kelekçi S, Can H, Cribbs AP, Yıldız AB, Yılmaz A, Ayar ES, Arabacı DH, Dunford JE, Ata D, Sigua LH, Qi J, Oppermann U, Onder TT. BRD9-containing non-canonical BAF complex maintains somatic cell transcriptome and acts as a barrier to human reprogramming. Stem Cell Reports 2022; 17:2629-2642. [PMID: 36332631 PMCID: PMC9768578 DOI: 10.1016/j.stemcr.2022.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Epigenetic reprogramming to pluripotency requires extensive remodeling of chromatin landscapes to silence existing cell-type-specific genes and activate pluripotency genes. ATP-dependent chromatin remodeling complexes are important regulators of chromatin structure and gene expression; however, the role of recently identified Bromodomain-containing protein 9 (BRD9) and the associated non-canonical BRG1-associated factors (ncBAF) complex in reprogramming remains unknown. Here, we show that genetic or chemical inhibition of BRD9, as well as ncBAF complex subunit GLTSCR1, but not the closely related BRD7, increase human somatic cell reprogramming efficiency and can replace KLF4 and c-MYC. We find that BRD9 is dispensable for human induced pluripotent stem cells under primed but not under naive conditions. Mechanistically, BRD9 inhibition downregulates fibroblast-related genes and decreases chromatin accessibility at somatic enhancers. BRD9 maintains the expression of transcriptional regulators MN1 and ZBTB38, both of which impede reprogramming. Collectively, these results establish BRD9 as an important safeguarding factor for somatic cell identity whose inhibition lowers chromatin-based barriers to reprogramming.
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Affiliation(s)
- Kenan Sevinç
- School of Medicine, Koç University, Istanbul, Turkey
| | | | - Ayşe Derya Cavga
- School of Medicine, Koç University, Istanbul, Turkey; Biostatistics, Bioinformatics and Data Management Core, KUTTAM, Koç University, Istanbul, Turkey
| | - Martin Philpott
- Botnar Research Centre, Oxford NIHR BRU, University of Oxford, Oxford, UK
| | - Simge Kelekçi
- School of Medicine, Koç University, Istanbul, Turkey
| | - Hazal Can
- School of Medicine, Koç University, Istanbul, Turkey
| | - Adam P Cribbs
- Botnar Research Centre, Oxford NIHR BRU, University of Oxford, Oxford, UK
| | | | | | | | | | - James E Dunford
- Botnar Research Centre, Oxford NIHR BRU, University of Oxford, Oxford, UK
| | - Deniz Ata
- School of Medicine, Koç University, Istanbul, Turkey
| | - Logan H Sigua
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Udo Oppermann
- Botnar Research Centre, Oxford NIHR BRU, University of Oxford, Oxford, UK; Centre for Medicine Discovery, University of Oxford, Oxford, UK; Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford OX3 7LD, UK
| | - Tamer T Onder
- School of Medicine, Koç University, Istanbul, Turkey.
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8
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Imprinting fidelity in mouse iPSCs depends on sex of donor cell and medium formulation. Nat Commun 2022; 13:5432. [PMID: 36114205 PMCID: PMC9481624 DOI: 10.1038/s41467-022-33013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Reprogramming of somatic cells into induced Pluripotent Stem Cells (iPSCs) is a major leap towards personalised approaches to disease modelling and cell-replacement therapies. However, we still lack the ability to fully control the epigenetic status of iPSCs, which is a major hurdle for their downstream applications. Epigenetic fidelity can be tracked by genomic imprinting, a phenomenon dependent on DNA methylation, which is frequently perturbed in iPSCs by yet unknown reasons. To try to understand the causes underlying these defects, we conducted a thorough imprinting analysis using IMPLICON, a high-throughput method measuring DNA methylation levels, in multiple female and male murine iPSC lines generated under different experimental conditions. Our results show that imprinting defects are remarkably common in iPSCs, but their nature depends on the sex of donor cells and their response to culture conditions. Imprints in female iPSCs resist the initial genome-wide DNA demethylation wave during reprogramming, but ultimately cells accumulate hypomethylation defects irrespective of culture medium formulations. In contrast, imprinting defects on male iPSCs depends on the experimental conditions and arise during reprogramming, being mitigated by the addition of vitamin C (VitC). Our findings are fundamental to further optimise reprogramming strategies and generate iPSCs with a stable epigenome. Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) is associated with epigenetic alterations. Here the authors assess DNA methylation in detail in multiple female and male mouse iPSC lines generated with different protocols and find that defects depend on the sex of donor cells and can be partially mitigated by Vitamin C.
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9
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Bauer M, Payer B, Filion GJ. Causality in transcription and genome folding: Insights from X inactivation. Bioessays 2022; 44:e2200105. [PMID: 36028473 DOI: 10.1002/bies.202200105] [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: 06/01/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 11/10/2022]
Abstract
The spatial organization of genomes is becoming increasingly understood. In mammals, where it is most investigated, this organization ties in with transcription, so an important research objective is to understand whether gene activity is a cause or a consequence of genome folding in space. In this regard, the phenomena of X-chromosome inactivation and reactivation open a unique window of investigation because of the singularities of the inactive X chromosome. Here we focus on the cause-consequence nexus between genome conformation and transcription and explain how recent results about the structural changes associated with inactivation and reactivation of the X chromosome shed light on this problem.
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Affiliation(s)
- Moritz Bauer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guillaume J Filion
- Dept. Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
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10
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A lifelong duty: how Xist maintains the inactive X chromosome. Curr Opin Genet Dev 2022; 75:101927. [PMID: 35717799 PMCID: PMC9472561 DOI: 10.1016/j.gde.2022.101927] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/10/2022] [Accepted: 05/14/2022] [Indexed: 11/22/2022]
Abstract
Female eutherians transcriptionally silence one X chromosome to balance gene dosage between the sexes. X-chromosome inactivation (XCI) is initiated by the lncRNA Xist, which assembles many proteins within the inactive X chromosome (Xi) to trigger gene silencing and heterochromatin formation. It is well established that gene silencing on the Xi is maintained through repressive epigenetic processes, including histone deacetylation and DNA methylation. Recent studies revealed a new mechanism where RNA-binding proteins that interact directly with the RNA contribute to the maintenance of Xist localization and gene silencing. In addition, a surprising plasticity of the Xi was uncovered with many genes becoming upregulated upon experimental deletion of Xist. Intriguingly, immune cells normally lose Xist from the Xi, suggesting that thisXist dependence is utilized in vivo to dynamically regulate gene expression from the Xi. These new studies expose fundamental regulatory mechanisms for the chromatin association of RNAs, highlight the need for studying the maintenance of XCI and Xist localization in a gene- and cell-type-specific manner, and are likely to have clinical impact.
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11
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XIST loss impairs mammary stem cell differentiation and increases tumorigenicity through Mediator hyperactivation. Cell 2022; 185:2164-2183.e25. [PMID: 35597241 DOI: 10.1016/j.cell.2022.04.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 01/10/2022] [Accepted: 04/27/2022] [Indexed: 12/27/2022]
Abstract
X inactivation (XCI) is triggered by upregulation of XIST, which coats the chromosome in cis, promoting formation of a heterochromatic domain (Xi). XIST role beyond initiation of XCI is only beginning to be elucidated. Here, we demonstrate that XIST loss impairs differentiation of human mammary stem cells (MaSCs) and promotes emergence of highly tumorigenic and metastatic carcinomas. On the Xi, XIST deficiency triggers epigenetic changes and reactivation of genes overlapping Polycomb domains, including Mediator subunit MED14. MED14 overdosage results in increased Mediator levels and hyperactivation of the MaSC enhancer landscape and transcriptional program, making differentiation less favorable. We further demonstrate that loss of XIST and Xi transcriptional instability is common among human breast tumors of poor prognosis. We conclude that XIST is a gatekeeper of human mammary epithelium homeostasis, thus unveiling a paradigm in the control of somatic cell identity with potential consequences for our understanding of gender-specific malignancies.
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12
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Severino J, Bauer M, Mattimoe T, Arecco N, Cozzuto L, Lorden P, Hamada N, Nosaka Y, Nagaoka SI, Audergon P, Tarruell A, Heyn H, Hayashi K, Saitou M, Payer B. Controlled X-chromosome dynamics defines meiotic potential of female mouse in vitro germ cells. EMBO J 2022; 41:e109457. [PMID: 35603814 PMCID: PMC9194795 DOI: 10.15252/embj.2021109457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 11/23/2022] Open
Abstract
The mammalian germline is characterized by extensive epigenetic reprogramming during its development into functional eggs and sperm. Specifically, the epigenome requires resetting before parental marks can be established and transmitted to the next generation. In the female germline, X‐chromosome inactivation and reactivation are among the most prominent epigenetic reprogramming events, yet very little is known about their kinetics and biological function. Here, we investigate X‐inactivation and reactivation dynamics using a tailor‐made in vitro system of primordial germ cell‐like cell (PGCLC) differentiation from mouse embryonic stem cells. We find that X‐inactivation in PGCLCs in vitro and in germ cell‐competent epiblast cells in vivo is moderate compared to somatic cells, and frequently characterized by escaping genes. X‐inactivation is followed by step‐wise X‐reactivation, which is mostly completed during meiotic prophase I. Furthermore, we find that PGCLCs which fail to undergo X‐inactivation or reactivate too rapidly display impaired meiotic potential. Thus, our data reveal fine‐tuned X‐chromosome remodelling as a critical feature of female germ cell development towards meiosis and oogenesis.
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Affiliation(s)
- Jacqueline Severino
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Moritz Bauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Tom Mattimoe
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Niccolò Arecco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Patricia Lorden
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Norio Hamada
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshiaki Nosaka
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - So I Nagaoka
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Pauline Audergon
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Tarruell
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
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13
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Mira-Bontenbal H, Tan B, Gontan C, Goossens S, Boers RG, Boers JB, Dupont C, van Royen ME, IJcken WFJ, French P, Bedalov A, Gribnau J. Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells. Stem Cell Reports 2022; 17:693-706. [PMID: 35148843 PMCID: PMC9039756 DOI: 10.1016/j.stemcr.2022.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 01/17/2023] Open
Abstract
Rett syndrome may be treated by reactivating the silent copy of Mecp2 from the inactive X chromosome in female cells. Most studies that model Mecp2 reactivation have used mouse fibroblasts rather than neural cells, which would be critical for phenotypic reversal, and rely on fluorescent reporters that lack adequate sensitivity. Here, we present a mouse model based on a dual bioluminescent and fluorescent reporter to assess the level of reactivation of Mecp2 and the inactive X chromosome by treating neural stem cells with 5-azacytidine and Xist knockdown. We show that reactivation of Mecp2 and other X-linked genes correlates with CpG density, with distance from escapees, and, very strongly, with the presence of short interspersed nuclear elements. In addition, X-linked genes reactivated in neural stem cells overlap substantially with early reactivating genes by induced pluripotent stem cell reprogramming of fibroblasts or neuronal progenitors, indicating that X chromosome reactivation follows similar paths regardless of the technique or cell type used.
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Affiliation(s)
- H Mira-Bontenbal
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands.
| | - B Tan
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - C Gontan
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - S Goossens
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - R G Boers
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - J B Boers
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - C Dupont
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - M E van Royen
- Department of Pathology, Erasmus MC, Rotterdam, the Netherlands
| | - W F J IJcken
- Center for Biomics, Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands
| | - P French
- Department of Neurology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
| | - A Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
| | - J Gribnau
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands.
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14
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X-chromosome reactivation: a concise review. Biochem Soc Trans 2021; 49:2797-2805. [PMID: 34821360 DOI: 10.1042/bst20210777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Mammalian females (XX) silence transcription on one of the two X chromosomes to compensate the expression dosage with males (XY). This process - named X-chromosome inactivation - entails a variety of epigenetic modifications that act synergistically to maintain silencing and make it heritable through cell divisions. Genes along the inactive X chromosome are, indeed, refractory to reactivation. Nonetheless, X-chromosome reactivation can occur alongside with epigenome reprogramming or by perturbing multiple silencing pathways. Here we review the events associated with X-chromosome reactivation during in vivo and in vitro reprogramming and highlight recent efforts in inducing Xi reactivation by molecular perturbations. This provides us with a first understanding of the mechanisms underlying X-chromosome reactivation, which could be tackled for therapeutic purposes.
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15
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Early reactivation of clustered genes on the inactive X chromosome during somatic cell reprogramming. Stem Cell Reports 2021; 17:53-67. [PMID: 34919813 PMCID: PMC8758948 DOI: 10.1016/j.stemcr.2021.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 12/04/2022] Open
Abstract
Reprogramming of murine female somatic cells to induced pluripotent stem cells (iPSCs) is accompanied by X chromosome reactivation (XCR), by which the inactive X chromosome (Xi) in female somatic cells becomes reactivated. However, how Xi initiates reactivation during reprogramming remains poorly defined. Here, we used a Sendai virus-based reprogramming system to generate partially reprogrammed iPSCs that appear to be undergoing the initial phase of XCR. Allele-specific RNA-seq of these iPSCs revealed that XCR initiates at a subset of genes clustered near the centromere region. The initial phase of XCR occurs when the cells transit through mesenchymal-epithelial transition (MET) before complete shutoff of Xist expression. Moreover, regulatory regions of these genes display dynamic changes in lysine-demethylase 1a (KDM1A) occupancy. Our results identified clustered genes on the Xi that show reactivation in the initial phase of XCR during reprogramming and suggest a possible role for histone demethylation in this process. Partially reprogrammed iPSCs enabled analyses of early events in XCR XCR initiates at a subset of genes clustered near the centromere region XCR occurs before complete shutoff of Xist expression during reprogramming KDM1A inhibition appears to directly reactivate transcription from the Xi
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16
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Talon I, Janiszewski A, Theeuwes B, Lefevre T, Song J, Bervoets G, Vanheer L, De Geest N, Poovathingal S, Allsop R, Marine JC, Rambow F, Voet T, Pasque V. Enhanced chromatin accessibility contributes to X chromosome dosage compensation in mammals. Genome Biol 2021; 22:302. [PMID: 34724962 PMCID: PMC8558763 DOI: 10.1186/s13059-021-02518-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/13/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Precise gene dosage of the X chromosomes is critical for normal development and cellular function. In mice, XX female somatic cells show transcriptional X chromosome upregulation of their single active X chromosome, while the other X chromosome is inactive. Moreover, the inactive X chromosome is reactivated during development in the inner cell mass and in germ cells through X chromosome reactivation, which can be studied in vitro by reprogramming of somatic cells to pluripotency. How chromatin processes and gene regulatory networks evolved to regulate X chromosome dosage in the somatic state and during X chromosome reactivation remains unclear. RESULTS Using genome-wide approaches, allele-specific ATAC-seq and single-cell RNA-seq, in female embryonic fibroblasts and during reprogramming to pluripotency, we show that chromatin accessibility on the upregulated mammalian active X chromosome is increased compared to autosomes. We further show that increased accessibility on the active X chromosome is erased by reprogramming, accompanied by erasure of transcriptional X chromosome upregulation and the loss of increased transcriptional burst frequency. In addition, we characterize gene regulatory networks during reprogramming and X chromosome reactivation, revealing changes in regulatory states. Our data show that ZFP42/REX1, a pluripotency-associated gene that evolved specifically in placental mammals, targets multiple X-linked genes, suggesting an evolutionary link between ZFP42/REX1, X chromosome reactivation, and pluripotency. CONCLUSIONS Our data reveal the existence of intrinsic compensatory mechanisms that involve modulation of chromatin accessibility to counteract X-to-Autosome gene dosage imbalances caused by evolutionary or in vitro X chromosome loss and X chromosome inactivation in mammalian cells.
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Affiliation(s)
- Irene Talon
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Adrian Janiszewski
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Bart Theeuwes
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Thomas Lefevre
- Laboratory of Reproductive Genomics, Centre for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Juan Song
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Lotte Vanheer
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Natalie De Geest
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Suresh Poovathingal
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Ryan Allsop
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Jean-Christophe Marine
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Florian Rambow
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Thierry Voet
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory of Reproductive Genomics, Centre for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
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17
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Chromosome compartments on the inactive X guide TAD formation independently of transcription during X-reactivation. Nat Commun 2021; 12:3499. [PMID: 34108480 PMCID: PMC8190187 DOI: 10.1038/s41467-021-23610-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 05/10/2021] [Indexed: 12/21/2022] Open
Abstract
A hallmark of chromosome organization is the partition into transcriptionally active A and repressed B compartments, and into topologically associating domains (TADs). Both structures were regarded to be absent from the inactive mouse X chromosome, but to be re-established with transcriptional reactivation and chromatin opening during X-reactivation. Here, we combine a tailor-made mouse iPSC reprogramming system and high-resolution Hi-C to produce a time course combining gene reactivation, chromatin opening and chromosome topology during X-reactivation. Contrary to previous observations, we observe A/B-like compartments on the inactive X harbouring multiple subcompartments. While partial X-reactivation initiates within a compartment rich in X-inactivation escapees, it then occurs rapidly along the chromosome, concomitant with downregulation of Xist. Importantly, we find that TAD formation precedes transcription and initiates from Xist-poor compartments. Here, we show that TAD formation and transcriptional reactivation are causally independent during X-reactivation while establishing Xist as a common denominator.
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18
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Bansal P, Ahern DT, Kondaveeti Y, Qiu CW, Pinter SF. Contiguous erosion of the inactive X in human pluripotency concludes with global DNA hypomethylation. Cell Rep 2021; 35:109215. [PMID: 34107261 PMCID: PMC8267460 DOI: 10.1016/j.celrep.2021.109215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/18/2020] [Accepted: 05/13/2021] [Indexed: 01/21/2023] Open
Abstract
Female human pluripotent stem cells (hPSCs) routinely undergo inactive X (Xi) erosion. This progressive loss of key repressive features follows the loss of XIST expression, the long non-coding RNA driving X inactivation, and causes reactivation of silenced genes across the eroding X (Xe). To date, the sporadic and progressive nature of erosion has obscured its scale, dynamics, and key transition events. To address this problem, we perform an integrated analysis of DNA methylation (DNAme), chromatin accessibility, and gene expression across hundreds of hPSC samples. Differential DNAme orders female hPSCs across a trajectory from initiation to terminal Xi erosion. Our results identify a cis-regulatory element crucial for XIST expression, trace contiguously growing reactivated domains to a few euchromatic origins, and indicate that the late-stage Xe impairs DNAme genome-wide. Surprisingly, from this altered regulatory landscape emerge select features of naive pluripotency, suggesting that its link to X dosage may be partially conserved in human embryonic development. Reactivation of the silenced X in human female iPSC/ESCs compromises their utility. Bansal et al. perform an integrated genomics analysis to reveal a prevalent X erosion trajectory that they validate in long-term culture. Starting with XIST loss, this trajectory indicates that reactivation may spread contiguously from escapees to silenced genes.
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Affiliation(s)
- Prakhar Bansal
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Darcy T Ahern
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Catherine W Qiu
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Stefan F Pinter
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA.
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19
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Brown KE, Fisher AG. Reprogramming lineage identity through cell-cell fusion. Curr Opin Genet Dev 2021; 70:15-23. [PMID: 34087754 DOI: 10.1016/j.gde.2021.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/12/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022]
Abstract
The conversion of differentiated cells to a pluripotent state through somatic cell nuclear transfer provided the first unequivocal evidence that differentiation was reversible. In more recent times, introducing a combination of key transcription factors into terminally differentiated mammalian cells was shown to drive their conversion to induced pluripotent stem cells (iPSCs). These discoveries were transformative, but the relatively slow speed (2-3 weeks) and low efficiency of reprogramming (0.1-1%) made deciphering the underlying molecular mechanisms difficult and complex. Cell fusion provides an alternative reprogramming approach that is both efficient and tractable, particularly when combined with modern multi-omics analysis of individual cells. Here we review the history and the recent advances in cell-cell fusion that are enabling a better understanding cell fate conversion, and we discuss how this knowledge could be used to shape improved strategies for regenerative medicine.
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Affiliation(s)
- Karen E Brown
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London W12 0NN, UK.
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London W12 0NN, UK
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20
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Haramoto Y, Sakata M, Kobayashi S. Visualization of X chromosome reactivation in mouse primordial germ cells in vivo. Biol Open 2021; 10:261692. [PMID: 33913476 PMCID: PMC8096617 DOI: 10.1242/bio.058602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/30/2021] [Indexed: 02/01/2023] Open
Abstract
X chromosome inactivation (XCI), determined during development, remains stable after embryonic cell divisions. However, primordial germ cells (PGCs) are exceptions in that XCI is reprogrammed and inactivated X chromosomes are reactivated. Although interactions between PGCs and somatic cells are thought to be important for PGC development, little is known about them. Here, we performed imaging of X chromosome reactivation (XCR) using the ‘Momiji’ mouse system, which can monitor the X chromosome's inactive and active states using two color fluorescence reporter genes, and investigated whether interactions would affect XCR in PGCs. Based on their expression levels, we found that XCR of the Pgk1 locus began at embryonic day (E)10.5 and was almost complete by E13.5. During this period, PGCs became distributed uniformly in the genital ridge, proliferated, and formed clusters; XCR progressed accordingly. In addition, XCR of the Pgk1 locus preceded that of the Hprt locus, indicating that the timing of epigenetic memory erasure varied according to the locus of each of these X-linked genes. Our results indicate that XCR proceeds along with the proliferation of PGCs clustered within the genital ridge. This article has an associated First Person interview with the first author of the paper. Summary: Imaging of mouse X chromosome activities reveals that they undergo reprogramming and reactivation while the primordial germ cells form clusters and proliferate in the genital ridge.
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Affiliation(s)
- Yoshikazu Haramoto
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Mino Sakata
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shin Kobayashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koutou-ku, Tokyo 135-0064, Japan.,Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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21
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Van Bergen NJ, Massey S, Stait T, Ellery M, Reljić B, Formosa LE, Quigley A, Dottori M, Thorburn D, Stroud DA, Christodoulou J. Abnormalities of mitochondrial dynamics and bioenergetics in neuronal cells from CDKL5 deficiency disorder. Neurobiol Dis 2021; 155:105370. [PMID: 33905871 DOI: 10.1016/j.nbd.2021.105370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/01/2021] [Accepted: 04/20/2021] [Indexed: 01/29/2023] Open
Abstract
CDKL5 deficiency disorder (CDD) is a rare neurodevelopmental disorder caused by pathogenic variants in the Cyclin-dependent kinase-like 5 (CDKL5) gene, resulting in dysfunctional CDKL5 protein. It predominantly affects females and causes seizures in the first few months of life, ultimately resulting in severe intellectual disability. In the absence of targeted therapies, treatment is currently only symptomatic. CDKL5 is a serine/threonine kinase that is highly expressed in the brain, with a critical role in neuronal development. Evidence of mitochondrial dysfunction in CDD is gathering, but has not been studied extensively. We used human patient-derived induced pluripotent stem cells with a pathogenic truncating mutation (p.Arg59*) and CRISPR/Cas9 gene-corrected isogenic controls, differentiated into neurons, to investigate the impact of CDKL5 mutation on cellular function. Quantitative proteomics indicated mitochondrial defects in CDKL5 p.Arg59* neurons, and mitochondrial bioenergetics analysis confirmed decreased activity of mitochondrial respiratory chain complexes. Additionally, mitochondrial trafficking velocity was significantly impaired, and there was a higher percentage of stationary mitochondria. We propose mitochondrial dysfunction is contributing to CDD pathology, and should be a focus for development of targeted treatments for CDD.
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Affiliation(s)
- Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Tegan Stait
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Molly Ellery
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Boris Reljić
- Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Anita Quigley
- Electrical and Biomedical Engineering, College of Science, Engineering and Health, RMIT University, Melbourne, Victoria 3000, Australia; Department of Medicine, University of Melbourne, St Vincent's Hospital Melbourne, Fitzroy, Victoria 3065, Australia; BioFab3D@ACMD, St Vincent's Hospital Melbourne, Fitzroy, Victoria 3065, Australia
| | - Mirella Dottori
- Centre for Neural Engineering, The University of Melbourne, Carlton, VIC 3010, Australia; Illawarra Health and Medical Research Institute, Centre for Molecular and Medical Bioscience, University of Wollongong, Wollongong, New South Wales 2500, Australia
| | - David Thorburn
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Australia; Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia.
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22
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Posfai E, Schell JP, Janiszewski A, Rovic I, Murray A, Bradshaw B, Yamakawa T, Pardon T, El Bakkali M, Talon I, De Geest N, Kumar P, To SK, Petropoulos S, Jurisicova A, Pasque V, Lanner F, Rossant J. Evaluating totipotency using criteria of increasing stringency. Nat Cell Biol 2021. [PMID: 33420491 DOI: 10.1101/2020.1103.1102.972893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Totipotency is the ability of a single cell to give rise to all of the differentiated cell types that build the conceptus, yet how to capture this property in vitro remains incompletely understood. Defining totipotency relies on a variety of assays of variable stringency. Here, we describe criteria to define totipotency. We explain how distinct criteria of increasing stringency can be used to judge totipotency by evaluating candidate totipotent cell types in mice, including early blastomeres and expanded or extended pluripotent stem cells. Our data challenge the notion that expanded or extended pluripotent states harbour increased totipotent potential relative to conventional embryonic stem cells under in vitro and in vivo conditions.
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Affiliation(s)
- Eszter Posfai
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - John Paul Schell
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Adrian Janiszewski
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Isidora Rovic
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Alexander Murray
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brian Bradshaw
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tatsuya Yamakawa
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tine Pardon
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Mouna El Bakkali
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Irene Talon
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Natalie De Geest
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Pankaj Kumar
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - San Kit To
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Sophie Petropoulos
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Andrea Jurisicova
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Departments of Obstetrics and Gynecology and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Vincent Pasque
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium.
| | - Fredrik Lanner
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden.
- Ming Wai Lau Center for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden.
| | - Janet Rossant
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.
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23
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Posfai E, Schell JP, Janiszewski A, Rovic I, Murray A, Bradshaw B, Yamakawa T, Pardon T, El Bakkali M, Talon I, De Geest N, Kumar P, To SK, Petropoulos S, Jurisicova A, Pasque V, Lanner F, Rossant J. Evaluating totipotency using criteria of increasing stringency. Nat Cell Biol 2021; 23:49-60. [PMID: 33420491 DOI: 10.1038/s41556-020-00609-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 11/17/2020] [Indexed: 01/28/2023]
Abstract
Totipotency is the ability of a single cell to give rise to all of the differentiated cell types that build the conceptus, yet how to capture this property in vitro remains incompletely understood. Defining totipotency relies on a variety of assays of variable stringency. Here, we describe criteria to define totipotency. We explain how distinct criteria of increasing stringency can be used to judge totipotency by evaluating candidate totipotent cell types in mice, including early blastomeres and expanded or extended pluripotent stem cells. Our data challenge the notion that expanded or extended pluripotent states harbour increased totipotent potential relative to conventional embryonic stem cells under in vitro and in vivo conditions.
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Affiliation(s)
- Eszter Posfai
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - John Paul Schell
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Adrian Janiszewski
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Isidora Rovic
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Alexander Murray
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brian Bradshaw
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tatsuya Yamakawa
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tine Pardon
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Mouna El Bakkali
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Irene Talon
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Natalie De Geest
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Pankaj Kumar
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - San Kit To
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Sophie Petropoulos
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Andrea Jurisicova
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Departments of Obstetrics and Gynecology and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Vincent Pasque
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium.
| | - Fredrik Lanner
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden.
- Ming Wai Lau Center for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden.
| | - Janet Rossant
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.
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24
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Panda A, Zylicz JJ, Pasque V. New Insights into X-Chromosome Reactivation during Reprogramming to Pluripotency. Cells 2020; 9:E2706. [PMID: 33348832 PMCID: PMC7766869 DOI: 10.3390/cells9122706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Dosage compensation between the sexes results in one X chromosome being inactivated during female mammalian development. Chromosome-wide transcriptional silencing from the inactive X chromosome (Xi) in mammalian cells is erased in a process termed X-chromosome reactivation (XCR), which has emerged as a paradigm for studying the reversal of chromatin silencing. XCR is linked with germline development and induction of naive pluripotency in the epiblast, and also takes place upon reprogramming somatic cells to induced pluripotency. XCR depends on silencing of the long non-coding RNA (lncRNA) X inactive specific transcript (Xist) and is linked with the erasure of chromatin silencing. Over the past years, the advent of transcriptomics and epigenomics has provided new insights into the transcriptional and chromatin dynamics with which XCR takes place. However, multiple questions remain unanswered about how chromatin and transcription related processes enable XCR. Here, we review recent work on establishing the transcriptional and chromatin kinetics of XCR, as well as discuss a model by which transcription factors mediate XCR not only via Xist repression, but also by direct targeting of X-linked genes.
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Affiliation(s)
- Amitesh Panda
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
| | - Jan J. Zylicz
- The Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Vincent Pasque
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
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