1
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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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2
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Ziemka-Nalecz M, Pawelec P, Ziabska K, Zalewska T. Sex Differences in Brain Disorders. Int J Mol Sci 2023; 24:14571. [PMID: 37834018 PMCID: PMC10572175 DOI: 10.3390/ijms241914571] [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: 09/06/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
A remarkable feature of the brain is its sexual dimorphism. Sexual dimorphism in brain structure and function is associated with clinical implications documented previously in healthy individuals but also in those who suffer from various brain disorders. Sex-based differences concerning some features such as the risk, prevalence, age of onset, and symptomatology have been confirmed in a range of neurological and neuropsychiatric diseases. The mechanisms responsible for the establishment of sex-based differences between men and women are not fully understood. The present paper provides up-to-date data on sex-related dissimilarities observed in brain disorders and highlights the most relevant features that differ between males and females. The topic is very important as the recognition of disparities between the sexes might allow for the identification of therapeutic targets and pharmacological approaches for intractable neurological and neuropsychiatric disorders.
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Affiliation(s)
| | | | | | - Teresa Zalewska
- NeuroRepair Department, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5, A. Pawinskiego Str., 02-106 Warsaw, Poland; (M.Z.-N.); (P.P.); (K.Z.)
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3
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Gutierrez WR, Scherer A, Rytlewski JD, Laverty EA, Sheehan AP, McGivney GR, Brockman QR, Knepper-Adrian V, Roughton GA, Quelle DE, Gordon DJ, Monga V, Dodd RD. Augmenting chemotherapy with low-dose decitabine through an immune-independent mechanism. JCI Insight 2022; 7:e159419. [PMID: 36227698 PMCID: PMC9746804 DOI: 10.1172/jci.insight.159419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 10/11/2022] [Indexed: 12/15/2022] Open
Abstract
The DNA methyltransferase inhibitor decitabine has classically been used to reactivate silenced genes and as a pretreatment for anticancer therapies. In a variation of this idea, this study explores the concept of adding low-dose decitabine (DAC) following administration of chemotherapy to bolster therapeutic efficacy. We find that addition of DAC following treatment with the chemotherapy agent gemcitabine improves survival and slows tumor growth in a mouse model of high-grade sarcoma. Unlike prior studies in epithelial tumor models, DAC did not induce a robust antitumor T cell response in sarcoma. Furthermore, DAC synergizes with gemcitabine independently of the immune system. Mechanistic analyses demonstrate that the combination therapy induces biphasic cell cycle arrest and apoptosis. Therapeutic efficacy was sequence dependent, with gemcitabine priming cells for treatment with DAC through inhibition of ribonucleotide reductase. This study identifies an apparently unique application of DAC to augment the cytotoxic effects of conventional chemotherapy in an immune-independent manner. The concepts explored in this study represent a promising paradigm for cancer treatment by augmenting chemotherapy through addition of DAC to increase tolerability and improve patient response. These findings have widespread implications for the treatment of sarcomas and other aggressive malignancies.
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Affiliation(s)
- Wade R. Gutierrez
- Cancer Biology Graduate Program
- Medical Scientist Training Program
- Holden Comprehensive Cancer Center
- Department of Internal Medicine
| | - Amanda Scherer
- Holden Comprehensive Cancer Center
- Department of Internal Medicine
| | | | | | - Alexa P. Sheehan
- Holden Comprehensive Cancer Center
- Department of Internal Medicine
- Molecular Medicine Graduate Program
| | - Gavin R. McGivney
- Cancer Biology Graduate Program
- Holden Comprehensive Cancer Center
- Department of Internal Medicine
- Department of Molecular Physiology and Biophysics
| | - Qierra R. Brockman
- Holden Comprehensive Cancer Center
- Department of Internal Medicine
- Molecular Medicine Graduate Program
| | | | | | - Dawn E. Quelle
- Cancer Biology Graduate Program
- Medical Scientist Training Program
- Holden Comprehensive Cancer Center
- Molecular Medicine Graduate Program
- Department of Neuroscience and Pharmacology
- Department of Pathology, and
| | - David J. Gordon
- Holden Comprehensive Cancer Center
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Varun Monga
- Holden Comprehensive Cancer Center
- Department of Internal Medicine
| | - Rebecca D. Dodd
- Cancer Biology Graduate Program
- Medical Scientist Training Program
- Holden Comprehensive Cancer Center
- Department of Internal Medicine
- Molecular Medicine Graduate Program
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4
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Lin C, Xie Y, Huang W, Lin D, Lin L. 5-Aza-dC promotes T-cell acute lymphoblastic leukemia cell invasion via downregulation of DNMT1 and upregulation of MMP-2 and MMP-9. Exp Hematol 2022; 114:43-53.e2. [PMID: 35908628 DOI: 10.1016/j.exphem.2022.07.301] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/04/2022]
Abstract
5-Aza-2'-deoxycytidine (5-Aza-dC) is a demethylation agent known to deplete DNA methyltransferases (DNMTs) in leukemia cancer cells, and can restore the expression of their target genes in Jurkat cells. The goal of this study was to discern the potential effect of 5-Aza-dC on the invasion of T-ALL cells in acute lymphoblastic leukemia (ALL). The role of matrix metallopeptidase (MMP)-2, MMP-9, and DNMT1 in cell invasion was determined using loss- and gain-of-function investigations in Jurkat- and Sup-T1-R cells. A nude mouse model of ALL was established for further exploration of their roles in vivo. MMP-2 and MMP-9 exhibited high expression and low DNA methylation levels in 5-Aza-dC-resistant T-ALL cells. DNMT1 was poorly expressed in 5-Aza-dC-resistant T-ALL cells and exhibited decreased enrichment in the promoter region of MMP-2 and MMP-9. Silencing of MMP-2 and MMP-9 or DNMT1 overexpression reduced T-ALL cell invasion. After treatment of Sup-T1 cells with 5-Aza-dC, MMP-2 and MMP-9 presented with reduced DNA methylation levels but increased expression, and DNMT1 expression was identified to be suppressed. Further, in vivo assays revealed that DNMT1 alleviated T-ALL by reducing the expression of MMP-2 and MMP-9 in vivo. All in all, 5-Aza-dC activates MMP-2 and MMP-9 expression by reducing DNMT1-dependent DNA methylation levels and, hence, promotes the invasion of T-ALL cells.
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Affiliation(s)
- Congmeng Lin
- Department of Hematology, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, China
| | - Yongxin Xie
- Department of Hematology, Second Hospital of Longyan, Longyan, China
| | - Wenwen Huang
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China.
| | - Dayi Lin
- Department of Hematology, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, China
| | - Luhui Lin
- Department of Hematology, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, China
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5
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Grimm NB, Lee JT. Selective Xi reactivation and alternative methods to restore MECP2 function in Rett syndrome. Trends Genet 2022; 38:920-943. [PMID: 35248405 PMCID: PMC9915138 DOI: 10.1016/j.tig.2022.01.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
Abstract
The human X-chromosome harbors only 4% of our genome but carries over 20% of genes associated with intellectual disability. Given that they inherit only one X-chromosome, males are more frequently affected by X-linked neurodevelopmental genetic disorders than females. However, despite inheriting two X-chromosomes, females can also be affected because X-chromosome inactivation enables only one of two X-chromosomes to be expressed per cell. For Rett syndrome and similar X-linked disorders affecting females, disease-specific treatments have remained elusive. However, a cure may be found within their own cells because every sick cell carries a healthy copy of the affected gene on the inactive X (Xi). Therefore, selective Xi reactivation may be a viable approach that would address the root cause of various X-linked disorders. Here, we discuss Rett syndrome and compare current approaches in the pharmaceutical pipeline to restore MECP2 function. We then focus on Xi reactivation and review available methods, lessons learned, and future directions.
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Affiliation(s)
- Niklas-Benedikt Grimm
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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6
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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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7
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BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation. Nat Commun 2022; 13:1658. [PMID: 35351876 PMCID: PMC8964718 DOI: 10.1038/s41467-022-29333-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/10/2022] [Indexed: 12/12/2022] Open
Abstract
The process of epigenetic silencing, while fundamentally important, is not yet completely understood. Here we report a replenishable female mouse embryonic stem cell (mESC) system, Xmas, that allows rapid assessment of X chromosome inactivation (XCI), the epigenetic silencing mechanism of one of the two X chromosomes that enables dosage compensation in female mammals. Through a targeted genetic screen in differentiating Xmas mESCs, we reveal that the BAF complex is required to create nucleosome-depleted regions at promoters on the inactive X chromosome during the earliest stages of establishment of XCI. Without this action gene silencing fails. Xmas mESCs provide a tractable model for screen-based approaches that enable the discovery of unknown facets of the female-specific process of XCI and epigenetic silencing more broadly. Female embryonic stem cells (ESCs) are the ideal model to study X chromosome inactivation (XCI) establishment; however, these cells are challenging to keep in culture. Here the authors create fluorescent ‘Xmas’ reporter mice as a renewable source of ESCs and show nucleosome remodelers Smarcc1 and Smarca4 create a nucleosome-free promoter region prior to the establishment of silencing.
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8
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Good KV, Vincent JB, Ausió J. MeCP2: The Genetic Driver of Rett Syndrome Epigenetics. Front Genet 2021; 12:620859. [PMID: 33552148 PMCID: PMC7859524 DOI: 10.3389/fgene.2021.620859] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Mutations in methyl CpG binding protein 2 (MeCP2) are the major cause of Rett syndrome (RTT), a rare neurodevelopmental disorder with a notable period of developmental regression following apparently normal initial development. Such MeCP2 alterations often result in changes to DNA binding and chromatin clustering ability, and in the stability of this protein. Among other functions, MeCP2 binds to methylated genomic DNA, which represents an important epigenetic mark with broad physiological implications, including neuronal development. In this review, we will summarize the genetic foundations behind RTT, and the variable degrees of protein stability exhibited by MeCP2 and its mutated versions. Also, past and emerging relationships that MeCP2 has with mRNA splicing, miRNA processing, and other non-coding RNAs (ncRNA) will be explored, and we suggest that these molecules could be missing links in understanding the epigenetic consequences incurred from genetic ablation of this important chromatin modifier. Importantly, although MeCP2 is highly expressed in the brain, where it has been most extensively studied, the role of this protein and its alterations in other tissues cannot be ignored and will also be discussed. Finally, the additional complexity to RTT pathology introduced by structural and functional implications of the two MeCP2 isoforms (MeCP2-E1 and MeCP2-E2) will be described. Epigenetic therapeutics are gaining clinical popularity, yet treatment for Rett syndrome is more complicated than would be anticipated for a purely epigenetic disorder, which should be taken into account in future clinical contexts.
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Affiliation(s)
- Katrina V. Good
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John B. Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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9
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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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10
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Lu Z, Guo JK, Wei Y, Dou DR, Zarnegar B, Ma Q, Li R, Zhao Y, Liu F, Choudhry H, Khavari PA, Chang HY. Structural modularity of the XIST ribonucleoprotein complex. Nat Commun 2020; 11:6163. [PMID: 33268787 PMCID: PMC7710737 DOI: 10.1038/s41467-020-20040-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs are thought to regulate gene expression by organizing protein complexes through unclear mechanisms. XIST controls the inactivation of an entire X chromosome in female placental mammals. Here we develop and integrate several orthogonal structure-interaction methods to demonstrate that XIST RNA-protein complex folds into an evolutionarily conserved modular architecture. Chimeric RNAs and clustered protein binding in fRIP and eCLIP experiments align with long-range RNA secondary structure, revealing discrete XIST domains that interact with distinct sets of effector proteins. CRISPR-Cas9-mediated permutation of the Xist A-repeat location shows that A-repeat serves as a nucleation center for multiple Xist-associated proteins and m6A modification. Thus modular architecture plays an essential role, in addition to sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and suggests a general strategy for mechanistic studies of large ribonucleoprotein assemblies.
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Affiliation(s)
- Zhipeng Lu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, 90089, USA.
| | - Jimmy K Guo
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Diana R Dou
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Brian Zarnegar
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Qing Ma
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Synthetic Biology Department, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, PR China
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Yang Zhao
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Fan Liu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Hani Choudhry
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, 22252, Saudi Arabia
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA.
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11
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Janiszewski A, Talon I, Chappell J, Collombet S, Song J, De Geest N, To SK, Bervoets G, Marin-Bejar O, Provenzano C, Vanheer L, Marine JC, Rambow F, Pasque V. Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming. Genome Res 2019; 29:1659-1672. [PMID: 31515287 PMCID: PMC6771397 DOI: 10.1101/gr.249706.119] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022]
Abstract
Induction and reversal of chromatin silencing is critical for successful development, tissue homeostasis, and the derivation of induced pluripotent stem cells (iPSCs). X-Chromosome inactivation (XCI) and reactivation (XCR) in female cells represent chromosome-wide transitions between active and inactive chromatin states. Although XCI has long been studied, providing important insights into gene regulation, the dynamics and mechanisms underlying the reversal of stable chromatin silencing of X-linked genes are much less understood. Here, we use allele-specific transcriptomics to study XCR during mouse iPSC reprogramming in order to elucidate the timing and mechanisms of chromosome-wide reversal of gene silencing. We show that XCR is hierarchical, with subsets of genes reactivating early, late, and very late during reprogramming. Early genes are activated before the onset of late pluripotency genes activation. Early genes are located genomically closer to genes that escape XCI, unlike genes reactivating late. Early genes also show increased pluripotency transcription factor (TF) binding. We also reveal that histone deacetylases (HDACs) restrict XCR in reprogramming intermediates and that the severe hypoacetylation state of the inactive X Chromosome (Xi) persists until late reprogramming stages. Altogether, these results reveal the timing of transcriptional activation of monoallelically repressed genes during iPSC reprogramming, and suggest that allelic activation involves the combined action of chromatin topology, pluripotency TFs, and chromatin regulators. These findings are important for our understanding of gene silencing, maintenance of cell identity, reprogramming, and disease.
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Affiliation(s)
- Adrian Janiszewski
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Irene Talon
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Joel Chappell
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Samuel Collombet
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Juan Song
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Natalie De Geest
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - San Kit To
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Oskar Marin-Bejar
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Caterina Provenzano
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Lotte Vanheer
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Vincent Pasque
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
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12
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Talon I, Janiszewski A, Chappell J, Vanheer L, Pasque V. Recent Advances in Understanding the Reversal of Gene Silencing During X Chromosome Reactivation. Front Cell Dev Biol 2019; 7:169. [PMID: 31552244 PMCID: PMC6733891 DOI: 10.3389/fcell.2019.00169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/07/2019] [Indexed: 12/24/2022] Open
Abstract
Dosage compensation between XX female and XY male cells is achieved by a process known as X chromosome inactivation (XCI) in mammals. XCI is initiated early during development in female cells and is subsequently stably maintained in most somatic cells. Despite its stability, the robust transcriptional silencing of XCI is reversible, in the embryo and also in a number of reprogramming settings. Although XCI has been intensively studied, the dynamics, factors, and mechanisms of X chromosome reactivation (XCR) remain largely unknown. In this review, we discuss how new sequencing technologies and reprogramming approaches have enabled recent advances that revealed the timing of transcriptional activation during XCR. We also discuss the factors and chromatin features that might be important to understand the dynamics and mechanisms of the erasure of transcriptional gene silencing on the inactive X chromosome (Xi).
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Affiliation(s)
| | | | | | | | - Vincent Pasque
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
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13
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Repele A. Robust Normalization of Luciferase Reporter Data. Methods Protoc 2019; 2:mps2030062. [PMID: 31349610 PMCID: PMC6789503 DOI: 10.3390/mps2030062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/14/2019] [Accepted: 07/22/2019] [Indexed: 11/26/2022] Open
Abstract
Transient Luciferase reporter assays are widely used in the study of gene regulation and intracellular cell signaling. In order to control for sample-to-sample variation in luminescence arising from variability in transfection efficiency and other sources, an internal control reporter is co-transfected with the experimental reporter. The luminescence of the experimental reporter is normalized against the control by taking the ratio of the two. Here we show that this method of normalization, “ratiometric”, performs poorly when the transfection efficiency is low and leads to biased estimates of relative activity. We propose an alternative methodology based on linear regression that is much better suited for the normalization of reporter data, especially when transfection efficiency is low. We compare the ratiometric method against three regression methods on both simulated and empirical data. Our results suggest that robust errors-in-variables (REIV) regression performs the best in normalizing Luciferase reporter data. We have made the R code for Luciferase data normalization using REIV available on GitHub.
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Affiliation(s)
- Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, ND 58202, USA
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14
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Giri AK, Aittokallio T. DNMT Inhibitors Increase Methylation in the Cancer Genome. Front Pharmacol 2019; 10:385. [PMID: 31068808 PMCID: PMC6491738 DOI: 10.3389/fphar.2019.00385] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/27/2019] [Indexed: 01/16/2023] Open
Abstract
DNA methyltransferase inhibitors (DNMTi) decitabine and azacytidine are approved therapies for myelodysplastic syndrome and acute myeloid leukemia, and their combinations with other anticancer agents are being tested as therapeutic options for multiple solid cancers such as colon, ovarian, and lung cancer. However, the current therapeutic challenges of DNMTis include development of resistance, severe side effects and no or partial treatment responses, as observed in more than half of the patients. Therefore, there is a critical need to better understand the mechanisms of action of these drugs. In order to discover molecular targets of DNMTi therapy, we identified 638 novel CpGs with an increased methylation in response to decitabine treatment in HCT116 cell lines and validated the findings in multiple cancer types (e.g., bladder, ovarian, breast, and lymphoma) cell lines, bone marrow mononuclear cells from primary leukemia patients, as well as peripheral blood mononuclear cells and ascites from platinum resistance epithelial ovarian cancer patients. Azacytidine treatment also increased methylation of these CpGs in colon, ovarian, breast, and lymphoma cancer cell lines. Methylation at 166 identified CpGs strongly correlated (|r|≥ 0.80) with corresponding gene expression in HCT116 cell line. Differences in methylation at some of the identified CpGs and expression changes of the corresponding genes was observed in TCGA colon cancer tissue as compared to adjacent healthy tissue. Our analysis revealed that hypermethylated CpGs are involved in cancer cell proliferation and apoptosis by P53 and olfactory receptor pathways, hence influencing DNMTi responses. In conclusion, we showed hypermethylation of CpGs as a novel mechanism of action for DNMTi agents and identified 638 hypermethylated molecular targets (CpGs) common to decitabine and azacytidine therapy. These novel results suggest that hypermethylation of CpGs should be considered when predicting the DNMTi responses and side effects in cancer patients.
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Affiliation(s)
- Anil K Giri
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,Helsinki Institute for Information Technology, Department of Computer Science, Aalto University, Espoo, Finland.,Department of Mathematics and Statistics, University of Turku, Turku, Finland
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15
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Yamamoto-Shimojima K, Imaizumi T, Aoki Y, Inoue K, Kaname T, Okuno Y, Muramatsu H, Kato K, Yamamoto T. Elucidation of the pathogenic mechanism and potential treatment strategy for a female patient with spastic paraplegia derived from a single-nucleotide deletion in PLP1. J Hum Genet 2019; 64:665-671. [PMID: 31004103 DOI: 10.1038/s10038-019-0600-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/24/2019] [Accepted: 04/04/2019] [Indexed: 11/09/2022]
Abstract
Pelizaeus-Merzbacher disease (PMD) is an X-linked recessive disorder caused by abnormalities in the gene PLP1. Most females harboring heterozygous PLP1 abnormalities are basically asymptomatic. However, as a result of abnormal patterns of X-chromosome inactivation, it is possible for some female carriers to be symptomatic. Whole-exome sequencing of a female patient with unknown spastic paraplegia was performed to obtain a molecular diagnosis. As a result, a de novo heterozygous single-nucleotide deletion in PLP1 [NM_000533.5(PLP1_v001):c.783del; p.Thr262Leufs*20] was identified. RNA sequencing was performed in a patient-derived lymphoblastoid cell line, confirming mono-allelic expression of the mutated allele and abnormal inactivation of the wild-type allele. The patient-derived lymphoblastoid cell line was then treated with VX680 or 5azadC, which resulted in restored expression of the wild-type allele. These two agents thus have the potential to reverse inappropriately-skewed inactivation of the X-chromosome.
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Affiliation(s)
- Keiko Yamamoto-Shimojima
- Japan Society for the Promotion of Science (RPD), Tokyo, 160-8582, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.,Tokyo Women's Medical University, Institute of Integrated Medical Sciences, Tokyo, 162-8666, Japan
| | - Taichi Imaizumi
- Department of Gene Medicine, Graduate school of Medicine, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.,Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, 216-8511, Japan
| | - Yusuke Aoki
- Department of Neurology, Aichi Children's Health and Medical Center, Aichi, 474-8710, Japan
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, 187-0031, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, 157-8535, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Department of Advanced Medicine, Nagoya University Hospital, Nagoya, 466-8560, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, 466-8560, Japan
| | - Kohji Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, 466-8560, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, 162-8666, Japan. .,Tokyo Women's Medical University, Institute of Integrated Medical Sciences, Tokyo, 162-8666, Japan. .,Department of Gene Medicine, Graduate school of Medicine, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
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16
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Treating Rett syndrome: from mouse models to human therapies. Mamm Genome 2019; 30:90-110. [PMID: 30820643 PMCID: PMC6606665 DOI: 10.1007/s00335-019-09793-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/09/2019] [Indexed: 02/06/2023]
Abstract
Rare diseases are very difficult to study mechanistically and to develop therapies for because of the scarcity of patients. Here, the rare neuro-metabolic disorder Rett syndrome (RTT) is discussed as a prototype for precision medicine, demonstrating how mouse models have led to an understanding of the development of symptoms. RTT is caused by mutations in the X-linked gene methyl-CpG-binding protein 2 (MECP2). Mecp2-mutant mice are being used in preclinical studies that target the MECP2 gene directly, or its downstream pathways. Importantly, this work may improve the health of RTT patients. Clinical presentation may vary widely among individuals based on their mutation, but also because of the degree of X chromosome inactivation and the presence of modifier genes. Because it is a complex disorder involving many organ systems, it is likely that recovery of RTT patients will involve a combination of treatments. Precision medicine is warranted to provide the best efficacy to individually treat RTT patients.
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17
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Jégu T, Blum R, Cochrane JC, Yang L, Wang CY, Gilles ME, Colognori D, Szanto A, Marr SK, Kingston RE, Lee JT. Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome. Nat Struct Mol Biol 2019; 26:96-109. [PMID: 30664740 PMCID: PMC6421574 DOI: 10.1038/s41594-018-0176-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/03/2018] [Indexed: 02/08/2023]
Abstract
The noncoding RNA Xist recruits silencing factors to the inactive X chromosome (Xi) and facilitates re-organization of Xi structure. Here, we examine the mouse epigenomic landscape of Xi and assess how Xist alters chromatin accessibility. Interestingly, Xist deletion triggers a gain of accessibility of selective chromatin regions that is regulated by BRG1, an ATPase subunit of the SWI/SNF chromatin remodeling complex. In vitro, RNA binding inhibits nucleosome remodeling and ATPase activities of BRG1, while in cell culture Xist directly interacts with BRG1 and expels BRG1 from the Xi. Xist ablation leads to a selective return of BRG1 in cis, starting from pre-existing BRG1 sites that are free of Xist. BRG1 re-association correlates with cohesin binding and restoration of topologically associated domains (TADs), and results in formation of de novo Xi “superloops.” Thus, Xist binding inhibits BRG1’s nucleosome remodeling activity and results in expulsion of the SWI/SNF complex from the Xi.
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Affiliation(s)
- Teddy Jégu
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Roy Blum
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jesse C Cochrane
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lin Yang
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chen-Yu Wang
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maud-Emmanuelle Gilles
- Institute for RNA Medicine, Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - David Colognori
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Attila Szanto
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sharon K Marr
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute, Boston, MA, USA. .,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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18
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Tsix-Mecp2 female mouse model for Rett syndrome reveals that low-level MECP2 expression extends life and improves neuromotor function. Proc Natl Acad Sci U S A 2018; 115:8185-8190. [PMID: 30038001 DOI: 10.1073/pnas.1800931115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rett syndrome (RTT) is a severe neurodevelopmental disorder caused by a mutation in the X-linked methyl-CpG-binding protein 2 (MECP2). There is currently no disease-specific treatment, but MECP2 restoration through reactivation of the inactive X (Xi) has been of considerable interest. Progress toward an Xi-reactivation therapy has been hampered by a lack of suitable female mouse models. Because of cellular mosaicism due to random X-chromosome inactivation (XCI), Mecp2+/- heterozygous females develop only mild RTT. Here, we create an improved female mouse model by introducing a mutation in Tsix, the antisense regulator of XCI allelic choice. Tsix-Mecp2 mice show reduced MECP2 mosaicism and closely phenocopy the severely affected Mecp2-null males. Tsix-Mecp2 females demonstrate shortened lifespan, motor weakness, tremors, and gait disturbance. Intriguingly, they also exhibit repetitive behaviors, as is often seen in human RTT, including excessive grooming and biting that result in self-injury. With a Tsix allelic series, we vary MECP2 levels in brain and demonstrate a direct, but nonlinear correlation between MECP2 levels and phenotypic improvement. As little as 5-10% MECP2 restoration improves neuromotor function and extends lifespan five- to eightfold. Our study thus guides future pharmacological strategies and suggests that partial MECP2 restoration could have disproportionate therapeutic benefit.
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19
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Mougeot JL, Noll BD, Bahrani Mougeot FK. Sjögren's syndrome X-chromosome dose effect: An epigenetic perspective. Oral Dis 2018; 25:372-384. [PMID: 29316023 DOI: 10.1111/odi.12825] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/12/2017] [Accepted: 12/20/2017] [Indexed: 02/06/2023]
Abstract
Sjögren's syndrome (SS) is a chronic autoimmune disease affecting exocrine glands leading to mouth and eyes dryness. The extent to which epigenetic DNA methylation changes are responsible for an X-chromosome dose effect has yet to be determined. Our objectives were to (i) describe how epigenetic DNA methylation changes could explain an X-chromosome dose effect in SS for women with normal 46,XX genotype and (ii) determine the relevant relationships to this dose effect, between X-linked genes, genes controlling X-chromosome inactivation (XCI) and genes encoding associated transcription factors, all of which are differentially expressed and/or differentially methylated in the salivary glands of patients with SS. We identified 58 upregulated X-chromosome genes, including 22 genes previously shown to escape XCI, based on the analysis of SS patient salivary gland GEO2R gene expression datasets. Moreover, we found XIST and its cis regulators RLIM, FTX, and CHIC1, and polycomb repressor genes of the PRC1/2 complexes to be upregulated. Many of the X-chromosome genes implicated in SS pathogenesis can be regulated by transcription factors which we found to be overexpressed and/or differentially methylated in patients with SS. Determination of the mechanisms underlying methylation-dependent gene expression and impaired XCI is needed to further elucidate the etiopathogenesis of SS.
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Affiliation(s)
- J-Lc Mougeot
- Department of Oral Medicine-Cannon Research Center, Carolinas HealthCare System, Charlotte, NC, USA.,Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - B D Noll
- Department of Oral Medicine-Cannon Research Center, Carolinas HealthCare System, Charlotte, NC, USA.,Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - F K Bahrani Mougeot
- Department of Oral Medicine-Cannon Research Center, Carolinas HealthCare System, Charlotte, NC, USA.,Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
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20
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Zhu KW, Chen P, Zhang DY, Yan H, Liu H, Cen LN, Liu YL, Cao S, Zhou G, Zeng H, Chen SP, Zhao XL, Chen XP. Association of genetic polymorphisms in genes involved in Ara-C and dNTP metabolism pathway with chemosensitivity and prognosis of adult acute myeloid leukemia (AML). J Transl Med 2018; 16:90. [PMID: 29631596 PMCID: PMC5892020 DOI: 10.1186/s12967-018-1463-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
Background Cytarabine arabinoside (Ara-C) has been the core of chemotherapy for adult acute myeloid leukemia (AML). Ara-C undergoes a three-step phosphorylation into the active metabolite Ara-C triphosphosphate (ara-CTP). Several enzymes are involved directly or indirectly in either the formation or detoxification of ara-CTP. Methods A total of 12 eQTL (expression Quantitative Trait Loci) single nucleotide polymorphisms (SNPs) or tag SNPs in 7 genes including CMPK1, NME1, NME2, RRM1, RRM2, SAMHD1 and E2F1 were genotyped in 361 Chinese non-M3 AML patients by using the Sequenom Massarray system. Association of the SNPs with complete remission (CR) rate after Ara-C based induction therapy, relapse-free survival (RFS) and overall survival (OS) were analyzed. Results Three SNPs were observed to be associated increased risk of chemoresistance indicated by CR rate (NME2 rs3744660, E2F1 rs3213150, and RRM2 rs1130609), among which two (rs3744660 and rs1130609) were eQTL. Combined genotypes based on E2F1 rs3213150 and RRM2 rs1130609 polymorphisms further increased the risk of non-CR. The SAMHD1 eQTL polymorphism rs6102991 showed decreased risk of non-CR marginally (P = 0.055). Three SNPs (NME1 rs3760468 and rs2302254, and NME2 rs3744660) were associated with worse RFS, and the RRM2 rs1130609 polymorphism was marginally associated with worse RFS (P = 0.085) and OS (P = 0.080). Three SNPs (NME1 rs3760468, NME2 rs3744660, and RRM1 rs183484) were associated with worse OS in AML patients. Conclusion Data from our study demonstrated that SNPs in Ara-C and dNTP metabolic pathway predict chemosensitivity and prognosis of AML patients in China. Electronic supplementary material The online version of this article (10.1186/s12967-018-1463-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ke-Wei Zhu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China
| | - Peng Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China
| | - Dao-Yu Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China
| | - Han Yan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China
| | - Han Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China
| | - Li-Na Cen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China
| | - Yan-Ling Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China
| | - Shan Cao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China
| | - Gan Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China
| | - Hui Zeng
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China
| | - Shu-Ping Chen
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China
| | - Xie-Lan Zhao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China
| | - Xiao-Ping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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21
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Involvement of X-chromosome Reactivation in Augmenting Cancer Testis Antigens Expression: A Hypothesis. Curr Med Sci 2018; 38:19-25. [PMID: 30074147 DOI: 10.1007/s11596-018-1842-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/08/2018] [Indexed: 12/28/2022]
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22
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Leko V, Sripathy S, Adrianse RL, Loe T, Park A, Lao U, Foss EJ, Bartolomei MS, Bedalov A. Pooled shRNA Screen for Reactivation of MeCP2 on the Inactive X Chromosome. J Vis Exp 2018. [PMID: 29553562 DOI: 10.3791/56398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Forward genetic screens using reporter genes inserted into the heterochromatin have been extensively used to investigate mechanisms of epigenetic control in model organisms. Technologies including short hairpin RNAs (shRNAs) and clustered regularly interspaced short palindromic repeats (CRISPR) have enabled such screens in diploid mammalian cells. Here we describe a large-scale shRNA screen for regulators of X-chromosome inactivation (XCI), using a murine cell line with firefly luciferase and hygromycin resistance genes knocked in at the C-terminus of the methyl CpG binding protein 2 (MeCP2) gene on the inactive X-chromosome (Xi). Reactivation of the construct in the reporter cell line conferred survival advantage under hygromycin B selection, enabling us to screen a large shRNA library and identify hairpins that reactivated the reporter by measuring their post-selection enrichment using next-generation sequencing. The enriched hairpins were then individually validated by testing their ability to activate the luciferase reporter on Xi.
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Affiliation(s)
- Vid Leko
- Clinical Research Division, Fred Hutchinson Cancer Research Center; Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health
| | - Smitha Sripathy
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Robin L Adrianse
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Taylor Loe
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Angela Park
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Uyen Lao
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Eric J Foss
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Marisa S Bartolomei
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center; Departments of Medicine and Biochemistry, University of Washington;
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23
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A mixed modality approach towards Xi reactivation for Rett syndrome and other X-linked disorders. Proc Natl Acad Sci U S A 2017; 115:E668-E675. [PMID: 29282321 DOI: 10.1073/pnas.1715124115] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The X-chromosome harbors hundreds of disease genes whose associated diseases predominantly affect males. However, a subset, including neurodevelopmental disorders, Rett syndrome (RTT), fragile X syndrome, and CDKL5 syndrome, also affects females. These disorders lack disease-specific treatment. Because female cells carry two X chromosomes, an emerging treatment strategy has been to reawaken the healthy allele on the inactive X (Xi). Here, we focus on methyl-CpG binding protein 2 (MECP2) restoration for RTT and combinatorially target factors in the interactome of Xist, the noncoding RNA responsible for X inactivation. We identify a mixed modality approach combining an Xist antisense oligonucleotide and a small-molecule inhibitor of DNA methylation, which, together, achieve 30,000-fold MECP2 up-regulation from the Xi in cultured cells. Combining a brain-specific genetic Xist ablation with short-term 5-aza-2'-deoxycytidine (Aza) treatment models the synergy in vivo without evident toxicity. The Xi is selectively reactivated. These experiments provide proof of concept for a mixed modality approach for treating X-linked disorders in females.
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24
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Rugg-Gunn PJ. Naive pluripotent stem cells as a model for studying human developmental epigenomics: opportunities and limitations. Epigenomics 2017; 9:1485-1488. [DOI: 10.2217/epi-2017-0115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Babraham, Cambridge, CB22 3AT, UK
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25
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Association of Smoking, Alcohol Use, and Betel Quid Chewing with Epigenetic Aberrations in Cancers. Int J Mol Sci 2017; 18:ijms18061210. [PMID: 28587272 PMCID: PMC5486033 DOI: 10.3390/ijms18061210] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 12/16/2022] Open
Abstract
Numerous environmental factors such as diet, alcohol use, stress, and environmental chemicals are known to elicit epigenetic changes, leading to increased rates of cancers and other diseases. The incidence of head and neck cancer, one of the most common cancers in Taiwanese males, is increasing: oral cancer and nasopharyngeal carcinoma are ranked fourth and tenth respectively, among the top ten cancers in this group, and a major cause of cancer-related deaths in Taiwanese males. Previous studies have identified smoking, alcohol use, and betel quid chewing as the three major causes of head and neck cancers; these three social habits are commonly observed in Taiwanese males, resulting in an increasing morbidity rate of head and neck cancers in this population. In this literature review, we discuss the association between specific components of betel quid, alcohol, and tobacco, and the occurrence of head and neck cancers, lung cancer, gastrointestinal cancers, and urethral cancer. We focus on regulatory mechanisms at the epigenetic level and their oncogenic effects. The review further discusses the application of FDA-approved epigenetic drugs as therapeutic strategies against cancer.
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26
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Abstract
X chromosome inactivation (XCI) is a dosage compensation process that was adopted by female mammals to balance gene dosage between XX females and XY males. XCI starts with the upregulation of the non-coding RNA Xist, after which most X-linked genes are silenced and acquire a repressive chromatin state. Even though the chromatin marks of the inactive X have been fairly well described, the mechanisms responsible for the initiation of XCI remain largely unknown. In this review, we discuss recent developments that revealed unexpected factors playing a role in XCI and that might be of crucial importance to understand the mechanisms responsible for the very first steps of this chromosome-wide gene-silencing event.
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Affiliation(s)
- Ines Pinheiro
- Mammalian Developmental Epigenetics Group (équipe labellisée La Ligue), Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 26 Rue d'Ulm, 11 75248 Paris Cedex 05, France
| | - Edith Heard
- Mammalian Developmental Epigenetics Group (équipe labellisée La Ligue), Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 26 Rue d'Ulm, 11 75248 Paris Cedex 05, France
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Screen for reactivation of MeCP2 on the inactive X chromosome identifies the BMP/TGF-β superfamily as a regulator of XIST expression. Proc Natl Acad Sci U S A 2017; 114:1619-1624. [PMID: 28143937 DOI: 10.1073/pnas.1621356114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rett syndrome (RS) is a debilitating neurological disorder affecting mostly girls with heterozygous mutations in the gene encoding the methyl-CpG-binding protein MeCP2 on the X chromosome. Because restoration of MeCP2 expression in a mouse model reverses neurologic deficits in adult animals, reactivation of the wild-type copy of MeCP2 on the inactive X chromosome (Xi) presents a therapeutic opportunity in RS. To identify genes involved in MeCP2 silencing, we screened a library of 60,000 shRNAs using a cell line with a MeCP2 reporter on the Xi and found 30 genes clustered in seven functional groups. More than half encoded proteins with known enzymatic activity, and six were members of the bone morphogenetic protein (BMP)/TGF-β pathway. shRNAs directed against each of these six genes down-regulated X-inactive specific transcript (XIST), a key player in X-chromosome inactivation that encodes an RNA that coats the silent X chromosome, and modulation of regulators of this pathway both in cell culture and in mice demonstrated robust regulation of XIST. Moreover, we show that Rnf12, an X-encoded ubiquitin ligase important for initiation of X-chromosome inactivation and XIST transcription in ES cells, also plays a role in maintenance of the inactive state through regulation of BMP/TGF-β signaling. Our results identify pharmacologically suitable targets for reactivation of MeCP2 on the Xi and a genetic circuitry that maintains XIST expression and X-chromosome inactivation in differentiated cells.
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Lessing D, Dial TO, Wei C, Payer B, Carrette LLG, Kesner B, Szanto A, Jadhav A, Maloney DJ, Simeonov A, Theriault J, Hasaka T, Bedalov A, Bartolomei MS, Lee JT. A high-throughput small molecule screen identifies synergism between DNA methylation and Aurora kinase pathways for X reactivation. Proc Natl Acad Sci U S A 2016; 113:14366-14371. [PMID: 28182563 PMCID: PMC5167172 DOI: 10.1073/pnas.1617597113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
X-chromosome inactivation is a mechanism of dosage compensation in which one of the two X chromosomes in female mammals is transcriptionally silenced. Once established, silencing of the inactive X (Xi) is robust and difficult to reverse pharmacologically. However, the Xi is a reservoir of >1,000 functional genes that could be potentially tapped to treat X-linked disease. To identify compounds that could reactivate the Xi, here we screened ∼367,000 small molecules in an automated high-content screen using an Xi-linked GFP reporter in mouse fibroblasts. Given the robust nature of silencing, we sensitized the screen by "priming" cells with the DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5azadC). Compounds that elicited GFP activity include VX680, MLN8237, and 5azadC, which are known to target the Aurora kinase and DNA methylation pathways. We demonstrate that the combinations of VX680 and 5azadC, as well as MLN8237 and 5azadC, synergistically up-regulate genes on the Xi. Thus, our work identifies a synergism between the DNA methylation and Aurora kinase pathways as being one of interest for possible pharmacological reactivation of the Xi.
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Affiliation(s)
- Derek Lessing
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Thomas O Dial
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Chunyao Wei
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | - Lieselot L G Carrette
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Barry Kesner
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Attila Szanto
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Ajit Jadhav
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - David J Maloney
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | | | | | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Jeannie T Lee
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114;
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
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Payer B. Developmental regulation of X-chromosome inactivation. Semin Cell Dev Biol 2016; 56:88-99. [PMID: 27112543 DOI: 10.1016/j.semcdb.2016.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/13/2016] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Abstract
With the emergence of sex-determination by sex chromosomes, which differ in composition and number between males and females, appeared the need to equalize X-chromosomal gene dosage between the sexes. Mammals have devised the strategy of X-chromosome inactivation (XCI), in which one of the two X-chromosomes is rendered transcriptionally silent in females. In the mouse, the best-studied model organism with respect to XCI, this inactivation process occurs in different forms, imprinted and random, interspersed by periods of X-chromosome reactivation (XCR), which is needed to switch between the different modes of XCI. In this review, I describe the recent advances with respect to the developmental control of XCI and XCR and in particular their link to differentiation and pluripotency. Furthermore, I review the mechanisms, which influence the timing and choice, with which one of the two X-chromosomes is chosen for inactivation during random XCI. This has an impact on how females are mosaics with regard to which X-chromosome is active in different cells, which has implications on the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra (UPF), Dr. Aiguader, 88, Barcelona 08003, Spain.
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30
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Vacca M, Della Ragione F, Scalabrì F, D'Esposito M. X inactivation and reactivation in X-linked diseases. Semin Cell Dev Biol 2016; 56:78-87. [PMID: 26994527 DOI: 10.1016/j.semcdb.2016.03.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 12/22/2022]
Abstract
X chromosome inactivation (XCI) is the phenomenon by which mammals compensate for dosage of X-linked genes in females (XX) versus males (XY). XCI patterns can be random or show extreme skewing, and can modify the mode of inheritance of X-driven phenotypes, which contributes to the variability of human pathologies. Recent findings have shown reversibility of the XCI process, which has opened new avenues in the approaches used for the treatment of X-linked diseases.
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Affiliation(s)
- Marcella Vacca
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy.
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | | | - Maurizio D'Esposito
- Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, via Pietro Castellino, 111, 80131, Naples, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
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