1
|
Wang HS, Ma XR, Guo YH. Development and application of haploid embryonic stem cells. Stem Cell Res Ther 2024; 15:116. [PMID: 38654389 DOI: 10.1186/s13287-024-03727-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Haploid cells are a kind of cells with only one set of chromosomes. Compared with traditional diploid cells, haploid cells have unique advantages in gene screening and drug-targeted therapy, due to their phenotype being equal to the genotype. Embryonic stem cells are a kind of cells with strong differentiation potential that can differentiate into various types of cells under specific conditions in vitro. Therefore, haploid embryonic stem cells have the characteristics of both haploid cells and embryonic stem cells, which makes them have significant advantages in many aspects, such as reproductive developmental mechanism research, genetic screening, and drug-targeted therapy. Consequently, establishing haploid embryonic stem cell lines is of great significance. This paper reviews the progress of haploid embryonic stem cell research and briefly discusses the applications of haploid embryonic stem cells.
Collapse
Affiliation(s)
- Hai-Song Wang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 40 Daxue Road, 450052, Zhengzhou, Henan Province, China.
| | - Xin-Rui Ma
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 40 Daxue Road, 450052, Zhengzhou, Henan Province, China
| | - Yi-Hong Guo
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 40 Daxue Road, 450052, Zhengzhou, Henan Province, China.
| |
Collapse
|
2
|
Liang M, Zhang L, Lai L, Li Z. Unraveling the role of Xist in X chromosome inactivation: insights from rabbit model and deletion analysis of exons and repeat A. Cell Mol Life Sci 2024; 81:156. [PMID: 38551746 PMCID: PMC10980640 DOI: 10.1007/s00018-024-05151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 04/01/2024]
Abstract
X chromosome inactivation (XCI) is a process that equalizes the expression of X-linked genes between males and females. It relies on Xist, continuously expressed in somatic cells during XCI maintenance. However, how Xist impacts XCI maintenance and its functional motifs remain unclear. In this study, we conducted a comprehensive analysis of Xist, using rabbits as an ideal non-primate model. Homozygous knockout of exon 1, exon 6, and repeat A in female rabbits resulted in embryonic lethality. However, X∆ReAX females, with intact X chromosome expressing Xist, showed no abnormalities. Interestingly, there were no significant differences between females with homozygous knockout of exons 2-5 and wild-type rabbits, suggesting that exons 2, 3, 4, and 5 are less important for XCI. These findings provide evolutionary insights into Xist function.
Collapse
Affiliation(s)
- Mingming Liang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Lichao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, 100039, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences, Guangzhou, 510530, China.
| | - Zhanjun Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| |
Collapse
|
3
|
Chen X, Yun L, Long Y, Sun Y, Chen T. First report on female monozygotic twins discordant for congenital nephrogenic diabetes insipidus. Am J Med Genet A 2024; 194:e63407. [PMID: 37909842 DOI: 10.1002/ajmg.a.63407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 11/03/2023]
Abstract
Ninety percent of congenital nephrogenic diabetes insipidus (NDI) are X-linked inherited and are caused by mutations in the vasopressin type 2 receptor gene (AVPR2). Most affected individuals are males. Only sporadic female cases have been reported. Here, we first reported a female monozygotic twin with discordant phenotypes for NDI carrying a missense variant c.845T>C (p.Leu282Pro) in exon 4 of AVPR2. Intracellular cAMP concentrations in COS7 cells transfected with AVPR2-L282P were significantly decreased by about 60% compared with those in wild-type AVPR2 plasmid transfected cells, suggesting this variation was pathogenic. The X-inactivation pattern was investigated in peripheral leukocytes and urine sediments in both the unaffected and affected pair. Results showed that the affected pair had a skewed X chromosome inactivation (XCI) pattern in urine sediments and a random XCI pattern in leukocytes, while the unaffected pair showed a random XCI pattern both in leukocytes and urine sediments. This was the first report of monozygotic twins who developed different phenotypes of NDI. Our study suggested that the development of NDI symptoms is more closely associated with the XCI pattern in urine sediments compared with the XCI pattern in peripheral leukocytes. Analysis of XCI in peripheral leukocytes may not be enough to explore possible mechanisms.
Collapse
Affiliation(s)
- Xiang Chen
- Department of Endocrinology and Metabolism, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Laboratory of Endocrinology and Metabolism, Department of Endocrinology and Metabolism, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Libing Yun
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yang Long
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yuxia Sun
- Department of Endocrinology and Metabolism, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Tao Chen
- Department of Endocrinology and Metabolism, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
4
|
Luchsinger-Morcelle SJ, Gribnau J, Mira-Bontenbal H. Orchestrating Asymmetric Expression: Mechanisms behind Xist Regulation. Epigenomes 2024; 8:6. [PMID: 38390897 PMCID: PMC10885031 DOI: 10.3390/epigenomes8010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Compensation for the gene dosage disequilibrium between sex chromosomes in mammals is achieved in female cells by repressing one of its X chromosomes through a process called X chromosome inactivation (XCI), exemplifying the control of gene expression by epigenetic mechanisms. A critical player in this mechanism is Xist, a long, non-coding RNA upregulated from a single X chromosome during early embryonic development in female cells. Over the past few decades, many factors involved at different levels in the regulation of Xist have been discovered. In this review, we hierarchically describe and analyze the different layers of Xist regulation operating concurrently and intricately interacting with each other to achieve asymmetric and monoallelic upregulation of Xist in murine female cells. We categorize these into five different classes: DNA elements, transcription factors, other regulatory proteins, long non-coding RNAs, and the chromatin and topological landscape surrounding Xist.
Collapse
Affiliation(s)
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Hegias Mira-Bontenbal
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands
| |
Collapse
|
5
|
San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. Cell Genom 2024; 4:100462. [PMID: 38190107 PMCID: PMC10794785 DOI: 10.1016/j.xgen.2023.100462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/15/2023] [Accepted: 11/14/2023] [Indexed: 01/09/2024]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors-ZFX and ZFY-encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
Collapse
Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Alexander K Godfrey
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neha V Bokil
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Shanlee M Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Developmental Pediatrics, eXtraOrdinarY Kids Program, Children's Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA; Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA.
| |
Collapse
|
6
|
Dror I, Chitiashvili T, Tan SYX, Cano CT, Sahakyan A, Markaki Y, Chronis C, Collier AJ, Deng W, Liang G, Sun Y, Afasizheva A, Miller J, Xiao W, Black DL, Ding F, Plath K. XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells. Cell 2024; 187:110-129.e31. [PMID: 38181737 PMCID: PMC10783549 DOI: 10.1016/j.cell.2023.11.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/01/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024]
Abstract
X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.
Collapse
Affiliation(s)
- Iris Dror
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tsotne Chitiashvili
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shawn Y X Tan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Clara T Cano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Sahakyan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yolanda Markaki
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Amanda J Collier
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Weixian Deng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Guohao Liang
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA
| | - Yu Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Afasizheva
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jarrett Miller
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fangyuan Ding
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
7
|
Wang F, Chander A, Yoon Y, Welton JM, Wallingford MC, Espejo-Serrano C, Bustos F, Findlay GM, Mager J, Bach I. Roles of the Rlim-Rex1 axis during X chromosome inactivation in mice. Proc Natl Acad Sci U S A 2023; 120:e2313200120. [PMID: 38113263 PMCID: PMC10756295 DOI: 10.1073/pnas.2313200120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023] Open
Abstract
In female mice, the gene dosage from X chromosomes is adjusted by a process called X chromosome inactivation (XCI) that occurs in two steps. An imprinted form of XCI (iXCI) that silences the paternally inherited X chromosome (Xp) is initiated at the 2- to 4-cell stages. As extraembryonic cells including trophoblasts keep the Xp silenced, epiblast cells that give rise to the embryo proper reactivate the Xp and undergo a random form of XCI (rXCI) around implantation. Both iXCI and rXCI require the lncRNA Xist, which is expressed from the X to be inactivated. The X-linked E3 ubiquitin ligase Rlim (Rnf12) in conjunction with its target protein Rex1 (Zfp42), a critical repressor of Xist, have emerged as major regulators of iXCI. However, their roles in rXCI remain controversial. Investigating early mouse development, we show that the Rlim-Rex1 axis is active in pre-implantation embryos. Upon implantation Rex1 levels are downregulated independently of Rlim specifically in epiblast cells. These results provide a conceptual framework of how the functional dynamics between Rlim and Rex1 ensures regulation of iXCI but not rXCI in female mice.
Collapse
Affiliation(s)
- Feng Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Ashmita Chander
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA01003
| | - Yeonsoo Yoon
- Division of Genes and Development, Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Janelle M. Welton
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA01003
| | - Mary C. Wallingford
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA01003
| | - Carmen Espejo-Serrano
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
| | - Francisco Bustos
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
| | - Greg M. Findlay
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA01003
| | - Ingolf Bach
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA01605
| |
Collapse
|
8
|
Abstract
The eukaryotic nucleus displays a variety of membraneless compartments with distinct biomolecular composition and specific cellular activities. Emerging evidence indicates that protein-based liquid-liquid phase separation (LLPS) plays an essential role in the formation and dynamic regulation of heterochromatin compartmentalization. This feature is especially conspicuous at the pericentric heterochromatin domains. In this review, we will describe our understanding of heterochromatin organization and LLPS. In addition, we will highlight the increasing importance of multivalent weak homo- and heteromolecular interactions in LLPS-mediated heterochromatin compartmentalization in the complex environment inside living cells.
Collapse
Affiliation(s)
- Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Hector Romero
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany,CONTACT M. Cristina Cardoso Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287Darmstadt, Germany
| |
Collapse
|
9
|
Kaufmann C, Wutz A. IndiSPENsable for X Chromosome Inactivation and Gene Silencing. Epigenomes 2023; 7:28. [PMID: 37987303 PMCID: PMC10660550 DOI: 10.3390/epigenomes7040028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
For about 30 years, SPEN has been the subject of research in many different fields due to its variety of functions and its conservation throughout a wide spectrum of species, like worms, arthropods, and vertebrates. To date, 216 orthologues have been documented. SPEN had been studied for its role in gene regulation in the context of cell signaling, including the NOTCH or nuclear hormone receptor signaling pathways. More recently, SPEN has been identified as a major regulator of initiation of chromosome-wide gene silencing during X chromosome inactivation (XCI) in mammals, where its function remains to be fully understood. Dependent on the biological context, SPEN functions via mechanisms which include different domains. While some domains of SPEN are highly conserved in sequence and secondary structure, species-to-species differences exist that might lead to mechanistic differences. Initiation of XCI appears to be different between humans and mice, which raises additional questions about the extent of generalization of SPEN's function in XCI. In this review, we dissect the mechanism of SPEN in XCI. We discuss its subregions and domains, focusing on its role as a major regulator. We further highlight species-related research, specifically of mouse and human SPEN, with the aim to reveal and clarify potential species-to-species differences in SPEN's function.
Collapse
Affiliation(s)
| | - Anton Wutz
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology ETH Hönggerberg, 8093 Zurich, Switzerland;
| |
Collapse
|
10
|
Liu C, Ma J, Lu Y, Lu Y, Mai J, Bai L, Wang Y, Zheng Y, Yu M, Zheng Y, Deng J, Meng L, Zhang W, Wang Z, Yuan Y, Xie Z. Clinical, pathological, and genetic characterization in a large Chinese cohort with female dystrophinopathy. Neuromuscul Disord 2023; 33:728-736. [PMID: 37716855 DOI: 10.1016/j.nmd.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 09/18/2023]
Abstract
We aimed to investigate the clinical, pathological, and genetic characteristics of Chinese female dystrophinopathy and to identify possible correlations among them. One hundred forty genetically and/or pathologically confirmed female DMD variant carriers were enrolled, including 104 asymptomatic carriers and 36 symptomatic carriers. Twenty of 36 symptomatic and 16 of 104 asymptomatic carriers were sporadic with no family history. Muscle pathological analysis was performed in 53 carriers and X chromosome inactivation (XCI) analysis in 19 carriers. In asymptomatic carriers, the median age was 35.0 (range 2.0-58.0) years, and the serum creatine kinase (CK) level was 131 (range 60-15,745) IU/L. The median age, age of onset, and CK level of symptomatic carriers were 15.5 (range 1.8-62.0) years, 6.3 (range 1.0-54.0) years, and 6,659 (range 337-58,340) IU/L, respectively. Four female carriers with X-autosome translocation presented with a Duchenne muscular dystrophy (DMD) phenotype. Skewed XCI was present in 70.0% of symptomatic carriers. Compared to Becker muscular dystrophy (BMD)-like carriers, DMD-like carriers were more likely to have an early onset age, rapidly progressive muscle weakness, delayed walking, elevated CK levels, severe reduction of dystrophin, and skewed XCI. Our study reports the largest series of symptomatic female DMD carriers and suggests that delayed walking, elevated CK levels, severe reduction of dystrophin, X-autosome translocation, and skewed XCI pattern are associated with a severe phenotype in female dystrophinopathy.
Collapse
Affiliation(s)
- Chang Liu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Jiajian Ma
- School of Data Science, The Chinese University of Hong Kong (Shenzhen), Shenzhen, China
| | - Yanyu Lu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Yunlong Lu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Jiahui Mai
- Department of Neurology, Shenzhen Children's Hospital, Shenzhen, China
| | - Li Bai
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Yikang Wang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Yilei Zheng
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Yiming Zheng
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Lingchao Meng
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing 100034, China.
| | - Zhiying Xie
- Department of Neurology, Peking University First Hospital, Beijing 100034, China.
| |
Collapse
|
11
|
Wang Y, Bai M, Zhang P, Peng Y, Chen Z, He Z, Xu J, Zhu Y, Yan D, Wang R, Zhang Z. Identification and functional analysis of a novel de novo missense mutation located in the initiation codon of LAMP2 associated with early onset female Danon disease. Mol Genet Genomic Med 2023; 11:e2216. [PMID: 37288668 PMCID: PMC10496070 DOI: 10.1002/mgg3.2216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Danon disease is characterized by the failure of lysosomal biogenesis, maturation, and function due to a deficiency of lysosomal membrane structural protein (LAMP2). METHODS The current report describes a female patient with a sudden syncope and hypertrophic cardiomyopathy phenotype. We identified the pathogenic mutations in patients by whole-exon sequencing, followed by a series of molecular biology and genetic approaches to identify and functional analysis of the mutations. RESULTS Suggestive findings by cardiac magnetic resonance (CMR), electrocardiogram (ECG), and laboratory examination suggested Danon disease which was confirmed by genetic testing. The patient carried a novel de novo mutation, LAMP2 c.2T>C located at the initiation codon. The quantitative polymerase chain reaction (qPCR) and Western blot (WB) analysis of peripheral blood leukocytes from the patients revealed evidence of LAMP2 haploinsufficiency. Labeling of the new initiation codon predicted by the software with green fluorescent protein followed by fluorescence microscopy and Western blotting showed that the first ATG downstream from the original initiation codon became the new translational initiation codon. The three-dimensional structure of the mutated protein predicted by alphafold2 revealed that it consisted of only six amino acids and failed to form a functional polypeptide or protein. Overexpression of the mutated LAMP2 c.2T>C showed a loss of function of the protein, as assessed by the dual-fluorescence autophagy indicator system. The mutation was confirmed to be null, AR experiments and sequencing results confirmed that 28% of the mutant X chromosome remained active. CONCLUSION We propose possible mechanisms of mutations associated with haploinsufficiency of LAMP2: (1) The inactivation X chromosome carrying the mutation was not significantly skewed. However, it decreased in the mRNA level and the expression ratio of the mutant transcripts; (2) The identified mutation is null, and the active mutant transcript fails to translate into the normal LAMP2 proteins. The presence of haploinsufficiency in LAMP2 and the X chromosome inactivation pattern were crucial factors contributing to the early onset of Danon disease in this female patient.
Collapse
Affiliation(s)
- Yongxiang Wang
- Heart CenterThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Key Laboratory of Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Provincial Clinical Research Center for Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Ming Bai
- Heart CenterThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Key Laboratory of Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Provincial Clinical Research Center for Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Piyi Zhang
- Heart CenterThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- The First Clinical Medical School, Lanzhou UniversityLanzhouGansuChina
| | - Yu Peng
- Heart CenterThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Key Laboratory of Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Provincial Clinical Research Center for Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Zixian Chen
- Heart CenterThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Department of RadiologyThe First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Zhiyu He
- Heart CenterThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Key Laboratory of Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Provincial Clinical Research Center for Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Jin Xu
- Heart CenterThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- The First Clinical Medical School, Lanzhou UniversityLanzhouGansuChina
| | - Youqi Zhu
- Heart CenterThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Key Laboratory of Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Provincial Clinical Research Center for Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Dongdong Yan
- Heart CenterThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Key Laboratory of Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Provincial Clinical Research Center for Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Runqing Wang
- Heart CenterThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- The First Clinical Medical School, Lanzhou UniversityLanzhouGansuChina
| | - Zheng Zhang
- Heart CenterThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Key Laboratory of Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
- Gansu Provincial Clinical Research Center for Cardiovascular DiseasesThe First Hospital of Lanzhou UniversityLanzhouGansuChina
| |
Collapse
|
12
|
Li YD, Huang H, Ren ZJ, Yuan Y, Wu H, Liu C. Pan-cancer analysis identifies SPEN mutation as a predictive biomarker with the efficacy of immunotherapy. BMC Cancer 2023; 23:793. [PMID: 37620924 PMCID: PMC10463702 DOI: 10.1186/s12885-023-11235-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
The association between specific genetic mutations and immunotherapy benefits has been widely known, while such studies in pan-cancer are still limited. SPEN, mainly involved in X chromosome inactivation (XCI), plays an essential in tumorigenesis and sex differences in cancer. Thus, we firstly analyzed the potential role of SPEN in the TCGA pan-cancer cohort and clinical samples. Bioinformatics analysis and immunohistochemistry (IHC) staining confirm that the expression of SPEN is significantly different in various cancers and may involve RNA splicing and processing via enrichment analysis. Then, our data further revealed that those patients with SPEN mutation could predict a better prognosis in pan-cancer and had distinct immune signatures, higher tumor mutation burden (TMB), and microsatellite instability (MSI) in common cancer types. Finally, the cancer patients from 9 studies treated with immune checkpoint inhibitors were included to investigate the efficacy of immunotherapy. The results further showed that SPEN mutation was associated with better clinical outcomes (HR, 0.74; 95%CI, 0.59-0.93, P = 0.01), and this association remained existed in female patients (HR, 0.60; 95%CI, 0.38-0.94 P = 0.024), but not in male patients (HR, 0.82; 95%CI, 0.62-1.08 P = 0.150). Our findings demonstrated that SPEN mutation might strongly predict immunotherapy efficacy in pan-cancer.
Collapse
Affiliation(s)
- Ya-Dong Li
- Department of Urology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hao Huang
- Department of Urology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Zheng-Ju Ren
- Department of Urology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ye Yuan
- Department of Urology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hao Wu
- Department of Urology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Chuan Liu
- Department of Urology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
| |
Collapse
|
13
|
Mori T, Zhou M, Tabuchi K. Diverse Clinical Phenotypes of CASK-Related Disorders and Multiple Functional Domains of CASK Protein. Genes (Basel) 2023; 14:1656. [PMID: 37628707 PMCID: PMC10454856 DOI: 10.3390/genes14081656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
CASK-related disorders are a form of rare X-linked neurological diseases and most of the patients are females. They are characterized by several symptoms, including microcephaly with pontine and cerebellar hypoplasia (MICPCH), epilepsy, congenital nystagmus, and neurodevelopmental disorders. Whole-genome sequencing has identified various mutations, including nonsense and missense mutations, from patients with CASK-related disorders, revealing correlations between specific mutations and clinical phenotypes. Notably, missense mutations associated with epilepsy and intellectual disability were found throughout the whole region of the CASK protein, while missense mutations related to microcephaly and MICPCH were restricted in certain domains. To investigate the pathophysiology of CASK-related disorders, research groups have employed diverse methods, including the generation of CASK knockout mice and the supplementation of CASK to rescue the phenotypes. These approaches have yielded valuable insights into the identification of functional domains of the CASK protein associated with a specific phenotype. Additionally, recent advancements in the AI-based prediction of protein structure, such as AlphaFold2, and the application of genome-editing techniques to generate CASK mutant mice carrying missense mutations from patients with CASK-related disorders, allow us to understand the pathophysiology of CASK-related disorders in more depth and to develop novel therapeutic methods for the fundamental treatment of CASK-related disorders.
Collapse
Affiliation(s)
- Takuma Mori
- Department of Neuroinnovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto 390-8621, Japan;
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
| | - Mengyun Zhou
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
| | - Katsuhiko Tabuchi
- Department of Neuroinnovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto 390-8621, Japan;
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
| |
Collapse
|
14
|
Dardik R, Janczar S, Lalezari S, Avishai E, Levy-Mendelovich S, Barg AA, Martinowitz U, Babol-Pokora K, Mlynarski W, Kenet G. Four Decades of Carrier Detection and Prenatal Diagnosis in Hemophilia A: Historical Overview, State of the Art and Future Directions. Int J Mol Sci 2023; 24:11846. [PMID: 37511607 PMCID: PMC10380558 DOI: 10.3390/ijms241411846] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/09/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Hemophilia A (HA), a rare recessive X-linked bleeding disorder, is caused by either deficiency or dysfunction of coagulation factor VIII (FVIII) resulting from deleterious mutations in the F8 gene encoding FVIII. Over the last 4 decades, the methods aimed at determining the HA carrier status in female relatives of HA patients have evolved from phenotypic studies based on coagulation tests providing merely probabilistic results, via genetic linkage studies based on polymorphic markers providing more accurate results, to next generation sequencing studies enabling highly precise identification of the causative F8 mutation. In parallel, the options for prenatal diagnosis of HA have progressed from examination of FVIII levels in fetal blood samples at weeks 20-22 of pregnancy to genetic analysis of fetal DNA extracted from chorionic villus tissue at weeks 11-14 of pregnancy. In some countries, in vitro fertilization (IVF) combined with preimplantation genetic diagnosis (PGD) has gradually become the procedure of choice for HA carriers who wish to prevent further transmission of HA without the need to undergo termination of pregnancies diagnosed with affected fetuses. In rare cases, genetic analysis of a HA carrier might be complicated by skewed X chromosome inactivation (XCI) of her non-hemophilic X chromosome, thus leading to the phenotypic manifestation of moderate to severe HA. Such skewed XCI may be associated with deleterious mutations in X-linked genes located on the non-hemophilic X chromosome, which should be considered in the process of genetic counseling and PGD planning for the symptomatic HA carrier. Therefore, whole exome sequencing, combined with X-chromosome targeted bioinformatic analysis, is highly recommended for symptomatic HA carriers diagnosed with skewed XCI in order to identify additional deleterious mutations potentially involved in XCI skewing. Identification of such mutations, which may profoundly impact the reproductive choices of HA carriers with skewed XCI, is extremely important.
Collapse
Affiliation(s)
- Rima Dardik
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Szymon Janczar
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 90-419 Lodz, Poland
| | - Shadan Lalezari
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Einat Avishai
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Sarina Levy-Mendelovich
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Assaf Arie Barg
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| | - Uri Martinowitz
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Katarzyna Babol-Pokora
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 90-419 Lodz, Poland
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 90-419 Lodz, Poland
| | - Gili Kenet
- National Hemophilia Center, Sheba Medical Center, Ramat Gan 52621, Israel
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Sackler School of Medicine, Tel Aviv University, Tel Aviv 52621, Israel
| |
Collapse
|
15
|
Caserta S, Gangemi S, Murdaca G, Allegra A. Gender Differences and miRNAs Expression in Cancer: Implications on Prognosis and Susceptibility. Int J Mol Sci 2023; 24:11544. [PMID: 37511303 PMCID: PMC10380791 DOI: 10.3390/ijms241411544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
MicroRNAs are small, noncoding molecules of about twenty-two nucleotides with crucial roles in both healthy and pathological cells. Their expression depends not only on genetic factors, but also on epigenetic mechanisms like genomic imprinting and inactivation of X chromosome in females that influence in a sex-dependent manner onset, progression, and response to therapy of different diseases like cancer. There is evidence of a correlation between miRNAs, sex, and cancer both in solid tumors and in hematological malignancies; as an example, in lymphomas, with a prevalence rate higher in men than women, miR-142 is "silenced" because of its hypermethylation by DNA methyltransferase-1 and it is blocked in its normal activity of regulating the migration of the cell. This condition corresponds in clinical practice with a more aggressive tumor. In addition, cancer treatment can have advantages from the evaluation of miRNAs expression; in fact, therapy with estrogens in hepatocellular carcinoma determines an upregulation of the oncosuppressors miR-26a, miR-92, and miR-122 and, consequently, apoptosis. The aim of this review is to present an exhaustive collection of scientific data about the possible role of sex differences on the expression of miRNAs and the mechanisms through which miRNAs influence cancerogenesis, autophagy, and apoptosis of cells from diverse types of tumors.
Collapse
Affiliation(s)
- Santino Caserta
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, Via Consolare Valeria, 98125 Messina, Italy
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria, 98125 Messina, Italy
| | - Giuseppe Murdaca
- Department of Internal Medicine, University of Genova, Viale Benedetto XV, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
| | - Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, Via Consolare Valeria, 98125 Messina, Italy
| |
Collapse
|
16
|
San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. bioRxiv 2023:2023.06.05.543763. [PMID: 37333288 PMCID: PMC10274745 DOI: 10.1101/2023.06.05.543763] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex-chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors - ZFX and ZFY - encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
Collapse
Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Alexander K. Godfrey
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Neha V. Bokil
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute; Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892 USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | | | | | - Shanlee M. Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E. Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R. Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Developmental Pediatrics, eXtraOrdinarY Kids Program, Children’s Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA
- Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - David C. Page
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| |
Collapse
|
17
|
Kudo R, Yoshida I, Matiz Ceron L, Mizushima S, Kuroki Y, Jogahara T, Kuroiwa A. The Neo-X Does Not Form a Barr Body but Shows a Slightly Condensed Structure in the Okinawa Spiny Rat (Tokudaia muenninki). Cytogenet Genome Res 2023; 162:632-643. [PMID: 37271129 DOI: 10.1159/000531275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/27/2023] [Indexed: 06/06/2023] Open
Abstract
X chromosome inactivation (XCI) is an essential mechanism for gene dosage compensation between male and female cells in mammals. The Okinawa spiny rat (Tokudaia muenninki) is a native rodent in Japan with XX/XY sex chromosomes, like most mammals; however, the X chromosome has acquired a neo-X region (Xp) by fusion with an autosome. We previously reported that dosage compensation has not yet evolved in the neo-X region; however, X-inactive-specific transcript (Xist) RNA (long non-coding RNA required for the initiation of XCI) is partially localized in the region. Here, we show that the neo-X region represents an early chromosomal state in the acquisition of XCI by analyses of heterochromatin and Barr body formation. We found no evidence for heterochromatin formation in the neo-X region by R-banding by acridine orange (RBA) assays and immunostaining of H3K27me3. Double-immunostaining of H3K27me3 and HP1, a component of the Barr body, revealed that the entire ancestral X chromosome region (Xq) showed a bipartite folded structure. By contrast, HP1 was not localized to the neo-X region. However, BAC-FISH revealed that the signals of genes on the neo-X region of the inactive X chromosome were concentrated in a narrow region. These findings indicated that although the neo-X region of the inactive X chromosome does not form a complete Barr body structure (e.g., it lacks HP1), it forms a slightly condensed structure. These findings combined with the previously reported partial binding of Xist RNA suggest that the neo-X region exhibits incomplete inactivation. This may represent an early chromosomal state in the acquisition of the XCI mechanism.
Collapse
Affiliation(s)
- Ryoma Kudo
- Reproductive and Developmental Sciences, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Ikuya Yoshida
- Reproductive and Developmental Sciences, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Luisa Matiz Ceron
- Reproductive and Developmental Sciences, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shusei Mizushima
- Reproductive and Developmental Sciences, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Yoko Kuroki
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
- Division of Collaborative Research, National Center for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Takamichi Jogahara
- Faculty of Law, Economics and Management, Okinawa University, Naha, Japan
| | - Asato Kuroiwa
- Reproductive and Developmental Sciences, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| |
Collapse
|
18
|
Krueger K, Lamenza F, Gu H, El-Hodiri H, Wester J, Oberdick J, Fischer AJ, Oghumu S. Sex differences in susceptibility to substance use disorder: Role for X chromosome inactivation and escape? Mol Cell Neurosci 2023; 125:103859. [PMID: 37207894 DOI: 10.1016/j.mcn.2023.103859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
There is a sex-based disparity associated with substance use disorders (SUDs) as demonstrated by clinical and preclinical studies. Females are known to escalate from initial drug use to compulsive drug-taking behavior (telescoping) more rapidly, and experience greater negative withdrawal effects than males. Although these biological differences have largely been attributed to sex hormones, there is evidence for non-hormonal factors, such as the influence of the sex chromosome, which underlie sex disparities in addiction behavior. However, genetic and epigenetic mechanisms underlying sex chromosome influences on substance abuse behavior are not completely understood. In this review, we discuss the role that escape from X-chromosome inactivation (XCI) in females plays in sex-associated differences in addiction behavior. Females have two X chromosomes (XX), and during XCI, one X chromosome is randomly chosen to be transcriptionally silenced. However, some X-linked genes escape XCI and display biallelic gene expression. We generated a mouse model using an X-linked gene specific bicistronic dual reporter mouse as a tool to visualize allelic usage and measure XCI escape in a cell specific manner. Our results revealed a previously undiscovered X-linked gene XCI escaper (CXCR3), which is variable and cell type dependent. This illustrates the highly complex and context dependent nature of XCI escape which is largely understudied in the context of SUD. Novel approaches such as single cell RNA sequencing will provide a global molecular landscape and impact of XCI escape in addiction and facilitate our understanding of the contribution of XCI escape to sex disparities in SUD.
Collapse
Affiliation(s)
- Kate Krueger
- Department of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Felipe Lamenza
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Howard Gu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Heithem El-Hodiri
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - Jason Wester
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - John Oberdick
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - Andy J Fischer
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - Steve Oghumu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
| |
Collapse
|
19
|
Yoon SH, Kim GY, Choi GT, Do JT. Organ Abnormalities Caused by Turner Syndrome. Cells 2023; 12:1365. [PMID: 37408200 DOI: 10.3390/cells12101365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/22/2023] [Accepted: 05/10/2023] [Indexed: 07/07/2023] Open
Abstract
Turner syndrome (TS), a genetic disorder due to incomplete dosage compensation of X-linked genes, affects multiple organ systems, leading to hypogonadotropic hypogonadism, short stature, cardiovascular and vascular abnormalities, liver disease, renal abnormalities, brain abnormalities, and skeletal problems. Patients with TS experience premature ovarian failure with a rapid decline in ovarian function caused by germ cell depletion, and pregnancies carry a high risk of adverse maternal and fetal outcomes. Aortic abnormalities, heart defects, obesity, hypertension, and liver abnormalities, such as steatosis, steatohepatitis, biliary involvement, liver cirrhosis, and nodular regenerative hyperplasia, are commonly observed in patients with TS. The SHOX gene plays a crucial role in short stature and abnormal skeletal phenotype in patients with TS. Abnormal structure formation of the ureter and kidney is also common in patients with TS, and a non-mosaic 45,X karyotype is significantly associated with horseshoe kidneys. TS also affects brain structure and function. In this review, we explore various phenotypic and disease manifestations of TS in different organs, including the reproductive system, cardiovascular system, liver, kidneys, brain, and skeletal system.
Collapse
Affiliation(s)
- Sang Hoon Yoon
- Department of Stem Cell and Regenerative Biotechnology, KU Institute of Technology, Konkuk University, Seoul 05029, Republic of Korea
| | - Ga Yeon Kim
- Department of Stem Cell and Regenerative Biotechnology, KU Institute of Technology, Konkuk University, Seoul 05029, Republic of Korea
| | - Gyu Tae Choi
- Department of Stem Cell and Regenerative Biotechnology, KU Institute of Technology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, KU Institute of Technology, Konkuk University, Seoul 05029, Republic of Korea
| |
Collapse
|
20
|
Soffer E, Coleman K, Batsuli G. The impact of concurrent X chromosome anomalies on diagnosis and bleeding phenotype in children with hemophilia: A single-institution case series. Pediatr Blood Cancer 2023; 70:e30400. [PMID: 37132158 DOI: 10.1002/pbc.30400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/28/2023] [Accepted: 04/13/2023] [Indexed: 05/04/2023]
Abstract
Hemophilia is an inherited X-linked bleeding disorder characterized by deficiencies of factors VIII or IX. Concomitant X chromosome disorders can impact bleeding phenotype, complicating timely diagnosis and disease management. Herein, we describe three cases of female and male pediatric patients with hemophilia A or B diagnosed between 6 days and 4 years old in the setting of skewed X chromosome inactivation, Turner syndrome, or Klinefelter syndrome. All of these cases had significant bleeding symptoms, and two patients required initiation of factor replacement therapy. One female patient developed a factor VIII inhibitor similar to that described in males with hemophilia A.
Collapse
Affiliation(s)
- Elizabeth Soffer
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Karlene Coleman
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Glaivy Batsuli
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| |
Collapse
|
21
|
Caylor RC. Nonrandom X Chromosome Inactivation Detection. Curr Protoc 2023; 3:e748. [PMID: 37074091 DOI: 10.1002/cpz1.748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
X chromosome inactivation patterns may be clinically useful in assessing tumor clonality, determining carrier status for certain X-linked disorders, and evaluating the pathogenicity of a genetic variant identified in an X-linked gene. The protocols in this article utilize the highly polymorphic trinucleotide repeat within the first exon of the human androgen receptor gene (AR) and the methylation-sensitive restriction enzyme HpaII to distinguish between the maternal and paternal alleles and simultaneously determine their methylation status. The data obtained from these protocols can be used to calculate the ratio of inactivation between the two alleles that ultimately reflects whether a female has a random or nonrandom pattern of X chromosome inactivation. © 2023 Wiley Periodicals LLC. Basic Protocol 1: X chromosome inactivation assay Basic Protocol 2: PCR amplification and labeling of digested and undigested DNA templates.
Collapse
Affiliation(s)
- Raymond C Caylor
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| |
Collapse
|
22
|
Miller RAJ, Williams AP, Kovats S. Sex chromosome complement and sex steroid signaling underlie sex differences in immunity to respiratory virus infection. Front Pharmacol 2023; 14:1150282. [PMID: 37063266 PMCID: PMC10097973 DOI: 10.3389/fphar.2023.1150282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/08/2023] [Indexed: 04/18/2023] Open
Abstract
Epidemiological studies have revealed sex differences in the incidence and morbidity of respiratory virus infection in the human population, and often these observations are correlated with sex differences in the quality or magnitude of the immune response. Sex differences in immunity and morbidity also are observed in animal models of respiratory virus infection, suggesting differential dominance of specific immune mechanisms. Emerging research shows intrinsic sex differences in immune cell transcriptomes, epigenomes, and proteomes that may regulate human immunity when challenged by viral infection. Here, we highlight recent research into the role(s) of sex steroids and X chromosome complement in immune cells and describe how these findings provide insight into immunity during respiratory virus infection. We focus on the regulation of innate and adaptive immune cells by receptors for androgen and estrogens, as well as genes with a propensity to escape X chromosome inactivation. A deeper mechanistic knowledge of these pathways will help us to understand the often significant sex differences in immunity to endemic or pandemic respiratory pathogens such as influenza viruses, respiratory syncytial viruses and pathogenic coronaviruses.
Collapse
Affiliation(s)
- Reegan A. J. Miller
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Abigael P. Williams
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Susan Kovats
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| |
Collapse
|
23
|
Strathmann EA, Hölker I, Tschernoster N, Hosseinibarkooie S, Come J, Martinat C, Altmüller J, Wirth B. Epigenetic regulation of plastin 3 expression by the macrosatellite DXZ4 and the transcriptional regulator CHD4. Am J Hum Genet 2023; 110:442-459. [PMID: 36812914 PMCID: PMC10027515 DOI: 10.1016/j.ajhg.2023.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 02/03/2023] [Indexed: 02/23/2023] Open
Abstract
Dysregulated Plastin 3 (PLS3) levels associate with a wide range of skeletal and neuromuscular disorders and the most common types of solid and hematopoietic cancer. Most importantly, PLS3 overexpression protects against spinal muscular atrophy. Despite its crucial role in F-actin dynamics in healthy cells and its involvement in many diseases, the mechanisms that regulate PLS3 expression are unknown. Interestingly, PLS3 is an X-linked gene and all asymptomatic SMN1-deleted individuals in SMA-discordant families who exhibit PLS3 upregulation are female, suggesting that PLS3 may escape X chromosome inactivation. To elucidate mechanisms contributing to PLS3 regulation, we performed a multi-omics analysis in two SMA-discordant families using lymphoblastoid cell lines and iPSC-derived spinal motor neurons originated from fibroblasts. We show that PLS3 tissue-specifically escapes X-inactivation. PLS3 is located ∼500 kb proximal to the DXZ4 macrosatellite, which is essential for X chromosome inactivation. By applying molecular combing in a total of 25 lymphoblastoid cell lines (asymptomatic individuals, individuals with SMA, control subjects) with variable PLS3 expression, we found a significant correlation between the copy number of DXZ4 monomers and PLS3 levels. Additionally, we identified chromodomain helicase DNA binding protein 4 (CHD4) as an epigenetic transcriptional regulator of PLS3 and validated co-regulation of the two genes by siRNA-mediated knock-down and overexpression of CHD4. We show that CHD4 binds the PLS3 promoter by performing chromatin immunoprecipitation and that CHD4/NuRD activates the transcription of PLS3 by dual-luciferase promoter assays. Thus, we provide evidence for a multilevel epigenetic regulation of PLS3 that may help to understand the protective or disease-associated PLS3 dysregulation.
Collapse
Affiliation(s)
- Eike A Strathmann
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Irmgard Hölker
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Nikolai Tschernoster
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Cologne Center for Genomics and West German Genome Center, University of Cologne, 50931 Cologne, Germany
| | - Seyyedmohsen Hosseinibarkooie
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Julien Come
- INSERM/ UEVE UMR 861, Université Paris Saclay, I-STEM, 91100 Corbeil-Essonnes, France
| | - Cecile Martinat
- INSERM/ UEVE UMR 861, Université Paris Saclay, I-STEM, 91100 Corbeil-Essonnes, France
| | - Janine Altmüller
- Cologne Center for Genomics and West German Genome Center, University of Cologne, 50931 Cologne, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50674 Cologne, Germany; Center for Rare Diseases, University Hospital of Cologne, 50931 Cologne, Germany.
| |
Collapse
|
24
|
Sierra I, Pyfrom S, Weiner A, Zhao G, Driscoll A, Yu X, Gregory BD, Vaughan AE, Anguera MC. Unusual X chromosome inactivation maintenance in female alveolar type 2 cells is correlated with increased numbers of X-linked escape genes and sex-biased gene expression. Stem Cell Reports 2023; 18:489-502. [PMID: 36638790 PMCID: PMC9968984 DOI: 10.1016/j.stemcr.2022.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/13/2023] Open
Abstract
Sex differences exist for many lung pathologies, including COVID-19 and pulmonary fibrosis, but the mechanistic basis for this remains unclear. Alveolar type 2 cells (AT2s), which play a key role in alveolar lung regeneration, express the X-linked Ace2 gene that has roles in lung repair and SARS-CoV-2 pathogenesis, suggesting that X chromosome inactivation (XCI) in AT2s might impact sex-biased lung pathology. Here we investigate XCI maintenance and sex-specific gene expression profiles using male and female AT2s. Remarkably, the inactive X chromosome (Xi) lacks robust canonical Xist RNA "clouds" and less enrichment of heterochromatic modifications in human and mouse AT2s. We demonstrate that about 68% of expressed X-linked genes in mouse AT2s, including Ace2, escape XCI. There are genome-wide expression differences between male and female AT2s, likely influencing both lung physiology and pathophysiologic responses. These studies support a renewed focus on AT2s as a potential contributor to sex-biased differences in lung disease.
Collapse
Affiliation(s)
- Isabel Sierra
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Pyfrom
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aaron Weiner
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gan Zhao
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Driscoll
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiang Yu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew E Vaughan
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Montserrat C Anguera
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
25
|
San Roman AK, Godfrey AK, Skaletsky H, Bellott DW, Groff AF, Harris HL, Blanton LV, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human inactive X chromosome modulates expression of the active X chromosome. Cell Genom 2023; 3:100259. [PMID: 36819663 DOI: 10.1016/j.xgen.2023.100259] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/12/2022] [Accepted: 01/06/2023] [Indexed: 02/11/2023]
Abstract
The "inactive" X chromosome (Xi) has been assumed to have little impact, in trans, on the "active" X (Xa). To test this, we quantified Xi and Xa gene expression in individuals with one Xa and zero to three Xis. Our linear modeling revealed modular Xi and Xa transcriptomes and significant Xi-driven expression changes for 38% (162/423) of expressed X chromosome genes. By integrating allele-specific analyses, we found that modulation of Xa transcript levels by Xi contributes to many of these Xi-driven changes (≥121 genes). By incorporating metrics of evolutionary constraint, we identified 10 X chromosome genes most likely to drive sex differences in common disease and sex chromosome aneuploidy syndromes. We conclude that human X chromosomes are regulated both in cis, through Xi-wide transcriptional attenuation, and in trans, through positive or negative modulation of individual Xa genes by Xi. The sum of these cis and trans effects differs widely among genes.
Collapse
|
26
|
Xiao X, Yang J, Li Y, Yang H, Zhu Y, Li L, Zhou Q, Lu D, Chen T, Tian Y. Identification of a Novel Frameshift Variant of ARR3 Related to X-Linked Female-Limited Early-Onset High Myopia and Study on the Effect of X Chromosome Inactivation on the Myopia Severity. J Clin Med 2023; 12:jcm12030835. [PMID: 36769483 PMCID: PMC9917903 DOI: 10.3390/jcm12030835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/11/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
X-linked myopia 26 (Myopia 26, MIM #301010), which is caused by the variants of ARR3 (MIM *301770), is characterized by female-limited early-onset high myopia (eo-HM). Clinical characteristics include a tigroid appearance in the fundus and a temporal crescent of the optic nerve head. At present, the limited literature on eo-HM caused by ARR3 mutations shows that its inheritance mode is complex, which brings certain difficulties to pre-pregnancy genetic counseling, pre-implantation genetic diagnosis, and prenatal diagnosis. Here, we investigated the genetic underpinning of a Chinese family with eo-HM. Whole exome sequencing of the proband revealed a novel frameshift mutation in ARR3 (NM_004312, exon10, c.666delC, p. Asn222LysfsTer22). Although the mode of inheritance of the eo-HM family fits the X-linked pattern of ARR3, the phenotypes of three patients deviate from the typical early-onset high myopia. Through X-chromosome inactivation experiments, the patient's different phenotypes can be precisely explained. In addition, this study not only enhanced the correlation between ARR3 and early-onset high myopia but also provided explanations for different phenotypes, which may inspire follow-up studies. Our results enrich the knowledge of the variant spectrum in ARR3 and provide critical information for preimplantation and prenatal genetic testing, diagnosis, and counseling.
Collapse
Affiliation(s)
- Xuan Xiao
- Department of Eye Center, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jingmin Yang
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 401120, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Shanghai WeHealth BioMedical Technology Co., Ltd., Shanghai 201210, China
| | - Ying Li
- Department of Eye Center, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Hongxia Yang
- Department of Eye Center, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yijian Zhu
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 401120, China
| | - Lianbing Li
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 401120, China
| | - Qinlinglan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Daru Lu
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 401120, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ting Chen
- Department of Eye Center, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Correspondence: (T.C.); (Y.T.)
| | - Yafei Tian
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing 401120, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Correspondence: (T.C.); (Y.T.)
| |
Collapse
|
27
|
Miquel CH, Faz-Lopez B, Guéry JC. Influence of X chromosome in sex-biased autoimmune diseases. J Autoimmun 2023:102992. [PMID: 36641351 DOI: 10.1016/j.jaut.2023.102992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/03/2023] [Indexed: 01/13/2023]
Abstract
Females have better ability to resolve infections, compared to males, but also, a greater susceptibility to develop autoimmunity. Besides the initial interest on the contribution of sex-steroid hormone signaling, the role of genetic factors linked to X chromosome has recently focused much attention. In human and mouse, the number of X chromosomes, rather than sex-steroid hormones, have been found associated with higher risk or susceptibility to develop autoimmunity, particularly rheumatic diseases, such as SLE, Sjögren's syndrome or Scleroderma. For all of these diseases, the Toll-like receptor TLR7 and TLR8, encoded on the same locus in the human Xp, have been demonstrated to be causal in disease development through gene dosage effect or gain of function mutations. During embryonic development in female mammals, one X chromosome is stochastically inactivated to balance X-linked gene expression between males and females, a process known as X chromosome inactivation (XCI). Nevertheless, some genes including immune related genes can escape XCI to variable degree and penetrance, resulting in a bi-allelic expression in some immune cells, such as TLR7. Because tight regulation of TLR expression is necessary for a healthy, self-tolerant immune environment, XCI escape has been proposed as a mechanism contributing to this sexual dimorphism. In this review, we will summarize general mechanisms of XCI, and describe the known escapee's genes in immune cells, the cellular diversity created by such mechanisms and its potential implication in autoimmune diseases, with a particular focus on the X-linked genes and immune cell populations involved in SLE. Whether dysregulated expression of X-linked genes could contribute to the enhanced susceptibility of females to develop such diseases remains to be proven. Shedding lights onto the X-linked genetic mechanisms contributing to modulation of immune cell functions will undoubtedly provide new insights into the intricate mechanisms underlying sex differences in immunity and autoimmunity.
Collapse
Affiliation(s)
- Charles-Henry Miquel
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITY), Université de Toulouse, INSERM, CNRS, UPS, 31300, France; Arthritis R&D, Neuilly-Sur-Seine, France
| | - Berenice Faz-Lopez
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITY), Université de Toulouse, INSERM, CNRS, UPS, 31300, France
| | - Jean-Charles Guéry
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITY), Université de Toulouse, INSERM, CNRS, UPS, 31300, France.
| |
Collapse
|
28
|
Hayden LP, Hobbs BD, Busch R, Cho MH, Liu M, Lopes-Ramos CM, Lomas DA, Bakke P, Gulsvik A, Silverman EK, Crapo JD, Beaty TH, Laird NM, Lange C, DeMeo DL. X chromosome associations with chronic obstructive pulmonary disease and related phenotypes: an X chromosome-wide association study. Respir Res 2023; 24:38. [PMID: 36726148 PMCID: PMC9891756 DOI: 10.1186/s12931-023-02337-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The association between genetic variants on the X chromosome to risk of COPD has not been fully explored. We hypothesize that the X chromosome harbors variants important in determining risk of COPD related phenotypes and may drive sex differences in COPD manifestations. METHODS Using X chromosome data from three COPD-enriched cohorts of adult smokers, we performed X chromosome specific quality control, imputation, and testing for association with COPD case-control status, lung function, and quantitative emphysema. Analyses were performed among all subjects, then stratified by sex, and subsequently combined in meta-analyses. RESULTS Among 10,193 subjects of non-Hispanic white or European ancestry, a variant near TMSB4X, rs5979771, reached genome-wide significance for association with lung function measured by FEV1/FVC ([Formula: see text] 0.020, SE 0.004, p 4.97 × 10-08), with suggestive evidence of association with FEV1 ([Formula: see text] 0.092, SE 0.018, p 3.40 × 10-07). Sex-stratified analyses revealed X chromosome variants that were differentially trending in one sex, with significantly different effect sizes or directions. CONCLUSIONS This investigation identified loci influencing lung function, COPD, and emphysema in a comprehensive genetic association meta-analysis of X chromosome genetic markers from multiple COPD-related datasets. Sex differences play an important role in the pathobiology of complex lung disease, including X chromosome variants that demonstrate differential effects by sex and variants that may be relevant through escape from X chromosome inactivation. Comprehensive interrogation of the X chromosome to better understand genetic control of COPD and lung function is important to further understanding of disease pathology. Trial registration Genetic Epidemiology of COPD Study (COPDGene) is registered at ClinicalTrials.gov, NCT00608764 (Active since January 28, 2008). Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints Study (ECLIPSE), GlaxoSmithKline study code SCO104960, is registered at ClinicalTrials.gov, NCT00292552 (Active since February 16, 2006). Genetics of COPD in Norway Study (GenKOLS) holds GlaxoSmithKline study code RES11080, Genetics of Chronic Obstructive Lung Disease.
Collapse
Affiliation(s)
- Lystra P. Hayden
- grid.38142.3c000000041936754XDivision of Pulmonary Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA ,grid.38142.3c000000041936754XChanning Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, 181 Longwood Ave, Boston, MA 02115 USA
| | - Brian D. Hobbs
- grid.38142.3c000000041936754XChanning Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, 181 Longwood Ave, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Robert Busch
- grid.417587.80000 0001 2243 3366Division of Pulmonology, Allergy, and Critical Care, U.S. Food and Drug Administration, Silver Spring, MD USA
| | - Michael H. Cho
- grid.38142.3c000000041936754XChanning Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, 181 Longwood Ave, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Ming Liu
- grid.268323.e0000 0001 1957 0327Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA USA
| | - Camila M. Lopes-Ramos
- grid.38142.3c000000041936754XChanning Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, 181 Longwood Ave, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - David A. Lomas
- grid.83440.3b0000000121901201UCL Respiratory, University College London, London, UK
| | - Per Bakke
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Edwin K. Silverman
- grid.38142.3c000000041936754XChanning Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, 181 Longwood Ave, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - James D. Crapo
- grid.240341.00000 0004 0396 0728Division of Pulmonary Sciences and Critical Care Medicine, National Jewish Health, Denver, CO USA
| | - Terri H. Beaty
- grid.21107.350000 0001 2171 9311Johns Hopkins School of Public Health, Baltimore, MD USA
| | - Nan M. Laird
- grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Christoph Lange
- grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Dawn L. DeMeo
- grid.38142.3c000000041936754XChanning Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, 181 Longwood Ave, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| |
Collapse
|
29
|
Abida O, Elloumi N, Bahloul E, Hachicha H, Sellami K, Fakhfakh R, Marzouk S, Ben Ayed I, Mahfoudh N, Turki H, Masmoudi H. Evaluation of X chromosome inactivation in endemic Tunisian pemphigus foliaceus. Mol Genet Genomic Med 2022; 10:e2080. [PMID: 36349750 DOI: 10.1002/mgg3.2080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 10/11/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Almost 5% of the world's population develops an autoimmune disease (AID), it is considered the fourth leading cause of disability for women, who represent 78% of cases. The sex ratio when it comes to the most prevalent AID varies from 9:1 in systemic lupus erythematosus (SLE) to 13:1 in endemic Tunisian pemphigus foliaceus (PF). METHODS To test the potential involvement of skewed x-inactivation in the pathogenesis of Tunisian PF, we analyzed the methylation status of a highly polymorphic CAG repeat in the androgen receptor gene and evaluated the x chromosome inactivation (XCI) patterns in peripheral blood-leukocyte-derived DNA samples of female patients with PF (n = 98) compared to healthy control (HC) subjects (n = 150), as well as female patients with SLE (n = 98) were enrolled as a reference group. RESULTS XCI status was informative for 50 of the 98 PF patients (51%) and 70 of the 150 HC women (47%). Extremely skewed XCI patterns were more frequent in PF and SLEwomen than HC, but the difference was statistically significant only in women with SLE. No statistical difference was observed in XCI patterns between PF and SLE patients. PF phenotype-XCI correlation analysis revealed that (i) skewed XCI patterns may be involved in the disease's subtype and (ii) it was more pronounced in the endemic group than the sporadic one. Furthermore, preferential XCI showed an increase in heterozygote genotypes of PF's susceptibility polymorphisms in immunity-related X genes (FOXP3, AR, and TLR7) in PF patients compared to HC. CONCLUSION Our results suggest that skewed XCI could lead to hemizygosity of X-linked alleles that might unmask X-linked deleterious alleles.
Collapse
Affiliation(s)
- Olfa Abida
- "Autoimmunity, Cancer and Immunogenetics" Research Laboratory (LR18SP12), Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Nesrine Elloumi
- "Autoimmunity, Cancer and Immunogenetics" Research Laboratory (LR18SP12), Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Emna Bahloul
- Dermatology Department, HediChaker Hospital, University of Sfax, Sfax, Tunisia
| | - Hend Hachicha
- "Autoimmunity, Cancer and Immunogenetics" Research Laboratory (LR18SP12), Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Khadija Sellami
- Dermatology Department, HediChaker Hospital, University of Sfax, Sfax, Tunisia
| | - Raouia Fakhfakh
- "Autoimmunity, Cancer and Immunogenetics" Research Laboratory (LR18SP12), Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - Sameh Marzouk
- Internal Medicine, HediChaker Hospital, University of Sfax, Sfax, Tunisia
| | - Ikhlas Ben Ayed
- Genetic Department, HediChaker Hospital, University of Sfax, Sfax, Tunisia
| | - Nadia Mahfoudh
- Immunology Department, HediChaker Hospital, University of Sfax, Sfax, Tunisia
| | - Hamida Turki
- Dermatology Department, HediChaker Hospital, University of Sfax, Sfax, Tunisia
| | - Hatem Masmoudi
- "Autoimmunity, Cancer and Immunogenetics" Research Laboratory (LR18SP12), Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| |
Collapse
|
30
|
Dong Y, Wu X, Peng X, Yang L, Tan B, Zhao H, Zheng E, Hong L, Cai G, Wu Z, Li Z. Knockdown of YY1 Inhibits XIST Expression and Enhances Cloned Pig Embryo Development. Int J Mol Sci 2022; 23. [PMID: 36498896 DOI: 10.3390/ijms232314572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
The technique of cloning has wide applications in animal husbandry and human biomedicine. However, the very low developmental efficiency of cloned embryos limits the application of cloning. Ectopic XIST-expression-induced abnormal X chromosome inactivation (XCI) is a primary cause of the low developmental competence of cloned mouse and pig embryos. Knockout or knockdown of XIST improves cloning efficiency in both pigs and mice. The transcription factor Yin yang 1(YY1) plays a critical role in XCI by triggering the transcription of X-inactive specific transcript (XIST) and facilitating the localization of XIST RNA on the X chromosome. This study aimed to investigate whether RNA interference to suppress the expression of YY1 can inhibit erroneous XIST expression, rescue abnormal XCI, and improve the developmental ability of cloned pig embryos. The results showed that YY1 binds to the 5' regulatory region of the porcine XIST gene in pig cells. The microinjection of YY1 siRNA into cloned pig embryos reduced the transcript abundance of XIST and upregulated the mRNA level of X-linked genes at the 4-cell and blastocyst stages. The siRNA-mediated knockdown of YY1 altered the transcriptome and enhanced the in vitro and in vivo developmental efficiency of cloned porcine embryos. These results suggested that YY1 participates in regulating XIST expression and XCI in cloned pig embryos and that the suppression of YY1 expression can increase the developmental rate of cloned pig embryos. The present study established a new method for improving the efficiency of pig cloning.
Collapse
|
31
|
Roberts AL, Morea A, Amar A, Zito A, El-Sayed Moustafa JS, Tomlinson M, Bowyer RCE, Zhang X, Christiansen C, Costeira R, Steves CJ, Mangino M, Bell JT, Wong CCY, Vyse TJ, Small KS. Age acquired skewed X chromosome inactivation is associated with adverse health outcomes in humans. eLife 2022; 11:78263. [PMID: 36412098 PMCID: PMC9681199 DOI: 10.7554/elife.78263] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Ageing is a heterogenous process characterised by cellular and molecular hallmarks, including changes to haematopoietic stem cells and is a primary risk factor for chronic diseases. X chromosome inactivation (XCI) randomly transcriptionally silences either the maternal or paternal X in each cell of 46, XX females to balance the gene expression with 46, XY males. Age acquired XCI-skew describes the preferential selection of cells across a tissue resulting in an imbalance of XCI, which is particularly prevalent in blood tissues of ageing females, and yet its clinical consequences are unknown. METHODS We assayed XCI in 1575 females from the TwinsUK population cohort using DNA extracted from whole blood. We employed prospective, cross-sectional, and intra-twin study designs to characterise the relationship of XCI-skew with molecular and cellular measures of ageing, cardiovascular disease risk, and cancer diagnosis. RESULTS We demonstrate that XCI-skew is independent of traditional markers of biological ageing and is associated with a haematopoietic bias towards the myeloid lineage. Using an atherosclerotic cardiovascular disease risk score, which captures traditional risk factors, XCI-skew is associated with an increased cardiovascular disease risk both cross-sectionally and within XCI-skew discordant twin pairs. In a prospective 10 year follow-up study, XCI-skew is predictive of future cancer incidence. CONCLUSIONS Our study demonstrates that age acquired XCI-skew captures changes to the haematopoietic stem cell population and has clinical potential as a unique biomarker of chronic disease risk. FUNDING KSS acknowledges funding from the Medical Research Council [MR/M004422/1 and MR/R023131/1]. JTB acknowledges funding from the ESRC [ES/N000404/1]. MM acknowledges funding from the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust in partnership with King's College London. TwinsUK is funded by the Wellcome Trust, Medical Research Council, European Union, Chronic Disease Research Foundation (CDRF), Zoe Global Ltd and the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust in partnership with King's College London.
Collapse
Affiliation(s)
- Amy L Roberts
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Alessandro Morea
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom.,Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Ariella Amar
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Antonino Zito
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | | | - Max Tomlinson
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom.,Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Ruth C E Bowyer
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Xinyuan Zhang
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Colette Christiansen
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Ricardo Costeira
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Claire J Steves
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom.,NIHR Biomedical Research Centre, Guy's and St Thomas' Foundation Trust, London, United Kingdom
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Chloe C Y Wong
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Kerrin S Small
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| |
Collapse
|
32
|
Sadagopan A, Nasim IT, Li J, Achom M, Zhang CZ, Viswanathan SR. Somatic XIST activation and features of X chromosome inactivation in male human cancers. Cell Syst 2022; 13:932-944.e5. [PMID: 36356577 DOI: 10.1016/j.cels.2022.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 05/09/2022] [Accepted: 10/04/2022] [Indexed: 11/11/2022]
Abstract
Expression of the non-coding RNA XIST is essential for initiating X chromosome inactivation (XCI) during early development in female mammals. As the main function of XCI is to enable dosage compensation of chromosome X genes between the sexes, XCI and XIST expression are generally absent in male normal tissues, except in germ cells and in individuals with supernumerary X chromosomes. Via a systematic analysis of public sequencing data of both cancerous and normal tissues, we report that XIST is somatically activated in a subset of male human cancers across diverse lineages. Some of these cancers display hallmarks of XCI, including silencing of gene expression, reduced chromatin accessibility, and increased DNA methylation across chromosome X, suggesting that the developmentally restricted, female-specific program of XCI can be somatically accessed in male cancers.
Collapse
|
33
|
Keniry A, Jansz N, Hickey PF, Breslin KA, Iminitoff M, Beck T, Gouil Q, Ritchie ME, Blewitt ME. A method for stabilising the XX karyotype in female mESC cultures. Development 2022; 149:285125. [PMID: 36355065 PMCID: PMC10112917 DOI: 10.1242/dev.200845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/30/2022] [Indexed: 11/12/2022]
Abstract
Female mouse embryonic stem cells (mESCs) present differently from male mESCs in several fundamental ways; however, complications with their in vitro culture have resulted in an under-representation of female mESCs in the literature. Recent studies show that the second X chromosome in female, and more specifically the transcriptional activity from both of these chromosomes due to absent X chromosome inactivation, sets female and male mESCs apart. To avoid this undesirable state, female mESCs in culture preferentially adopt an XO karyotype, with this adaption leading to loss of their unique properties in favour of a state that is near indistinguishable from male mESCs. If female pluripotency is to be studied effectively in this system, it is crucial that high-quality cultures of XX mESCs are available. Here, we report a method for better maintaining XX female mESCs in culture that also stabilises the male karyotype and makes study of female-specific pluripotency more feasible.
Collapse
Affiliation(s)
- Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Peter F Hickey
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Kelsey A Breslin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Quentin Gouil
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| |
Collapse
|
34
|
Huang Y, Ma L, Zhang Z, Nie S, Zhou Y, Zhang J, Wang C, Fang X, Quan Y, He T, Liu A, Peng D. Nance-Horan syndrome pedigree due to a novel microdeletion and skewed X chromosome inactivation. Mol Genet Genomic Med 2022; 11:e2100. [PMID: 36370055 PMCID: PMC9938751 DOI: 10.1002/mgg3.2100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/16/2022] [Accepted: 11/03/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Nance-Horan syndrome (NHS) is a rare and often overlooked X-linked dominant disorder characterized by dense congenital cataracts, dental abnormalities, and mental retardation. The majority of NHS variations include frameshift mutations, nonsense mutations, microdeletions, and insertions. METHODS Copy number variation sequencing was performed to determine the microdeletion. The expression of NHS was detected by RT-PCR. Four family members were tested for X chromosome inactivation. RESULTS In this study, all members were examined for systemic examinations and genetic testing of four members and two affected subjects are observed. We identified a heterozygous microdeletion of -0.52 Mb at Xp22.13 in a female proband presenting NHS phenotypically. The microdeletion contains the REPS2 and NHS genes and was inherited from a phenotypically normal mother. Of interest, the expression NHS of proband was reduced and the skewed X chromosome inactivation rate reached more than 85% compared with her mother and the control. It was concluded that the haploinsufficiency of the NHS gene may account for the majority of clinical symptoms in the affected subjects. The variability among female carriers presumably results from nonrandom X chromosome inactivation. CONCLUSION Our findings broaden the spectrum of NHS mutations and provide molecular insight into NHS clinical prenatal genetic diagnosis.
Collapse
Affiliation(s)
- Yazhou Huang
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Linya Ma
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Zhaoxia Zhang
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Shujuan Nie
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Yuan Zhou
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Jibo Zhang
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Chao Wang
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Xingxin Fang
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Yingting Quan
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Ting He
- Department of Medical GeneticsChangde First People's HospitalChangdeChina
| | - Anhui Liu
- Affiliated Hospital of Changde CityUniversity of South ChinaHengyangChina
| | - Dan Peng
- Department of Medical GeneticsChangde First People's HospitalChangdeChina,Affiliated Hospital of Changde CityUniversity of South ChinaHengyangChina
| |
Collapse
|
35
|
Ahern DT, Bansal P, Armillei MK, Faustino IV, Kondaveeti Y, Glatt-Deeley HR, Banda EC, Pinter SF. Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta. Proc Natl Acad Sci U S A 2022; 119:e2211073119. [PMID: 36161909 DOI: 10.1073/pnas.2211073119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mammalian sex chromosomes encode homologous X/Y gene pairs that were retained on the Y chromosome in males and escape X chromosome inactivation (XCI) in females. Inferred to reflect X/Y pair dosage sensitivity, monosomy X is a leading cause of miscarriage in humans with near full penetrance. This phenotype is shared with many other mammals but not the mouse, which offers sophisticated genetic tools to generate sex chromosomal aneuploidy but also tolerates its developmental impact. To address this critical gap, we generated X-monosomic human induced pluripotent stem cells (hiPSCs) alongside otherwise isogenic euploid controls from male and female mosaic samples. Phased genomic variants in these hiPSC panels enable systematic investigation of X/Y dosage-sensitive features using in vitro models of human development. Here, we demonstrate the utility of these validated hiPSC lines to test how X/Y-linked gene dosage impacts a widely used model for human syncytiotrophoblast development. While these isogenic panels trigger a GATA2/3- and TFAP2A/C-driven trophoblast gene circuit irrespective of karyotype, differential expression implicates monosomy X in altered levels of placental genes and in secretion of placental growth factor (PlGF) and human chorionic gonadotropin (hCG). Remarkably, weighted gene coexpression network modules that significantly reflect these changes are also preserved in first-trimester chorionic villi and term placenta. Our results suggest monosomy X may skew trophoblast cell type composition and function, and that the combined haploinsufficiency of the pseudoautosomal region likely plays a key role in these changes.
Collapse
|
36
|
Chang C, Ma G, Cheung E, Hutchins AP. A programmable system to methylate and demethylate N 6-Methyladenosine (m 6A) on specific RNA transcripts in mammalian cells. J Biol Chem 2022; 298:102525. [PMID: 36162509 PMCID: PMC9597892 DOI: 10.1016/j.jbc.2022.102525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/26/2022] Open
Abstract
RNA N6-methyladenosine (m6A) is the most abundant internal mRNA modification and forms part of an epitranscriptomic system that modulates RNA function. m6A is reversibly catalyzed by specific enzymes, and those modifications can be recognized by RNA-binding proteins that in turn regulate biological processes. Although there are many reports demonstrating m6A participation in critical biological functions, this exploration has mainly been conducted through the global KO or knockdown of the writers, erasers, or readers of m6A. Consequently, there is a lack of information about the role of m6A on single transcripts in biological processes, posing a challenge in understanding the biological functions of m6A. Here, we demonstrate a CRISPR/dCas13a-based RNA m6A editors, which can target RNAs using a single or multiple CRISPR RNA array to methylate or demethylate m6A in human 293T cells and mouse embryonic stem cells. We systematically assay its capabilities to enable the targeted rewriting of m6A dynamics, including modulation of circular RNA translation and transcript half-life. Finally, we use the system to specifically modulate m6A levels on the noncoding XIST (X-inactive specific transcript) to modulate X chromosome silencing and activation. The editors described here can be used to explore the roles of m6A in biological processes.
Collapse
Affiliation(s)
- Chen Chang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China; Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR
| | - Gang Ma
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Edwin Cheung
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR.
| | - Andrew P Hutchins
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| |
Collapse
|
37
|
Ichihara S, Nagao K, Sakaguchi T, Obuse C, Sado T. SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice. Development 2022; 149:275999. [PMID: 35831949 DOI: 10.1242/dev.200864] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/30/2022] [Indexed: 12/12/2022]
Abstract
Stable silencing of the inactive X chromosome (Xi) in female mammals is crucial for the development of embryos and their postnatal health. SmcHD1 is essential for stable silencing of the Xi, and its functional deficiency results in derepression of many X-inactivated genes. Although SmcHD1 has been suggested to play an important role in the formation of higher-order chromatin structure of the Xi, the underlying mechanism is largely unknown. Here, we explore the epigenetic state of the Xi in SmcHD1-deficient epiblast stem cells and mouse embryonic fibroblasts in comparison with their wild-type counterparts. The results suggest that SmcHD1 underlies the formation of H3K9me3-enriched blocks on the Xi, which, although the importance of H3K9me3 has been largely overlooked in mice, play a crucial role in the establishment of the stably silenced state. We propose that the H3K9me3 blocks formed on the Xi facilitate robust heterochromatin formation in combination with H3K27me3, and that the substantial loss of H3K9me3 caused by SmcHD1 deficiency leads to aberrant distribution of H3K27me3 on the Xi and derepression of X-inactivated genes.
Collapse
Affiliation(s)
- Saya Ichihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Koji Nagao
- Department of Biological Science, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Takehisa Sakaguchi
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Chikashi Obuse
- Department of Biological Science, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan.,Agricultural Technology and Innovation Research Institute, Kindai University, Nara 631-8505, Japan
| |
Collapse
|
38
|
Hierholzer A, Chureau C, Liverziani A, Ruiz NB, Cattanach BM, Young AN, Kumar M, Cerase A, Avner P. A long noncoding RNA influences the choice of the X chromosome to be inactivated. Proc Natl Acad Sci U S A 2022; 119:e2118182119. [PMID: 35787055 DOI: 10.1073/pnas.2118182119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X chromosome inactivation (XCI) is the process of silencing one of the X chromosomes in cells of the female mammal which ensures dosage compensation between the sexes. Although theoretically random in somatic tissues, the choice of which X chromosome is chosen to be inactivated can be biased in mice by genetic element(s) associated with the so-called X-controlling element (Xce). Although the Xce was first described and genetically localized nearly 40 y ago, its mode of action remains elusive. In the approach presented here, we identify a single long noncoding RNA (lncRNA) within the Xce locus, Lppnx, which may be the driving factor in the choice of which X chromosome will be inactivated in the developing female mouse embryo. Comparing weak and strong Xce alleles we show that Lppnx modulates the expression of Xist lncRNA, one of the key factors in XCI, by controlling the occupancy of pluripotency factors at Intron1 of Xist. This effect is counteracted by enhanced binding of Rex1 in DxPas34, another key element in XCI regulating the activity of Tsix lncRNA, the main antagonist of Xist, in the strong but not in the weak Xce allele. These results suggest that the different susceptibility for XCI observed in weak and strong Xce alleles results from differential transcription factor binding of Xist Intron 1 and DxPas34, and that Lppnx represents a decisive factor in explaining the action of the Xce.
Collapse
|
39
|
Karvas RM, Khan SA, Verma S, Yin Y, Kulkarni D, Dong C, Park KM, Chew B, Sane E, Fischer LA, Kumar D, Ma L, Boon ACM, Dietmann S, Mysorekar IU, Theunissen TW. Stem-cell-derived trophoblast organoids model human placental development and susceptibility to emerging pathogens. Cell Stem Cell 2022; 29:810-825.e8. [PMID: 35523141 PMCID: PMC9136997 DOI: 10.1016/j.stem.2022.04.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/13/2021] [Accepted: 03/01/2022] [Indexed: 12/28/2022]
Abstract
Trophoblast organoids derived from placental villi provide a 3D model system of human placental development, but access to first-trimester tissues is limited. Here, we report that trophoblast stem cells isolated from naive human pluripotent stem cells (hPSCs) can efficiently self-organize into 3D stem-cell-derived trophoblast organoids (SC-TOs) with a villous architecture similar to primary trophoblast organoids. Single-cell transcriptome analysis reveals the presence of distinct cytotrophoblast and syncytiotrophoblast clusters and a small cluster of extravillous trophoblasts, which closely correspond to trophoblast identities in the post-implantation embryo. These organoid cultures display clonal X chromosome inactivation patterns previously described in the human placenta. We further demonstrate that SC-TOs exhibit selective vulnerability to emerging pathogens (SARS-CoV-2 and Zika virus), which correlates with expression levels of their respective entry factors. The generation of trophoblast organoids from naive hPSCs provides an accessible 3D model system of the developing placenta and its susceptibility to emerging pathogens.
Collapse
Affiliation(s)
- Rowan M Karvas
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, 4515 McKinley Ave, Room 3313, St. Louis, MO 63110, USA
| | - Shafqat A Khan
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, 4515 McKinley Ave, Room 3313, St. Louis, MO 63110, USA
| | - Sonam Verma
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yan Yin
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Devesha Kulkarni
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chen Dong
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, 4515 McKinley Ave, Room 3313, St. Louis, MO 63110, USA
| | - Kyoung-Mi Park
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, 4515 McKinley Ave, Room 3313, St. Louis, MO 63110, USA
| | - Brian Chew
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, 4515 McKinley Ave, Room 3313, St. Louis, MO 63110, USA
| | - Eshan Sane
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, 4515 McKinley Ave, Room 3313, St. Louis, MO 63110, USA
| | - Laura A Fischer
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, 4515 McKinley Ave, Room 3313, St. Louis, MO 63110, USA
| | - Deepak Kumar
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Liang Ma
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Adrianus C M Boon
- Division of Infection Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sabine Dietmann
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, 4515 McKinley Ave, Room 3313, St. Louis, MO 63110, USA; Division of Nephrology and Institute for Informatics (I(2)), Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Indira U Mysorekar
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Thorold W Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, 4515 McKinley Ave, Room 3313, St. Louis, MO 63110, USA.
| |
Collapse
|
40
|
Lansdorp PM. Sex differences in telomere length, lifespan, and embryonic dyskerin levels. Aging Cell 2022; 21:e13614. [PMID: 35441417 PMCID: PMC9124296 DOI: 10.1111/acel.13614] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/20/2022] [Accepted: 04/03/2022] [Indexed: 01/22/2023] Open
Abstract
Telomerase levels in most human cells are insufficient to prevent loss of telomeric DNA with each replication cycle. The resulting “Hayflick” limit may have allowed lifespan to increase by suppressing the development of tumors early in life be it at the expense of compromised cellular responses late in life. At any given age, the average telomere length in leukocytes shows considerably variation between individuals with females having, on average, longer telomeres than males. Sex differences in average telomere length are already present at birth and correspond to reported differences in the average life expectancy between the sexes. Levels of telomerase RNA and dyskerin, encoded by DKC1, are known to limit telomerase activity in embryonic stem cells. X‐linked DKC1 is expressed from both alleles in female embryo cells and higher levels of dyskerin and telomerase could elongate telomeres prior to embryo implantation. The hypothesis that embryonic telomerase levels set the stage for the sex differences in telomere length and lifespan deserves further study.
Collapse
Affiliation(s)
- Peter M. Lansdorp
- Terry Fox Laboratory BC Cancer Agency Vancouver BC Canada
- Department of Medical Genetics University of British Columbia Vancouver BC Canada
| |
Collapse
|
41
|
Nicolì V, Tabano SM, Colapietro P, Maestri M, Ricciardi R, Stoccoro A, Fontana L, Guida M, Miozzo M, Coppedè F, Migliore L. Preferential X Chromosome Inactivation as a Mechanism to Explain Female Preponderance in Myasthenia Gravis. Genes (Basel) 2022; 13. [PMID: 35456502 DOI: 10.3390/genes13040696] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/04/2022] [Accepted: 04/13/2022] [Indexed: 11/17/2022] Open
Abstract
Myasthenia gravis (MG) is a neuromuscular autoimmune disease characterized by prevalence in young women (3:1). Several mechanisms proposed as explanations for gender bias, including skewed X chromosome inactivation (XCI) and dosage or sex hormones, are often involved in the development of autoimmunity. The skewed XCI pattern can lead to an unbalanced expression of some X-linked genes, as observed in several autoimmune disorders characterized by female predominance. No data are yet available regarding XCI and MG. We hypothesize that the preferential XCI pattern may contribute to the female bias observed in the onset of MG, especially among younger women. XCI analysis was performed on blood samples of 284 women between the ages of 20 and 82. XCI was tested using the Human Androgen Receptor Assay (HUMARA). XCI patterns were classified as random (XCI < 75%) and preferential (XCI ≥ 75%). In 121 informative patients, the frequency of skewed XCI patterns was 47%, significantly higher than in healthy controls (17%; p ≤ 0.00001). Interestingly, the phenomenon was observed mainly in younger patients (<45 years; p ≤ 0.00001). Furthermore, considering the XCI pattern and the other clinical characteristics of patients, no significant differences were found. In conclusion, we observed preferential XCI in MG female patients, suggesting its potential role in the aetiology of MG, as observed in other autoimmune diseases in women.
Collapse
|
42
|
Abstract
The etiology of autism spectrum disorders (ASD) is complex, involving different combinations of genetic and environmental factors. My lab's approach has been to investigate DNA methylation as a tractable genome-wide modification at the interface of these complex interactions, reflecting past and future events in the molecular pathogenesis of ASD. Since X-linked genes were enriched in DNA methylation differences discovered from cord blood from newborns later diagnosed with ASD, this has prompted me to review and revisit the recent advancements in the field of X chromosome inactivation (XCI), particularly in humans and other primates. In this Perspective, I compare XCI mechanisms in different mammalian species, including the finding of the noncoding transcript XACT associated with X chromosome erosion in human pluripotent stem cells and recent findings from non-human primate post-implantation embryos. I focus on the experimentally challenging peri- and post-implantation stages of human development when the timing of XCI is prolonged and imprecise in humans. Collectively, this research has raised some important unanswered questions involving biased sex ratios in human births and the male bias in the incidence of ASD.
Collapse
Affiliation(s)
- Janine M LaSalle
- Department of Medical Microbiology and Immunology, Perinatal Origins of Disparities Center, MIND Institute, Genome Center, Environmental Health Sciences Center, University of California, Davis, Davis, CA, United States
| |
Collapse
|
43
|
Siniscalchi C, Di Palo A, Russo A, Potenza N. The lncRNAs at X Chromosome Inactivation Center: Not Just a Matter of Sex Dosage Compensation. Int J Mol Sci 2022; 23:611. [PMID: 35054794 DOI: 10.3390/ijms23020611] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) constitute the majority of the transcriptome, as the result of pervasive transcription of the mammalian genome. Different RNA species, such as lncRNAs, miRNAs, circRNA, mRNAs, engage in regulatory networks based on their reciprocal interactions, often in a competitive manner, in a way denominated “competing endogenous RNA (ceRNA) networks” (“ceRNET”): miRNAs and other ncRNAs modulate each other, since miRNAs can regulate the expression of lncRNAs, which in turn regulate miRNAs, titrating their availability and thus competing with the binding to other RNA targets. The unbalancing of any network component can derail the entire regulatory circuit acting as a driving force for human diseases, thus assigning “new” functions to “old” molecules. This is the case of XIST, the lncRNA characterized in the early 1990s and well known as the essential molecule for X chromosome inactivation in mammalian females, thus preventing an imbalance of X-linked gene expression between females and males. Currently, literature concerning XIST biology is becoming dominated by miRNA associations and they are also gaining prominence for other lncRNAs produced by the X-inactivation center. This review discusses the available literature to explore possible novel functions related to ceRNA activity of lncRNAs produced by the X-inactivation center, beyond their role in dosage compensation, with prospective implications for emerging gender-biased functions and pathological mechanisms.
Collapse
|
44
|
Markaki Y, Gan Chong J, Wang Y, Jacobson EC, Luong C, Tan SYX, Jachowicz JW, Strehle M, Maestrini D, Banerjee AK, Mistry BA, Dror I, Dossin F, Schöneberg J, Heard E, Guttman M, Chou T, Plath K. Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell 2021; 184:6174-6192.e32. [PMID: 34813726 DOI: 10.1016/j.cell.2021.10.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 07/29/2021] [Accepted: 10/11/2021] [Indexed: 02/08/2023]
Abstract
The lncRNA Xist forms ∼50 diffraction-limited foci to transcriptionally silence one X chromosome. How this small number of RNA foci and interacting proteins regulate a much larger number of X-linked genes is unknown. We show that Xist foci are locally confined, contain ∼2 RNA molecules, and nucleate supramolecular complexes (SMACs) that include many copies of the critical silencing protein SPEN. Aggregation and exchange of SMAC proteins generate local protein gradients that regulate broad, proximal chromatin regions. Partitioning of numerous SPEN molecules into SMACs is mediated by their intrinsically disordered regions and essential for transcriptional repression. Polycomb deposition via SMACs induces chromatin compaction and the increase in SMACs density around genes, which propagates silencing across the X chromosome. Our findings introduce a mechanism for functional nuclear compartmentalization whereby crowding of transcriptional and architectural regulators enables the silencing of many target genes by few RNA molecules.
Collapse
|
45
|
Aizawa E, Kaufmann C, Sting S, Boigner S, Freimann R, Di Minin G, Wutz A. Haploid mouse germ cell precursors from embryonic stem cells reveal Xist activation from a single X chromosome. Stem Cell Reports 2021; 17:43-52. [PMID: 34919812 PMCID: PMC8758942 DOI: 10.1016/j.stemcr.2021.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 12/03/2022] Open
Abstract
Mammalian haploid cells have applications for genetic screening and substituting gametic genomes. Here, we characterize a culture system for obtaining haploid primordial germ cell-like cells (PGCLCs) from haploid mouse embryonic stem cells (ESCs). We find that haploid cells show predisposition for PGCLCs, whereas a large fraction of somatic cells becomes diploid. Characterization of the differentiating haploid ESCs (haESCs) reveals that Xist is activated from and colocalizes with the single X chromosome. This observation suggests that X chromosome inactivation (XCI) is initiated in haploid cells consistent with a model where autosomal blocking factors set a threshold for X-linked activators. We further find that Xist expression is lost at later timepoints in differentiation, which likely reflects the loss of X-linked activators. In vitro differentiation of haploid PGCLCs can be a useful approach for future studies of potential X-linked activators of Xist. A culture system for obtaining haploid PGCLCs Predisposition of haploid cells in the germline over somatic lineages A single X chromosome in haploid cells leads to activation of Xist Mutation of Xist is insufficient to prevent diploidization of haESCs
Collapse
Affiliation(s)
- Eishi Aizawa
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Corinne Kaufmann
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Sarah Sting
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Sarah Boigner
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Remo Freimann
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Giulio Di Minin
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
46
|
Enervald E, Powell LM, Boteva L, Foti R, Blanes Ruiz N, Kibar G, Piszczek A, Cavaleri F, Vingron M, Cerase A, Buonomo SBC. RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes. EMBO J 2021; 40:e105862. [PMID: 34786738 DOI: 10.15252/embj.2020105862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 11/09/2022] Open
Abstract
The onset of random X chromosome inactivation in mouse requires the switch from a symmetric to an asymmetric state, where the identities of the future inactive and active X chromosomes are assigned. This process is known as X chromosome choice. Here, we show that RIF1 and KAP1 are two fundamental factors for the definition of this transcriptional asymmetry. We found that at the onset of differentiation of mouse embryonic stem cells (mESCs), biallelic up-regulation of the long non-coding RNA Tsix weakens the symmetric association of RIF1 with the Xist promoter. The Xist allele maintaining the association with RIF1 goes on to up-regulate Xist RNA expression in a RIF1-dependent manner. Conversely, the promoter that loses RIF1 gains binding of KAP1, and KAP1 is required for the increase in Tsix levels preceding the choice. We propose that the mutual exclusion of Tsix and RIF1, and of RIF1 and KAP1, at the Xist promoters establish a self-sustaining loop that transforms an initially stochastic event into a stably inherited asymmetric X-chromosome state.
Collapse
Affiliation(s)
- Elin Enervald
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy
| | - Lynn Marie Powell
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Lora Boteva
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Rossana Foti
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy
| | - Nerea Blanes Ruiz
- Blizard Institute, Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Gözde Kibar
- Max-Planck-Institut fuer molekulare Genetik, Berlin, Germany
| | - Agnieszka Piszczek
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy
| | - Fatima Cavaleri
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy
| | - Martin Vingron
- Max-Planck-Institut fuer molekulare Genetik, Berlin, Germany
| | - Andrea Cerase
- Blizard Institute, Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sara B C Buonomo
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy
| |
Collapse
|
47
|
Matsuura R, Nakajima T, Ichihara S, Sado T. Ectopic Splicing Disturbs the Function of Xist RNA to Establish the Stable Heterochromatin State. Front Cell Dev Biol 2021; 9:751154. [PMID: 34722536 PMCID: PMC8551810 DOI: 10.3389/fcell.2021.751154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
Non-coding Xist RNA plays an essential role in X chromosome inactivation (XCI) in female mammals. It coats the X chromosome in cis and mediates the recruitment of many proteins involved in gene silencing and heterochromatinization. The molecular basis of how Xist RNA initiates chromosomal silencing and what proteins participate in this process has been extensively studied and elucidated. Its involvement in the establishment and maintenance of the X-inactivated state is, however, less understood. The XistIVS allele we previously reported is peculiar in that it can initiate XCI but fails to establish the inactive state that is stably maintained and, therefore, may provide an opportunity to explore how Xist RNA contributes to establish a robust heterochromatin state. Here we demonstrate that ectopic splicing taking place to produce XistIVS RNA disturbs its function to properly establish stable XCI state. This finding warrants the potential of XistIVS RNA to provide further insight into our understanding of how Xist RNA contributes to establish sustainable heterochromatin.
Collapse
Affiliation(s)
- Ruka Matsuura
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
| | - Tatsuro Nakajima
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Saya Ichihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan.,Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Japan
| |
Collapse
|
48
|
Yokobayashi S, Yabuta Y, Nakagawa M, Okita K, Hu B, Murase Y, Nakamura T, Bourque G, Majewski J, Yamamoto T, Saitou M. Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells. Cell Rep 2021; 37:109909. [PMID: 34731633 DOI: 10.1016/j.celrep.2021.109909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/24/2021] [Accepted: 10/08/2021] [Indexed: 01/13/2023] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) show variable differentiation potential due to their epigenomic heterogeneity, whose extent/attributes remain unclear, except for well-studied elements/chromosomes such as imprints and the X chromosomes. Here, we show that seven hiPSC lines with variable germline potential exhibit substantial epigenomic heterogeneity, despite their uniform transcriptomes. Nearly a quarter of autosomal regions bear potentially differential chromatin modifications, with promoters/CpG islands for H3K27me3/H2AK119ub1 and evolutionarily young retrotransposons for H3K4me3. We identify 145 large autosomal blocks (≥100 kb) with differential H3K9me3 enrichment, many of which are lamina-associated domains (LADs) in somatic but not in embryonic stem cells. A majority of these epigenomic heterogeneities are independent of genetic variations. We identify an X chromosome state with chromosome-wide H3K9me3 that stably prevents X chromosome erosion. Importantly, the germline potential of female hiPSCs correlates with X chromosome inactivation. We propose that inherent genomic properties, including CpG density, transposons, and LADs, engender epigenomic heterogeneity in hiPSCs.
Collapse
|
49
|
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: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
50
|
Lappala A, Wang CY, Kriz A, Michalk H, Tan K, Lee JT, Sanbonmatsu KY. Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome. Proc Natl Acad Sci U S A 2021; 118:e2107092118. [PMID: 34645712 DOI: 10.1073/pnas.2107092118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 12/14/2022] Open
Abstract
Chromosomes are segmented into domains and compartments, but how these structures are spatially related in three dimensions (3D) is unclear. Here, we developed tools that directly extract 3D information from Hi-C experiments and integrate the data across time. With our "4DHiC" method, we use X chromosome inactivation (XCI) as a model to examine the time evolution of 3D chromosome architecture during large-scale changes in gene expression. Our modeling resulted in several insights. Both A/B and S1/S2 compartments divide the X chromosome into hemisphere-like structures suggestive of a spatial phase-separation. During the XCI, the X chromosome transits through A/B, S1/S2, and megadomain structures by undergoing only partial mixing to assume new structures. Interestingly, when an active X chromosome (Xa) is reorganized into an inactive X chromosome (Xi), original underlying compartment structures are not fully eliminated within the Xi superstructure. Our study affirms slow mixing dynamics in the inner chromosome core and faster dynamics near the surface where escapees reside. Once established, the Xa and Xi resemble glassy polymers where mixing no longer occurs. Finally, Xist RNA molecules initially reside within the A compartment but transition to the interface between the A and B hemispheres and then spread between hemispheres via both surface and core to establish the Xi.
Collapse
|