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Yheskel M, Hatch HM, Pedrosa E, Terry BK, Siebels A, Zheng X, Blok LR, Fencková M, Sidoli S, Schenck A, Zheng D, Lachman H, Secombe J. KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons. Nucleic Acids Res 2024; 52:6201-6219. [PMID: 38597673 PMCID: PMC11194071 DOI: 10.1093/nar/gkae261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/11/2024] Open
Abstract
Genes encoding the KDM5 family of transcriptional regulators are disrupted in individuals with intellectual disability (ID). To understand the link between KDM5 and ID, we characterized five Drosophila strains harboring missense alleles analogous to those observed in patients. These alleles disrupted neuroanatomical development, cognition and other behaviors, and displayed a transcriptional signature characterized by the downregulation of many ribosomal protein genes. A similar transcriptional profile was observed in KDM5C knockout iPSC-induced human glutamatergic neurons, suggesting an evolutionarily conserved role for KDM5 proteins in regulating this class of gene. In Drosophila, reducing KDM5 changed neuronal ribosome composition, lowered the translation efficiency of mRNAs required for mitochondrial function, and altered mitochondrial metabolism. These data highlight the cellular consequences of altered KDM5-regulated transcriptional programs that could contribute to cognitive and behavioral phenotypes. Moreover, they suggest that KDM5 may be part of a broader network of proteins that influence cognition by regulating protein synthesis.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Bethany K Terry
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Aubrey A Siebels
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiang Yu Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laura E R Blok
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Michaela Fencková
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Ceske Budejovice 370 05, Czechia
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Hua W, Han X, Li F, Lu L, Sun Y, Hassanian-Moghaddam H, Tian M, Lu Y, Huang Q. Transgenerational Effects of Arsenic Exposure on Learning and Memory in Rats: Crosstalk between Arsenic Methylation, Hippocampal Metabolism, and Histone Modifications. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6475-6486. [PMID: 38578163 DOI: 10.1021/acs.est.3c07989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Arsenic (As) is widely present in the natural environment, and exposure to it can lead to learning and memory impairment. However, the underlying epigenetic mechanisms are still largely unclear. This study aimed to reveal the role of histone modifications in environmental levels of arsenic (sodium arsenite) exposure-induced learning and memory dysfunction in male rats, and the inter/transgenerational effects of paternal arsenic exposure were also investigated. It was found that arsenic exposure impaired the learning and memory ability of F0 rats and down-regulated the expression of cognition-related genes Bdnf, c-Fos, mGlur1, Nmdar1, and Gria2 in the hippocampus. We also observed that inorganic arsenite was methylated to DMA and histone modification-related metabolites were altered, contributing to the dysregulation of H3K4me1/2/3, H3K9me1/2/3, and H3K4ac in rat hippocampus after exposure. Therefore, it is suggested that arsenic methylation and hippocampal metabolism changes attenuated H3K4me1/2/3 and H3K4ac while enhancing H3K9me1/2/3, which repressed the key gene expressions, leading to cognitive impairment in rats exposed to arsenic. In addition, paternal arsenic exposure induced transgenerational effects of learning and memory disorder in F2 male rats through the regulation of H3K4me2 and H3K9me1/2/3, which inhibited c-Fos, mGlur1, and Nmdar1 expression. These results provide novel insights into the molecular mechanism of arsenic-induced neurotoxicity and highlight the risk of neurological deficits in offspring with paternal exposure to arsenic.
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Affiliation(s)
- Weizhen Hua
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Xuejingping Han
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Fuping Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Lu Lu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yiqiong Sun
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hossein Hassanian-Moghaddam
- Department of Clinical Toxicology, Shohada-e Tajrish Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | - Meiping Tian
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yanyang Lu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qingyu Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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Walkley SU, Molholm S, Jordan B, Marion RW, Wasserstein M. Using team-based precision medicine to advance understanding of rare genetic brain disorders. J Neurodev Disord 2024; 16:10. [PMID: 38491427 PMCID: PMC10941544 DOI: 10.1186/s11689-024-09518-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/07/2024] [Indexed: 03/18/2024] Open
Abstract
We describe a multidisciplinary teamwork approach known as "Operation IDD Gene Team" developed by the Rose F. Kennedy Intellectual and Developmental Disabilities Research Center (RFK IDDRC) at the Albert Einstein College of Medicine. This initiative brings families affected by rare genetic diseases that cause intellectual and developmental disability together with physicians, basic scientists, and their trainees. At team meetings, family members share their child's medical and personal history, physicians describe the broader clinical consequences of the condition, and scientists provide accessible tutorials focused on the fundamental biology of relevant genes. When appropriate, possible treatment approaches are also discussed. The outcomes of team meetings have been overwhelmingly positive, with families not only expressing deep gratitude, but also becoming empowered to establish foundations dedicated to their child's specific condition. Physicians, and in particular the scientists and their trainees, have gained a deeper understanding of challenges faced by affected families, broadening their perspective on how their research can extend beyond the laboratory. Remarkably, research by the scientists following the Gene Team meetings have often included focus on the actual gene variants exhibited by the participating children. As these investigations progress and newly created foundations expand their efforts, national as well as international collaborations are forged. These developments emphasize the importance of rare diseases as windows into previously unexplored molecular and cellular processes, which can offer fresh insights into both normal function as well as more common diseases. Elucidating the mechanisms of and treatments for rare and ultra-rare diseases thus has benefits for all involved-families, physicians, and scientists and their trainees, as well as the broader medical community. While the RFK IDDRC's Operation IDD Gene Team program has focused on intellectual disabilities affecting children, we believe it has the potential to be applied to rare genetic diseases impacting individuals of any age and encompassing a wide variety of developmental disorders affecting multiple organ systems.
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Affiliation(s)
- Steven U Walkley
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Department of Neuroscience, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Sophie Molholm
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Bryen Jordan
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Robert W Marion
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Melissa Wasserstein
- Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
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Karwacki-Neisius V, Jang A, Cukuroglu E, Tai A, Jiao A, Predes D, Yoon J, Brookes E, Chen J, Iberg A, Halbritter F, Õunap K, Gecz J, Schlaeger TM, Ho Sui S, Göke J, He X, Lehtinen MK, Pomeroy SL, Shi Y. WNT signalling control by KDM5C during development affects cognition. Nature 2024; 627:594-603. [PMID: 38383780 PMCID: PMC10954547 DOI: 10.1038/s41586-024-07067-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024]
Abstract
Although KDM5C is one of the most frequently mutated genes in X-linked intellectual disability1, the exact mechanisms that lead to cognitive impairment remain unknown. Here we use human patient-derived induced pluripotent stem cells and Kdm5c knockout mice to conduct cellular, transcriptomic, chromatin and behavioural studies. KDM5C is identified as a safeguard to ensure that neurodevelopment occurs at an appropriate timescale, the disruption of which leads to intellectual disability. Specifically, there is a developmental window during which KDM5C directly controls WNT output to regulate the timely transition of primary to intermediate progenitor cells and consequently neurogenesis. Treatment with WNT signalling modulators at specific times reveal that only a transient alteration of the canonical WNT signalling pathway is sufficient to rescue the transcriptomic and chromatin landscapes in patient-derived cells and to induce these changes in wild-type cells. Notably, WNT inhibition during this developmental period also rescues behavioural changes of Kdm5c knockout mice. Conversely, a single injection of WNT3A into the brains of wild-type embryonic mice cause anxiety and memory alterations. Our work identifies KDM5C as a crucial sentinel for neurodevelopment and sheds new light on KDM5C mutation-associated intellectual disability. The results also increase our general understanding of memory and anxiety formation, with the identification of WNT functioning in a transient nature to affect long-lasting cognitive function.
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Affiliation(s)
- Violetta Karwacki-Neisius
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Ahram Jang
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Engin Cukuroglu
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Albert Tai
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
- Data Intensive Studies Center, Tufts University, Medford, MA, USA
| | - Alan Jiao
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Danilo Predes
- Department of Neurology, F. M Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joon Yoon
- Department of Biostatistics, The Harvard Chan School of Public Health, Bioinformatics Core, Cambridge, MA, USA
| | - Emily Brookes
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Jiekai Chen
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Aimee Iberg
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Florian Halbritter
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria
| | - Katrin Õunap
- Department of Clinical Genetics, Genetic and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Thorsten M Schlaeger
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shannan Ho Sui
- Department of Biostatistics, The Harvard Chan School of Public Health, Bioinformatics Core, Cambridge, MA, USA
| | - Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Xi He
- Department of Neurology, F. M Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Scott L Pomeroy
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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Malcore RM, Kalantry S. A Comparative Analysis of Mouse Imprinted and Random X-Chromosome Inactivation. EPIGENOMES 2024; 8:8. [PMID: 38390899 PMCID: PMC10885068 DOI: 10.3390/epigenomes8010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
The mammalian sexes are distinguished by the X and Y chromosomes. Whereas males harbor one X and one Y chromosome, females harbor two X chromosomes. To equalize X-linked gene expression between the sexes, therian mammals have evolved X-chromosome inactivation as a dosage compensation mechanism. During X-inactivation, most genes on one of the two X chromosomes in females are transcriptionally silenced, thus equalizing X-linked gene expression between the sexes. Two forms of X-inactivation characterize eutherian mammals, imprinted and random. Imprinted X-inactivation is defined by the exclusive inactivation of the paternal X chromosome in all cells, whereas random X-inactivation results in the silencing of genes on either the paternal or maternal X chromosome in individual cells. Both forms of X-inactivation have been studied intensively in the mouse model system, which undergoes both imprinted and random X-inactivation early in embryonic development. Stable imprinted and random X-inactivation requires the induction of the Xist long non-coding RNA. Following its induction, Xist RNA recruits proteins and complexes that silence genes on the inactive-X. In this review, we present a current understanding of the mechanisms of Xist RNA induction, and, separately, the establishment and maintenance of gene silencing on the inactive-X by Xist RNA during imprinted and random X-inactivation.
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Affiliation(s)
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48105, USA
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Achiro JM, Tao Y, Gao F, Lin CH, Watanabe M, Neumann S, Coppola G, Black DL, Martin KC. Aging differentially alters the transcriptome and landscape of chromatin accessibility in the male and female mouse hippocampus. Front Mol Neurosci 2024; 17:1334862. [PMID: 38318533 PMCID: PMC10839115 DOI: 10.3389/fnmol.2024.1334862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Aging-related memory impairment and pathological memory disorders such as Alzheimer's disease differ between males and females, and yet little is known about how aging-related changes in the transcriptome and chromatin environment differ between sexes in the hippocampus. To investigate this question, we compared the chromatin accessibility landscape and gene expression/alternative splicing pattern of young adult and aged mouse hippocampus in both males and females using ATAC-seq and RNA-seq. We detected significant aging-dependent changes in the expression of genes involved in immune response and synaptic function and aging-dependent changes in the alternative splicing of myelin sheath genes. We found significant sex-bias in the expression and alternative splicing of hundreds of genes, including aging-dependent female-biased expression of myelin sheath genes and aging-dependent male-biased expression of genes involved in synaptic function. Aging was associated with increased chromatin accessibility in both male and female hippocampus, especially in repetitive elements, and with an increase in LINE-1 transcription. We detected significant sex-bias in chromatin accessibility in both autosomes and the X chromosome, with male-biased accessibility enriched at promoters and CpG-rich regions. Sex differences in gene expression and chromatin accessibility were amplified with aging, findings that may shed light on sex differences in aging-related and pathological memory loss.
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Affiliation(s)
- Jennifer M. Achiro
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Yang Tao
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Fuying Gao
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Chia-Ho Lin
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, United States
| | - Marika Watanabe
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Sylvia Neumann
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Giovanni Coppola
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Douglas L. Black
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, United States
| | - Kelsey C. Martin
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
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Terzi Cizmecioglu N. Roles and Regulation of H3K4 Methylation During Mammalian Early Embryogenesis and Embryonic Stem Cell Differentiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024. [PMID: 38231346 DOI: 10.1007/5584_2023_794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
From generation of germ cells, fertilization, and throughout early mammalian embryonic development, the chromatin undergoes significant alterations to enable precise regulation of gene expression and genome use. Methylation of histone 3 lysine 4 (H3K4) correlates with active regions of the genome, and it has emerged as a dynamic mark throughout this timeline. The pattern and the level of H3K4 methylation are regulated by methyltransferases and demethylases. These enzymes, as well as their protein partners, play important roles in early embryonic development and show phenotypes in embryonic stem cell self-renewal and differentiation. The various roles of H3K4 methylation are interpreted by dedicated chromatin reader proteins, linking this modification to broader molecular and cellular phenotypes. In this review, we discuss the regulation of different levels of H3K4 methylation, their distinct accumulation pattern, and downstream molecular roles with an early embryogenesis perspective.
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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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Rogers MF, Marshall OJ, Secombe J. KDM5-mediated activation of genes required for mitochondrial biology is necessary for viability in Drosophila. Development 2023; 150:dev202024. [PMID: 37800333 PMCID: PMC10651110 DOI: 10.1242/dev.202024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023]
Abstract
Histone-modifying proteins play important roles in the precise regulation of the transcriptional programs that coordinate development. KDM5 family proteins interact with chromatin through demethylation of H3K4me3 as well as demethylase-independent mechanisms that remain less understood. To gain fundamental insights into the transcriptional activities of KDM5 proteins, we examined the essential roles of the single Drosophila Kdm5 ortholog during development. KDM5 performs crucial functions in the larval neuroendocrine prothoracic gland, providing a model to study its role in regulating key gene expression programs. Integrating genome binding and transcriptomic data, we identify that KDM5 regulates the expression of genes required for the function and maintenance of mitochondria, and we find that loss of KDM5 causes morphological changes to mitochondria. This is key to the developmental functions of KDM5, as expression of the mitochondrial biogenesis transcription factor Ets97D, homolog of GABPα, is able to suppress the altered mitochondrial morphology as well as the lethality of Kdm5 null animals. Together, these data establish KDM5-mediated cellular functions that are important for normal development and could contribute to KDM5-linked disorders when dysregulated.
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Affiliation(s)
- Michael F. Rogers
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Owen J. Marshall
- Menzies Institute for Medical Research, University of Tasmania, Hobart TAS 7000, Australia
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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10
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Fazazi MR, Ruda GF, Brennan PE, Rangachari M. The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system. Brain Res Bull 2023; 202:110748. [PMID: 37657612 DOI: 10.1016/j.brainresbull.2023.110748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
T cell-driven autoimmune responses are subject to striking sex-dependent effects. While the contributions of sex hormones are well-understood, those of sex chromosomes are meeting with increased appreciation. Here, we outline what is known about the contribution of sex chromosome-linked factors to experimental autoimmune encephalomyelitis (EAE), a mouse model that recapitulates many of the T cell-driven mechanisms of multiple sclerosis (MS) pathology. Particular attention is paid to the KDM family of histone demethylases, several of which - KDM5C, KDM5D and KDM6A - are sex chromosome encoded. Finally, we provide evidence that functional inhibition of KDM5 molecules can suppress interferon (IFN)γ production from murine male effector T cells, and that an increased ratio of inflammatory Kdm6a to immunomodulatory Kdm5c transcript is observed in T helper 17 (Th17) cells from women with the autoimmune disorder ankylosing spondylitis (AS). Histone lysine demethlyases thus represent intriguing targets for the treatment of T cell-driven autoimmune disorders.
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Affiliation(s)
- Mohamed Reda Fazazi
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Gian Filippo Ruda
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Paul E Brennan
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Alzheimer's Research UK, Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Manu Rangachari
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada; Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada.
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11
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Qi S, Ngwa C, Al Mamun A, Romana S, Wu T, Marrelli SP, Arnold AP, McCullough LD, Liu F. X, but not Y, Chromosomal Complement Contributes to Stroke Sensitivity in Aged Animals. Transl Stroke Res 2023; 14:776-789. [PMID: 35906327 PMCID: PMC10490444 DOI: 10.1007/s12975-022-01070-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 01/16/2023]
Abstract
Post-menopausal women become vulnerable to stroke and have poorer outcomes and higher mortality than age-matched men, and previous studies suggested that sex chromosomes play a vital role in mediating stroke sensitivity in the aged. It is unknown if this is due to effects of the X or Y chromosome. The present study used the XY* mouse model (with four genotypes: XX and XO gonadal females and XY and XXY gonadal males) to compare the effect of the X vs. Y chromosome compliment in stroke. Aged (18-20 months) and gonadectomized young (8-12 weeks) mice were subjected to a 60-min middle cerebral artery occlusion. Infarct volume and behavioral deficits were quantified 3 days after stroke. Microglial activation and infiltration of peripheral leukocytes in the aged ischemic brain were assessed by flow cytometry. Plasma inflammatory cytokine levels by ELISA, and brain expression of two X chromosome-linked genes, KDM6A and KDM5C by immunochemistry, were also examined. Both aged and young XX and XXY mice had worse stroke outcomes compared to XO and XY mice, respectively; however, the difference between XX vs. XXY and XO vs. XY aged mice was minimal. Mice with two copies of the X chromosome showed more robust microglial activation, higher brain-infiltrating leukocytes, elevated plasma cytokine levels, and enhanced co-localization of KDM6A and KDM5C with Iba1+ cells after stroke than mice with one X chromosome. The number of X chromosomes mediates stroke sensitivity in aged mice, which might be processed through the X chromosome-linked genes and the inflammatory responses.
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Affiliation(s)
- Shaohua Qi
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, McGovern Medical School, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Conelius Ngwa
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, McGovern Medical School, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Abdullah Al Mamun
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, McGovern Medical School, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Sharmeen Romana
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, McGovern Medical School, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Ting Wu
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, McGovern Medical School, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Sean P Marrelli
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, McGovern Medical School, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Arthur P Arnold
- Department of Integrative Biology and Physiology, UCLA, 610 Charles Young Drive South, Los Angeles, CA, 90095, USA
| | - Louise D McCullough
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, McGovern Medical School, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Fudong Liu
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, McGovern Medical School, 6431 Fannin Street, Houston, TX, 77030, USA.
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12
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Tzeplaeff L, Seguin J, Le Gras S, Megat S, Cosquer B, Plassard D, Dieterlé S, Paiva I, Picchiarelli G, Decraene C, Alcala-Vida R, Cassel JC, Merienne K, Dupuis L, Boutillier AL. Mutant FUS induces chromatin reorganization in the hippocampus and alters memory processes. Prog Neurobiol 2023; 227:102483. [PMID: 37327984 DOI: 10.1016/j.pneurobio.2023.102483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/12/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Cytoplasmic mislocalization of the nuclear Fused in Sarcoma (FUS) protein is associated to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS accumulation is recapitulated in the frontal cortex and spinal cord of heterozygous Fus∆NLS/+ mice. Yet, the mechanisms linking FUS mislocalization to hippocampal function and memory formation are still not characterized. Herein, we show that in these mice, the hippocampus paradoxically displays nuclear FUS accumulation. Multi-omic analyses showed that FUS binds to a set of genes characterized by the presence of an ETS/ELK-binding motifs, and involved in RNA metabolism, transcription, ribosome/mitochondria and chromatin organization. Importantly, hippocampal nuclei showed a decompaction of the neuronal chromatin at highly expressed genes and an inappropriate transcriptomic response was observed after spatial training of Fus∆NLS/+ mice. Furthermore, these mice lacked precision in a hippocampal-dependent spatial memory task and displayed decreased dendritic spine density. These studies shows that mutated FUS affects epigenetic regulation of the chromatin landscape in hippocampal neurons, which could participate in FTD/ALS pathogenic events. These data call for further investigation in the neurological phenotype of FUS-related diseases and open therapeutic strategies towards epigenetic drugs.
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Affiliation(s)
- Laura Tzeplaeff
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France; Université de Strasbourg, INSERM, UMR-S1118, Strasbourg, France
| | - Jonathan Seguin
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Stéphanie Le Gras
- Université de Strasbourg, CNRS UMR 7104, INSERM U1258, GenomEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
| | - Salim Megat
- Université de Strasbourg, INSERM, UMR-S1118, Strasbourg, France
| | - Brigitte Cosquer
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Damien Plassard
- Université de Strasbourg, CNRS UMR 7104, INSERM U1258, GenomEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
| | | | - Isabel Paiva
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | | | - Charles Decraene
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Rafael Alcala-Vida
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Jean-Christophe Cassel
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Karine Merienne
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France; CNRS, UMR 7364, Strasbourg 67000, France
| | - Luc Dupuis
- Université de Strasbourg, INSERM, UMR-S1118, Strasbourg, France.
| | - Anne-Laurence Boutillier
- Université de Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg, France.
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13
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Tsompanidis A, Warrier V, Baron-Cohen S. The genetics of autism and steroid-related traits in prenatal and postnatal life. Front Endocrinol (Lausanne) 2023; 14:1126036. [PMID: 37223033 PMCID: PMC10200920 DOI: 10.3389/fendo.2023.1126036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/18/2023] [Indexed: 05/25/2023] Open
Abstract
Background Autism likelihood is a largely heritable trait. Autism prevalence has a skewed sex ratio, with males being diagnosed more often than females. Steroid hormones play a mediating role in this, as indicated by studies of both prenatal biology and postnatal medical conditions in autistic men and women. It is currently unclear if the genetics of steroid regulation or production interact with the genetic liability for autism. Methods To address this, two studies were conducted using publicly available datasets, which focused respectively on rare genetic variants linked to autism and neurodevelopmental conditions (study 1) and common genetic variants (study 2) for autism. In Study 1 an enrichment analysis was conducted, between autism-related genes (SFARI database) and genes that are differentially expressed (FDR<0.1) between male and female placentas, in 1st trimester chorionic villi samples of viable pregnancies (n=39). In Study 2 summary statistics of genome wide association studies (GWAS) were used to investigate the genetic correlation between autism and bioactive testosterone, estradiol and postnatal PlGF levels, as well as steroid-related conditions such as polycystic ovaries syndrome (PCOS), age of menarche, and androgenic alopecia. Genetic correlation was calculated based on LD Score regression and results were corrected for multiple testing with FDR. Results In Study 1, there was significant enrichment of X-linked autism genes in male-biased placental genes, independently of gene length (n=5 genes, p<0.001). In Study 2, common genetic variance associated with autism did not correlate to the genetics for the postnatal levels of testosterone, estradiol or PlGF, but was associated with the genotypes associated with early age of menarche in females (b=-0.109, FDR-q=0.004) and protection from androgenic alopecia for males (b=-0.135, FDR-q=0.007). Conclusion The rare genetic variants associated with autism appear to interact with placental sex differences, while the common genetic variants associated with autism appear to be involved in the regulation of steroid-related traits. These lines of evidence indicate that the likelihood for autism is partly linked to factors mediating physiological sex differences throughout development.
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Affiliation(s)
- Alex Tsompanidis
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
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14
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Liu H, Zhai L, Liu Y, Lu D, Vander Ark A, Yang T, Krawczyk CM. The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts. SCIENCE ADVANCES 2023; 9:eadg0731. [PMID: 37018401 PMCID: PMC10075994 DOI: 10.1126/sciadv.adg0731] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/06/2023] [Indexed: 05/28/2023]
Abstract
Women experience osteoporosis at higher rates than men. Aside from hormones, the mechanisms driving sex-dependent bone mass regulation are not well understood. Here, we demonstrate that the X-linked H3K4me2/3 demethylase KDM5C regulates sex-specific bone mass. Loss of KDM5C in hematopoietic stem cells or bone marrow monocytes increases bone mass in female but not male mice. Mechanistically, loss of KDM5C impairs the bioenergetic metabolism, resulting in impaired osteoclastogenesis. Treatment with the KDM5 inhibitor reduces osteoclastogenesis and energy metabolism of both female mice and human monocytes. Our report details a sex-dependent mechanism for bone homeostasis, connecting epigenetic regulation to osteoclast metabolism and positions KDM5C as a potential target for future treatment of osteoporosis in women.
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Affiliation(s)
- Huadie Liu
- Laboratory of Skeletal Biology, Department of Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Lukai Zhai
- Department of Metabolism and Nutritional Programming, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Ye Liu
- Laboratory of Skeletal Biology, Department of Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Di Lu
- Laboratory of Skeletal Biology, Department of Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Alexandra Vander Ark
- Department of Metabolism and Nutritional Programming, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Tao Yang
- Laboratory of Skeletal Biology, Department of Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Connie M. Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Research Institute, Grand Rapids, MI 49503, USA
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15
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The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529728. [PMID: 36865269 PMCID: PMC9980061 DOI: 10.1101/2023.02.23.529728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Women experience osteoporosis at higher rates than men. Aside from hormones, the mechanisms driving sex-dependent bone mass regulation are not well-understood. Here, we demonstrate that the X-linked H3K4me2/3 demethylase KDM5C regulates sex-specific bone mass. Loss of KDM5C in hematopoietic stem cells or bone marrow monocytes (BMM) increases bone mass in female but not male mice. Mechanistically, loss of KDM5C impairs the bioenergetic metabolism resulting in impaired osteoclastogenesis. Treatment with the KDM5 inhibitor reduces osteoclastogenesis and energy metabolism of both female mice and human monocytes. Our report details a novel sex-dependent mechanism for bone homeostasis, connecting epigenetic regulation to osteoclast metabolism, and positions KDM5C as a target for future treatment of osteoporosis in women. One-Sentence Summary KDM5C, an X-linked epigenetic regulator, controls female bone homeostasis by promoting energy metabolism in osteoclasts.
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16
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Yheskel M, Sidoli S, Secombe J. Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5. Epigenetics Chromatin 2023; 16:8. [PMID: 36803422 PMCID: PMC9938590 DOI: 10.1186/s13072-023-00481-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND KDM5 family proteins are multi-domain regulators of transcription that when dysregulated contribute to cancer and intellectual disability. KDM5 proteins can regulate transcription through their histone demethylase activity in addition to demethylase-independent gene regulatory functions that remain less characterized. To expand our understanding of the mechanisms that contribute to KDM5-mediated transcription regulation, we used TurboID proximity labeling to identify KDM5-interacting proteins. RESULTS Using Drosophila melanogaster, we enriched for biotinylated proteins from KDM5-TurboID-expressing adult heads using a newly generated control for DNA-adjacent background in the form of dCas9:TurboID. Mass spectrometry analyses of biotinylated proteins identified both known and novel candidate KDM5 interactors, including members of the SWI/SNF and NURF chromatin remodeling complexes, the NSL complex, Mediator, and several insulator proteins. CONCLUSIONS Combined, our data shed new light on potential demethylase-independent activities of KDM5. In the context of KDM5 dysregulation, these interactions may play key roles in the alteration of evolutionarily conserved transcriptional programs implicated in human disorders.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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17
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Bonefas KM, Vallianatos CN, Raines B, Tronson NC, Iwase S. Sexually Dimorphic Alterations in the Transcriptome and Behavior with Loss of Histone Demethylase KDM5C. Cells 2023; 12:cells12040637. [PMID: 36831303 PMCID: PMC9954040 DOI: 10.3390/cells12040637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Chromatin dysregulation has emerged as a major hallmark of neurodevelopmental disorders such as intellectual disability (ID) and autism spectrum disorders (ASD). The prevalence of ID and ASD is higher in males compared to females, with unknown mechanisms. Intellectual developmental disorder, X-linked syndromic, Claes-Jensen type (MRXSCJ), is caused by loss-of-function mutations of lysine demethylase 5C (KDM5C), a histone H3K4 demethylase gene. KDM5C escapes X-inactivation, thereby presenting at a higher level in females. Initially, MRXSCJ was exclusively reported in males, while it is increasingly evident that females with heterozygous KDM5C mutations can show cognitive deficits. The mouse model of MRXSCJ, male Kdm5c-hemizygous knockout animals, recapitulates key features of human male patients. However, the behavioral and molecular traits of Kdm5c-heterozygous female mice remain incompletely characterized. Here, we report that gene expression and behavioral abnormalities are readily detectable in Kdm5c-heterozygous female mice, demonstrating the requirement for a higher KDM5C dose in females. Furthermore, we found both shared and sex-specific consequences of a reduced KDM5C dose in social behavior, gene expression, and genetic interaction with the counteracting enzyme KMT2A. These observations provide an essential insight into the sex-biased manifestation of neurodevelopmental disorders and sex chromosome evolution.
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Affiliation(s)
- Katherine M. Bonefas
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christina N. Vallianatos
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Genetics and Genomics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brynne Raines
- Department of Psychology, College of LS&A, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natalie C. Tronson
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Psychology, College of LS&A, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence: (N.C.T.); (S.I.)
| | - Shigeki Iwase
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
- Genetics and Genomics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence: (N.C.T.); (S.I.)
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18
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Ugur FS, Kelly MJS, Fujimori DG. Chromatin Sensing by the Auxiliary Domains of KDM5C Regulates Its Demethylase Activity and Is Disrupted by X-linked Intellectual Disability Mutations. J Mol Biol 2023; 435:167913. [PMID: 36495919 PMCID: PMC10247153 DOI: 10.1016/j.jmb.2022.167913] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/10/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
The H3K4me3 chromatin modification, a hallmark of promoters of actively transcribed genes, is dynamically removed by the KDM5 family of histone demethylases. The KDM5 demethylases have a number of accessory domains, two of which, ARID and PHD1, lie between the segments of the catalytic domain. KDM5C, which has a unique role in neural development, harbors a number of mutations adjacent to its accessory domains that cause X-linked intellectual disability (XLID). The roles of these accessory domains remain unknown, limiting an understanding of how XLID mutations affect KDM5C activity. Through in vitro binding and kinetic studies using nucleosomes, we find that while the ARID domain is required for efficient nucleosome demethylation, the PHD1 domain alone has an inhibitory role in KDM5C catalysis. In addition, the unstructured linker region between the ARID and PHD1 domains interacts with PHD1 and is necessary for nucleosome binding. Our data suggests a model in which the PHD1 domain inhibits DNA recognition by KDM5C. This inhibitory effect is relieved by the H3 tail, enabling recognition of flanking DNA on the nucleosome. Importantly, we find that XLID mutations adjacent to the ARID and PHD1 domains break this regulation by enhancing DNA binding, resulting in the loss of specificity of substrate chromatin recognition and rendering demethylase activity lower in the presence of flanking DNA. Our findings suggest a model by which specific XLID mutations could alter chromatin recognition and enable euchromatin-specific dysregulation of demethylation by KDM5C.
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Affiliation(s)
- Fatima S Ugur
- Chemistry and Chemical Biology Graduate Program, 600 16th St., San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, 600 16th St., San Francisco, CA 94158, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, 600 16th St., San Francisco, CA 94158, USA
| | - Danica Galonić Fujimori
- Department of Pharmaceutical Chemistry, 600 16th St., San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, 600 16th St., San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, 600 16th St., San Francisco, CA 94158, USA.
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19
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Zhang SM, Cao J, Yan Q. KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:113-137. [PMID: 37751138 DOI: 10.1007/978-3-031-38176-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The histone lysine demethylase 5 (KDM5) family proteins are Fe2+ and α-ketoglutarate-dependent dioxygenases, with jumonji C (JmjC) domain as their catalytic core and several plant homeodomains (PHDs) to bind different histone methylation marks. These enzymes are capable of demethylating tri-, di- and mono-methylated lysine 4 in histone H3 (H3K4me3/2/1), the key epigenetic marks for active chromatin. Thus, this H3K4 demethylase family plays critical roles in cell fate determination during development as well as malignant transformation. KDM5 demethylases have both oncogenic and tumor suppressive functions in a cancer type-dependent manner. In solid tumors, KDM5A/B are generally oncogenic, whereas KDM5C/D have tumor suppressive roles. Their involvement in de-differentiation, cancer metastasis, drug resistance, and tumor immunoevasion indicated that KDM5 family proteins are promising drug targets for cancer therapy. Significant efforts from both academia and industry have led to the development of potent and selective KDM5 inhibitors for preclinical experiments and phase I clinical trials. However, a better understanding of the roles of KDM5 demethylases in different physiological and pathological conditions is critical for further developing KDM5 modulators for clinical applications.
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Affiliation(s)
- Shang-Min Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jian Cao
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
| | - Qin Yan
- Department of Pathology, Yale Cancer Center, Yale Stem Cell Center, Yale Center for Immuno-Oncology, Yale Center for Research on Aging, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA.
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20
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Shen R, Li Y, Liang A, Li S, Yang C, Huang H. A female case with novel KDM5C heterozygous variation presenting with Claes-Jensen type-like phonotype. BMC Neurol 2022; 22:491. [PMID: 36536324 PMCID: PMC9762001 DOI: 10.1186/s12883-022-03023-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lysine(K)-specific demethylase 5C (KDM5C) dysfunction causes X-linked syndromic intellectual developmental disorder Claes-Jensen type in male patients. The clinical presentations of female individuals with heterozygous KDM5C variations vary widely and are only now beginning to be characterized in detail. CASE PRESENTATION Herein, we identified a novel de novo heterozygous nonsense variation of KDM5C (c.3533C > A, p.S1178X) in a sporadic 4-year-old Chinese girl, who presented with Claes-Jensen type-like phenotypes, such as moderate developmental delay, serious expressive language delay, short stature, microcephaly, and typical facial particularities. Moreover, X-chromosome inactivation (XCI) analysis showed no significant skewed X-inactivation. CONCLUSION The report expands the genotype of KDM5C variation in female patients, delineates the phenotype of affected females in this well-known X-linked disorder, and also reinforces the necessity to consider this X-linked gene, KDM5C, in sporadic female patients.
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Affiliation(s)
- Ruiyun Shen
- grid.411609.b0000 0004 1758 4735Child Health Care Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, 100045 China
| | - Yanyang Li
- grid.256922.80000 0000 9139 560XPediatric Department, Huaihe Hospital of Henan University, Kaifeng, 475000 China
| | - Aiming Liang
- grid.411609.b0000 0004 1758 4735Child Health Care Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, 100045 China
| | - Shijie Li
- grid.411609.b0000 0004 1758 4735Child Health Care Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, 100045 China
| | - Chenlu Yang
- grid.411609.b0000 0004 1758 4735Child Health Care Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, 100045 China
| | - Hongmei Huang
- grid.411609.b0000 0004 1758 4735Child Health Care Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, 100045 China
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21
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Expanding the Spectrum of KDM5C Neurodevelopmental Disorder: A Novel De Novo Stop Variant in a Young Woman and Emerging Genotype-Phenotype Correlations. Genes (Basel) 2022; 13:genes13122266. [PMID: 36553533 PMCID: PMC9778367 DOI: 10.3390/genes13122266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
As a consequence of the implementation of NGS technologies, the diagnostic yield of neurodevelopmental disorders has dramatically increased during the past two decades. Among neurodevelopmental genes, transcription-related genes and chromatin remodeling genes are the most represented category of disease-causing genes. Indeed, the term "chromatinopathies" is now widely used to describe epigenetic disorders caused by mutations in these genes. We hereby describe a twenty-seven-year-old female patient diagnosed with moderate intellectual disability comorbid with other neuropsychiatric and behavioral issues carrying a de novo heterozygous stop variant in the KDM5C gene (NM_004187.5: c. 3847G>T, p.Glu1283*), encoding a histone demethylase that specifically acts on the H3K4 lysines. The gene is located on the X chromosome and has been associated with Claes-Jensen-type intellectual disability, an X-linked syndromic disorder. We discuss our case in relation to previously reported affected females harboring pathogenic mutations in the KDM5C gene with the objective of delineating genotype-phenotype correlations and further defining a common recognizable phenotype. We also highlight the importance of reverse phenotyping in relation to whole-exome sequencing results.
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Hatch HAM, Secombe J. Molecular and cellular events linking variants in the histone demethylase KDM5C to the intellectual disability disorder Claes-Jensen syndrome. FEBS J 2022; 289:7776-7787. [PMID: 34536985 PMCID: PMC8930784 DOI: 10.1111/febs.16204] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/02/2021] [Accepted: 09/16/2021] [Indexed: 01/14/2023]
Abstract
The widespread availability of genetic testing for those with neurodevelopmental disorders has highlighted the importance of many genes necessary for the proper development and function of the nervous system. One gene found to be genetically altered in the X-linked intellectual disability disorder Claes-Jensen syndrome is KDM5C, which encodes a histone demethylase that regulates transcription by altering chromatin. While the genetic link between KDM5C and cognitive (dys)function is clear, how KDM5C functions to control transcriptional programs within neurons to impact their growth and activity remains the subject of ongoing research. Here, we review our current knowledge of Claes-Jensen syndrome and discuss important new data using model organisms that have revealed the importance of KDM5C in regulating aspects of neuronal development and function. Continued research into the molecular and cellular activities regulated by KDM5C is expected to provide critical etiological insights into Claes-Jensen syndrome and highlight potential targets for developing therapies to improve the quality of life of those affected.
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Affiliation(s)
- Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Secombe
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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23
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Drongitis D, Verrillo L, De Marinis P, Orabona P, Caiola A, Turitto G, Alfieri A, Bruscella S, Gentile M, Moriello V, Sannino E, Di Muccio I, Costa V, Miano MG, de Bellis A. The Chromatin-Oxygen Sensor Gene KDM5C Associates with Novel Hypoxia-Related Signatures in Glioblastoma Multiforme. Int J Mol Sci 2022; 23:ijms231810250. [PMID: 36142158 PMCID: PMC9498997 DOI: 10.3390/ijms231810250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a fatal brain tumor without effective drug treatment. In this study, we highlight, for the first time, the contribution of chromatin remodeling gene Lysine (K)-specific demethylase 5C (KDM5C) in GBM via an extensive analysis of clinical, expression, and functional data, integrated with publicly available omic datasets. The expression analysis on GBM samples (N = 37) revealed two informative subtypes, namely KDM5CHigh and KDM5CLow, displaying higher/lower KDM5C levels compared to the controls. The former subtype displays a strong downregulation of brain-derived neurotrophic factor (BDNF)—a negative KDM5C target—and a robust overexpression of hypoxia-inducible transcription factor-1A (HIF1A) gene, a KDM5C modulator. Additionally, a significant co-expression among the prognostic markers HIF1A, Survivin, and p75 was observed. These results, corroborated by KDM5C overexpression and hypoxia-related functional assays in T98G cells, suggest a role for the HIF1A-KDM5C axis in the hypoxic response in this tumor. Interestingly, fluorescence-guided surgery on GBM sections further revealed higher KDM5C and HIF1A levels in the tumor rim niche compared to the adjacent tumor margin, indicating a regionally restricted hyperactivity of this regulatory axis. Analyzing the TCGA expression and methylation data, we found methylation changes between the subtypes in the genes, accounting for the hypoxia response, stem cell differentiation, and inflammation. High NANOG and IL6 levels highlight a distinctive stem cell-like and proinflammatory signature in the KDM5CHigh subgroup and GBM niches. Taken together, our results indicate HIF1A-KDM5C as a new, relevant cancer axis in GBM, opening a new, interesting field of investigation based on KDM5C as a potential therapeutic target of the hypoxic microenvironment in GBM.
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Affiliation(s)
- Denise Drongitis
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy
- Maria Rosaria Maglione Foundation Onlus, 80122 Naples, Italy
| | - Lucia Verrillo
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy
| | - Pasqualino De Marinis
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Pasquale Orabona
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Pathology, 81100 Caserta, Italy
| | - Agnese Caiola
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Pathology, 81100 Caserta, Italy
| | - Giacinto Turitto
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Oncology, 81100 Caserta, Italy
| | - Alessandra Alfieri
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Sara Bruscella
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Marisa Gentile
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Vania Moriello
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Ettore Sannino
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Ines Di Muccio
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Valerio Costa
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy
| | - Maria Giuseppina Miano
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy
- Correspondence: (M.G.M.); (A.d.B.)
| | - Alberto de Bellis
- Maria Rosaria Maglione Foundation Onlus, 80122 Naples, Italy
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
- Correspondence: (M.G.M.); (A.d.B.)
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24
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Epigenetic genes and epilepsy - emerging mechanisms and clinical applications. Nat Rev Neurol 2022; 18:530-543. [PMID: 35859062 DOI: 10.1038/s41582-022-00693-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 12/21/2022]
Abstract
An increasing number of epilepsies are being attributed to variants in genes with epigenetic functions. The products of these genes include factors that regulate the structure and function of chromatin and the placing, reading and removal of epigenetic marks, as well as other epigenetic processes. In this Review, we provide an overview of the various epigenetic processes, structuring our discussion around five function-based categories: DNA methylation, histone modifications, histone-DNA crosstalk, non-coding RNAs and chromatin remodelling. We provide background information on each category, describing the general mechanism by which each process leads to altered gene expression. We also highlight key clinical and mechanistic aspects, providing examples of genes that strongly associate with epilepsy within each class. We consider the practical applications of these findings, including tissue-based and biofluid-based diagnostics and precision medicine-based treatments. We conclude that variants in epigenetic genes are increasingly found to be causally involved in the epilepsies, with implications for disease mechanisms, treatments and diagnostics.
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25
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Coursimault J, Goldenberg A, Nicolas G, Saugier-Veber P, Coutant S, Vincent A, Pouliquen D, Feltin C, Aref-Eshghi E, Sadikovic B, Lecoquierre F. Contribution of DNA methylation profiling to the reclassification of a variant of uncertain significance in the KDM5C gene. Eur J Med Genet 2022; 65:104556. [PMID: 35781022 DOI: 10.1016/j.ejmg.2022.104556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/21/2022] [Accepted: 06/27/2022] [Indexed: 11/03/2022]
Abstract
KDM5C encodes a demethylase of the histone H3 lysine 4 residue, involved in chromatin regulation and gene expression. Hemizygous KDM5C pathogenic variants cause X-linked intellectual disability of Claes-Jensen type. Because of its mode of inheritance and the low specificity of the clinical phenotype, interpretation of variants can be difficult, hence the need for functional studies and biomarkers specific to this disorder. We present the case of a male patient with intellectual disability, behavioral abnormalities and subtle dysmorphic features, in which genetic investigation identified a hemizygous novel missense KDM5C variant of uncertain significance (VUS), inherited from his asymptomatic mother and present in his paucisymptomatic sister. We assessed the global genomic DNA methylation status from a whole blood sample of the proband. Global DNA methylation profiling specifically identified the recently discovered epi-signature of Claes-Jensen syndrome. This result served as a biomarker which independently highlighted KDM5C as the cause of the disorder in this patient. Because of the X-linked mode of inheritance, variant reclassification had a high impact on genetic counseling in this family. This example highlights the value of global methylome profiling in situations of variants of uncertain significance in genes with a known specific epi-signature.
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Affiliation(s)
- Juliette Coursimault
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Sophie Coutant
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France
| | - Anne Vincent
- Reference Centre for Learning Disorders, Rouen University Hospital, F-76031 Rouen Cedex, France; Department of Neonatology and Paediatric Intensive Care, Rouen University Hospital, F-76031 Cedex, France
| | | | - Cécile Feltin
- Institut de Psychiatrie - Centre Hospitalier du Rouvray, Sotteville-lès-Rouen, France
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Canada and Verspeeten Clinical Genome Centre, London Health Sciences, London, Ontario, Canada
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245, CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, F-76000, Rouen, France.
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26
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Samanta MK, Gayen S, Harris C, Maclary E, Murata-Nakamura Y, Malcore RM, Porter RS, Garay PM, Vallianatos CN, Samollow PB, Iwase S, Kalantry S. Activation of Xist by an evolutionarily conserved function of KDM5C demethylase. Nat Commun 2022; 13:2602. [PMID: 35545632 PMCID: PMC9095838 DOI: 10.1038/s41467-022-30352-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 04/26/2022] [Indexed: 12/03/2022] Open
Abstract
XX female and XY male therian mammals equalize X-linked gene expression through the mitotically-stable transcriptional inactivation of one of the two X chromosomes in female somatic cells. Here, we describe an essential function of the X-linked homolog of an ancestral X-Y gene pair, Kdm5c-Kdm5d, in the expression of Xist lncRNA, which is required for stable X-inactivation. Ablation of Kdm5c function in females results in a significant reduction in Xist RNA expression. Kdm5c encodes a demethylase that enhances Xist expression by converting histone H3K4me2/3 modifications into H3K4me1. Ectopic expression of mouse and human KDM5C, but not the Y-linked homolog KDM5D, induces Xist in male mouse embryonic stem cells (mESCs). Similarly, marsupial (opossum) Kdm5c but not Kdm5d also upregulates Xist in male mESCs, despite marsupials lacking Xist, suggesting that the KDM5C function that activates Xist in eutherians is strongly conserved and predates the divergence of eutherian and metatherian mammals. In support, prototherian (platypus) Kdm5c also induces Xist in male mESCs. Together, our data suggest that eutherian mammals co-opted the ancestral demethylase KDM5C during sex chromosome evolution to upregulate Xist for the female-specific induction of X-inactivation.
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Affiliation(s)
- Milan Kumar Samanta
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Srimonta Gayen
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Emily Maclary
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
| | - Yumie Murata-Nakamura
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Rebecca M Malcore
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Robert S Porter
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Patricia M Garay
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Christina N Vallianatos
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Paul B Samollow
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA.
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27
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Bonefas KM, Iwase S. Soma-to-germline transformation in chromatin-linked neurodevelopmental disorders? FEBS J 2022; 289:2301-2317. [PMID: 34514717 PMCID: PMC8918023 DOI: 10.1111/febs.16196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/16/2021] [Accepted: 09/10/2021] [Indexed: 01/22/2023]
Abstract
Mutations in numerous chromatin regulators cause neurodevelopmental disorders (NDDs) with unknown mechanisms. Understandably, most research has focused on how chromatin regulators control gene expression that is directly relevant to brain development and function, such as synaptic genes. However, some NDD models surprisingly show ectopic expression of germline genes in the brain. These germline genes are usually expressed only in the primordial germ cells, testis, and ovaries for germ cell development and sexual reproduction. Such ectopic germline gene expression has been reported in several NDDs, including immunodeficiency, centromeric instability, facial anomalies syndrome 1; Kleefstra syndrome 1; MeCP2 duplication syndrome; and mental retardation, X-linked syndromic, Claes-Jensen type. The responsible genes, DNMT3B, G9A/GLP, MECP2, and KDM5C, all encode chromatin regulators for gene silencing. These mutations may therefore lead to germline gene derepression and, in turn, a severe identity crisis of brain cells-potentially interfering with normal brain development. Thus, the ectopic expression of germline genes is a unique hallmark defining this NDD subset and further implicates the importance of germline gene silencing during brain development. The functional impact of germline gene expression on brain development, however, remains undetermined. This perspective article explores how this apparent soma-to-germline transformation arises and how it may interfere with neurodevelopment through genomic instability and impaired sensory cilium formation. Furthermore, we also discuss how to test these hypotheses experimentally to ultimately determine the contribution of ectopic germline transcripts to chromatin-linked NDDs.
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Affiliation(s)
- Katherine M. Bonefas
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109,The University of Michigan Neuroscience Graduate Program,Corresponding authors: Please address correspondence to: , and
| | - Shigeki Iwase
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109,The University of Michigan Neuroscience Graduate Program,Corresponding authors: Please address correspondence to: , and
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28
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Taylor-Papadimitriou J, Burchell JM. Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer. Cells 2022; 11:cells11071113. [PMID: 35406676 PMCID: PMC8997813 DOI: 10.3390/cells11071113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.
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Drosophila Model for Studying Gut Microbiota in Behaviors and Neurodegenerative Diseases. Biomedicines 2022; 10:biomedicines10030596. [PMID: 35327401 PMCID: PMC8945323 DOI: 10.3390/biomedicines10030596] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/01/2022] [Indexed: 01/14/2023] Open
Abstract
Mounting evidence indicates that the gut microbiota is linked to several physiological processes and disease development in mammals; however, the underlying mechanisms remained unexplored mostly due to the complexity of the mammalian gut microbiome. The fruit fly, Drosophila melanogaster, is a valuable animal model for studying host-gut microbiota interactions in translational aspects. The availability of powerful genetic tools and resources in Drosophila allowed the scientists to unravel the mechanisms by which the gut microbes affect fitness, health, and behavior of their hosts. Drosophila models have been extensively used not only to study animal behaviors (i.e., courtship, aggression, sleep, and learning & memory), but also some human related neurodegenerative diseases (i.e., Alzheimer’s disease and Parkinson’s disease) in the past. This review comprehensively summarizes the current understanding of the gut microbiota of Drosophila and its impact on fly behavior, physiology, and neurodegenerative diseases.
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30
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Wilson KD, Porter EG, Garcia BA. Reprogramming of the epigenome in neurodevelopmental disorders. Crit Rev Biochem Mol Biol 2022; 57:73-112. [PMID: 34601997 PMCID: PMC9462920 DOI: 10.1080/10409238.2021.1979457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.
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Affiliation(s)
- Khadija D. Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth G. Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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31
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Wu PM, Yu WH, Chiang CW, Wu CY, Chen JS, Tu YF. Novel Variations in the KDM5C Gene Causing X-Linked Intellectual Disability. Neurol Genet 2021; 8:e646. [PMID: 34877407 PMCID: PMC8641966 DOI: 10.1212/nxg.0000000000000646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/13/2021] [Indexed: 11/15/2022]
Abstract
Background and Objectives To investigate the pathogenicity of 2 novel KDM5C variations, report the clinical and neuroimaging findings, and review the available literature. Methods Physical examinations, structural neuroimaging studies, and exome sequence analysis were performed. KDM5C constructs were used to study the effect of the variations in transfected cells. Results We identified 2 novel variations c.2233C>G and c.3392_3393delAG in the KDM5C gene harboring from 2 Chinese families with X-linked intellectual disability (ID). The affected male patients exhibited severe ID, short stature, and facial dysmorphism. The 1 with c.3392_3393delAG additionally had epilepsy and autistic spectrum disorder (ASD). Transiently transfected mutant KDM5C constructs both reduced protein expression and stability and decreased histone demethylase activities in cells. Reviewing the available literature, we found that the associated ASD tended to occur in patients with variations near the C-terminus of KDM5C. Discussion We report the clinical, molecular genetic, and pathologic features in patients with novel variations of KDM5C. The variability of the clinical phenotype in addition to an ID may associate with altered particular parts of KDM5C.
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Affiliation(s)
- Po-Ming Wu
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Hao Yu
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chi-Wu Chiang
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chen-Yu Wu
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jia-Shing Chen
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Fang Tu
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
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32
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Chen J, Lambo ME, Ge X, Dearborn JT, Liu Y, McCullough KB, Swift RG, Tabachnick DR, Tian L, Noguchi K, Garbow JR, Constantino JN, Gabel HW, Hengen KB, Maloney SE, Dougherty JD. A MYT1L syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation. Neuron 2021; 109:3775-3792.e14. [PMID: 34614421 PMCID: PMC8668036 DOI: 10.1016/j.neuron.2021.09.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/07/2021] [Accepted: 09/08/2021] [Indexed: 02/06/2023]
Abstract
Human genetics have defined a new neurodevelopmental syndrome caused by loss-of-function mutations in MYT1L, a transcription factor known for enabling fibroblast-to-neuron conversions. However, how MYT1L mutation causes intellectual disability, autism, ADHD, obesity, and brain anomalies is unknown. Here, we developed a Myt1l haploinsufficient mouse model that develops obesity, white-matter thinning, and microcephaly, mimicking common clinical phenotypes. During brain development we discovered disrupted gene expression, mediated in part by loss of Myt1l gene-target activation, and identified precocious neuronal differentiation as the mechanism for microcephaly. In contrast, in adults we discovered that mutation results in failure of transcriptional and chromatin maturation, echoed in disruptions in baseline physiological properties of neurons. Myt1l haploinsufficiency also results in behavioral anomalies, including hyperactivity, muscle weakness, and social alterations, with more severe phenotypes in males. Overall, our findings provide insight into the mechanistic underpinnings of this disorder and enable future preclinical studies.
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Affiliation(s)
- Jiayang Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Mary E Lambo
- Department of Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xia Ge
- Department of Radiology, Washington University School of Medicine, St. Louis, MO USA
| | - Joshua T Dearborn
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Katherine B McCullough
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Raylynn G Swift
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Dora R Tabachnick
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Lucy Tian
- Department of Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kevin Noguchi
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Joel R Garbow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA; Alvin J Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO USA
| | - John N Constantino
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Keith B Hengen
- Department of Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan E Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA.
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Hatch HAM, O'Neil MH, Marion RW, Secombe J, Shulman LH. Caregiver-reported characteristics of children diagnosed with pathogenic variants in KDM5C. Am J Med Genet A 2021; 185:2951-2958. [PMID: 34089235 DOI: 10.1002/ajmg.a.62381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 05/08/2021] [Accepted: 05/22/2021] [Indexed: 11/09/2022]
Abstract
Loss of function variants in the lysine demethylase 5C (KDM5C) gene account for approximately 0.7-2.8% of X-linked intellectual disability (ID) cases and pose significant burdens for patients and their caregivers. To date, 45 unique variants in KDM5C have been reported in individuals with ID. As a rare disorder, its etiology and natural history remain an area of active investigation, with treatment limited to symptom management. Previous studies have found that males present with moderate to severe ID with significant syndromic comorbidities such as epilepsy, short stature, and craniofacial abnormalities. Although not as well characterized, females have been reported to predominantly display mild to moderate ID with approximately half being asymptomatic. Here, we present caregiver-reported data for 37 unrelated individuals with pathogenic variants in KDM5C; the largest cohort reported to-date. We find that up to 70% of affected females were reported to display syndromic features including gastrointestinal dysfunction and hearing impairment. Additionally, more than half of individuals reported a diagnosis of autism spectrum disorder or described features consistent with this spectrum. Our data thus provide further evidence of sexually dimorphic heterogeneity in disease presentation and suggest that pathogenic variants in KDM5C may be more common than previously assumed.
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Affiliation(s)
- Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Molly H O'Neil
- Rose F. Kennedy Children's Evaluation and Rehabilitation Center, The Children's Hospital at Montefiore, Bronx, New York, USA
| | - Robert W Marion
- Division of Genetic Medicine, The Children's Hospital at Montefiore, Bronx, New York, USA
| | - Julie Secombe
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Lisa H Shulman
- Rose F. Kennedy Children's Evaluation and Rehabilitation Center, The Children's Hospital at Montefiore, Bronx, New York, USA
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34
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Garay PM, Chen A, Tsukahara T, Rodríguez Díaz JC, Kohen R, Althaus JC, Wallner MA, Giger RJ, Jones KS, Sutton MA, Iwase S. RAI1 Regulates Activity-Dependent Nascent Transcription and Synaptic Scaling. Cell Rep 2021; 32:108002. [PMID: 32783930 PMCID: PMC7418709 DOI: 10.1016/j.celrep.2020.108002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/17/2020] [Accepted: 07/15/2020] [Indexed: 12/15/2022] Open
Abstract
Long-lasting forms of synaptic plasticity such as synaptic scaling are critically dependent on transcription. Activity-dependent transcriptional dynamics in neurons, however, remain incompletely characterized because most previous efforts relied on measurement of steady-state mRNAs. Here, we use nascent RNA sequencing to profile transcriptional dynamics of primary neuron cultures undergoing network activity shifts. We find pervasive transcriptional changes, in which ∼45% of expressed genes respond to network activity shifts. We further link retinoic acid-induced 1 (RAI1), the Smith-Magenis syndrome gene, to the transcriptional program driven by reduced network activity. Remarkable agreement among nascent transcriptomes, dynamic chromatin occupancy of RAI1, and electrophysiological properties of Rai1-deficient neurons demonstrates the essential roles of RAI1 in suppressing synaptic upscaling in the naive network, while promoting upscaling triggered by activity silencing. These results highlight the utility of bona fide transcription profiling to discover mechanisms of activity-dependent chromatin remodeling that underlie normal and pathological synaptic plasticity. BrU-seq reveals nascent transcription during synaptic up- or downscaling Smith-Magenis syndrome protein RAI1 regulates upscaling-associated transcription RAI1 departs chromatin in response to network activity shifts RAI1 blocks upscaling in naive networks and promotes inactivity-induced upscaling
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Affiliation(s)
- Patricia M Garay
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alex Chen
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Takao Tsukahara
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Rafi Kohen
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - J Christian Althaus
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Margarete A Wallner
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roman J Giger
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Cellular and Molecular Biology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kevin S Jones
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Michael A Sutton
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Shigeki Iwase
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
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Shen H, Zhang W, Huang Y, He Y, Hu G, Wang L, Peng B, Yi J, Li T, Rong R, Chen X, Liu J, Li W, Ohgi K, Li S, Rosenfeld MG, Liu W. The Dual Function of KDM5C in Both Gene Transcriptional Activation and Repression Promotes Breast Cancer Cell Growth and Tumorigenesis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004635. [PMID: 33977073 PMCID: PMC8097366 DOI: 10.1002/advs.202004635] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/25/2020] [Indexed: 06/01/2023]
Abstract
Emerging evidence suggested that epigenetic regulators can exhibit both activator and repressor activities in gene transcriptional regulation and disease development, such as cancer. However, how these dual activities are regulated and coordinated in specific cellular contexts remains elusive. Here, it is reported that KDM5C, a repressive histone demethylase, unexpectedly activates estrogen receptor alpha (ERα)-target genes, and meanwhile suppresses type I interferons (IFNs) and IFN-stimulated genes (ISGs) to promote ERα-positive breast cancer cell growth and tumorigenesis. KDM5C-interacting protein, ZMYND8, is found to be involved in both processes. Mechanistically, KDM5C binds to active enhancers and recruits the P-TEFb complex to activate ERα-target genes, while inhibits TBK1 phosphorylation in the cytosol to repress type I IFNs and ISGs. Pharmacological inhibition of both ERα and KDM5C is effective in inhibiting cell growth and tumorigenesis. Taken together, it is revealed that the dual activator and repressor nature of an epigenetic regulator together contributes to cancer development.
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Affiliation(s)
- Hai‐feng Shen
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Wen‐juan Zhang
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Ying Huang
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Yao‐hui He
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Guo‐sheng Hu
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Lei Wang
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Bing‐ling Peng
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Jia Yi
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Ting‐ting Li
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Rui Rong
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Xiao‐yan Chen
- School of Life SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Jun‐yi Liu
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Wen‐juan Li
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Kenny Ohgi
- Howard Hughes Medical InstituteDepartment of MedicineUniversity of California9500 Gilman Drive La JollaSan DiegoCA92093USA
| | - Shao‐Wei Li
- State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsXiamen UniversityXiang'an South RoadXiamenFujian361102China
| | - Michael G. Rosenfeld
- Howard Hughes Medical InstituteDepartment of MedicineUniversity of California9500 Gilman Drive La JollaSan DiegoCA92093USA
| | - Wen Liu
- State Key Laboratory of Cellular Stress BiologyFujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiang'an South RoadXiamenFujian361102China
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36
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Comorbidities associated with genetic abnormalities in children with intellectual disability. Sci Rep 2021; 11:6563. [PMID: 33753861 PMCID: PMC7985145 DOI: 10.1038/s41598-021-86131-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 02/02/2021] [Indexed: 12/03/2022] Open
Abstract
Intellectual disability (ID) has emerged as the commonest manifestation of underlying genomic abnormalities. Given that molecular genetic tests for diagnosis of ID usually require high costs and yield relatively low diagnostic rates, identification of additional phenotypes or comorbidities may increase the genetic diagnostic yield and are valuable clues for pediatricians in general practice. Here, we enrolled consecutively 61 children with unexplained moderate or severe ID and performed chromosomal microarray (CMA) and sequential whole-exome sequencing (WES) analysis on them. We identified 13 copy number variants in 12 probands and 24 variants in 25 probands, and the total diagnostic rate was 60.7%. The genetic abnormalities were commonly found in ID patients with movement disorder (100%) or with autistic spectrum disorder (ASD) (93.3%). Univariate analysis showed that ASD was the significant risk factor of genetic abnormality (P = 0.003; OR 14, 95% CI 1.7–115.4). At least 14 ID-ASD associated genes were identified, and the majority of ID-ASD associated genes (85.7%) were found to be expressed in the cerebellum based on database analysis. In conclusion, genetic testing on ID children, particularly in those with ASD is highly recommended. ID and ASD may share common cerebellar pathophysiology.
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37
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Hatch HAM, Belalcazar HM, Marshall OJ, Secombe J. A KDM5-Prospero transcriptional axis functions during early neurodevelopment to regulate mushroom body formation. eLife 2021; 10:63886. [PMID: 33729157 PMCID: PMC7997662 DOI: 10.7554/elife.63886] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Mutations in the lysine demethylase 5 (KDM5) family of transcriptional regulators are associated with intellectual disability, yet little is known regarding their spatiotemporal requirements or neurodevelopmental contributions. Utilizing the mushroom body (MB), a major learning and memory center within the Drosophila brain, we demonstrate that KDM5 is required within ganglion mother cells and immature neurons for proper axogenesis. Moreover, the mechanism by which KDM5 functions in this context is independent of its canonical histone demethylase activity. Using in vivo transcriptional and binding analyses, we identify a network of genes directly regulated by KDM5 that are critical modulators of neurodevelopment. We find that KDM5 directly regulates the expression of prospero, a transcription factor that we demonstrate is essential for MB morphogenesis. Prospero functions downstream of KDM5 and binds to approximately half of KDM5-regulated genes. Together, our data provide evidence for a KDM5-Prospero transcriptional axis that is essential for proper MB development.
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Affiliation(s)
- Hayden AM Hatch
- Dominick P. Purpura Department of Neuroscience Albert Einstein College of Medicine, Bronx, United States
| | - Helen M Belalcazar
- Department of Genetics Albert Einstein College of Medicine, Bronx, United States
| | - Owen J Marshall
- Menzies Institute for Medical Research University of Tasmania, Hobart, Australia
| | - Julie Secombe
- Dominick P. Purpura Department of Neuroscience Albert Einstein College of Medicine, Bronx, United States.,Department of Genetics Albert Einstein College of Medicine, Bronx, United States
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38
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Qi S, Al Mamun A, Ngwa C, Romana S, Ritzel R, Arnold AP, McCullough LD, Liu F. X chromosome escapee genes are involved in ischemic sexual dimorphism through epigenetic modification of inflammatory signals. J Neuroinflammation 2021; 18:70. [PMID: 33712031 PMCID: PMC7953638 DOI: 10.1186/s12974-021-02120-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/24/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Stroke is a sexually dimorphic disease. Previous studies have found that young females are protected against ischemia compared to males, partially due to the protective effect of ovarian hormones, particularly estrogen (E2). However, there are also genetic and epigenetic effects of X chromosome dosage that contribute to stroke sensitivity and neuroinflammation after injury, especially in the aged. Genes that escape from X chromosome inactivation (XCI) contribute to sex-specific phenotypes in many disorders. Kdm5c and kdm6a are X escapee genes that demethylate H3K4me3 and H3K27me3, respectively. We hypothesized that the two demethylases play critical roles in mediating the stroke sensitivity. METHODS To identify the X escapee genes involved in stroke, we performed RNA-seq in flow-sorted microglia from aged male and female wild type (WT) mice subjected to middle cerebral artery occlusion (MCAO). The expression of these genes (kdm5c/kdm6a) were confirmed in four core genotypes (FCG) mice and in post-mortem human stroke brains by immunohistochemistry (IHC), Western blot, and RT-PCR. Chromatin immunoprecipitation (ChIP) assays were conducted to detect DNA levels of inflammatory interferon regulatory factor (IRF) 4/5 precipitated by histone H3K4 and H3K27 antibodies. Manipulation of kdm5c/kdm6a expression with siRNA or lentivirus was performed in microglial culture, to determine downstream pathways and examine the regulatory roles in inflammatory cytokine production. RESULTS Kdm5c and kdm6a mRNA levels were significantly higher in aged WT female vs. male microglia, and the sex difference also existed in ischemic brains from FCG mice and human stroke patients. The ChIP assay showed the IRF 4/5 had higher binding levels to demethylated H3K4 or H3K27, respectively, in female vs. male ischemic microglia. Knockdown or over expression of kdm5c/kdm6a with siRNA or lentivirus altered the methylation of H3K4 or H3K27 at the IRF4/5 genes, which in turn, impacted the production of inflammatory cytokines. CONCLUSIONS The KDM-Histone-IRF pathways are suggested to mediate sex differences in cerebral ischemia. Epigenetic modification of stroke-related genes constitutes an important mechanism underlying the ischemic sexual dimorphism.
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Affiliation(s)
- Shaohua Qi
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Abdullah Al Mamun
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Conelius Ngwa
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Sharmeen Romana
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Rodney Ritzel
- Department of Anesthesiology, Center for Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Arthur P Arnold
- Department of Integrative Biology and Physiology, UCLA, 610 Charles Young Drive South, Los Angeles, CA, 90095, USA
| | - Louise D McCullough
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Fudong Liu
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
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39
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Belalcazar HM, Hendricks EL, Zamurrad S, Liebl FLW, Secombe J. The histone demethylase KDM5 is required for synaptic structure and function at the Drosophila neuromuscular junction. Cell Rep 2021; 34:108753. [PMID: 33596422 PMCID: PMC7945993 DOI: 10.1016/j.celrep.2021.108753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/14/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
Mutations in the genes encoding the lysine demethylase 5 (KDM5) family of histone demethylases are observed in individuals with intellectual disability (ID). Despite clear evidence linking KDM5 function to neurodevelopmental pathways, how this family of proteins impacts transcriptional programs to mediate synaptic structure and activity remains unclear. Using the Drosophila larval neuromuscular junction (NMJ), we show that KDM5 is required presynaptically for neuroanatomical development and synaptic function. The Jumonji C (JmjC) domain-encoded histone demethylase activity of KDM5, which is expected to be diminished by many ID-associated alleles, is required for appropriate synaptic morphology and neurotransmission. The activity of the C5HC2 zinc finger is also required, as an ID-associated mutation in this motif reduces NMJ bouton number, increases bouton size, and alters microtubule dynamics. KDM5 therefore uses demethylase-dependent and independent mechanisms to regulate NMJ structure and activity, highlighting the complex nature by which this chromatin modifier carries out its neuronal gene-regulatory programs.
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Affiliation(s)
- Helen M Belalcazar
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Emily L Hendricks
- Department of Biological Sciences, Southern Illinois University Edwardsville, 44 Circle Drive, Edwardsville, IL 62026, USA
| | - Sumaira Zamurrad
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Faith L W Liebl
- Department of Biological Sciences, Southern Illinois University Edwardsville, 44 Circle Drive, Edwardsville, IL 62026, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461, USA.
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40
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Agarwal S, Bonefas KM, Garay PM, Brookes E, Murata-Nakamura Y, Porter RS, Macfarlan TS, Ren B, Iwase S. KDM1A maintains genome-wide homeostasis of transcriptional enhancers. Genome Res 2021; 31:186-197. [PMID: 33414108 PMCID: PMC7849409 DOI: 10.1101/gr.234559.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 12/07/2020] [Indexed: 12/27/2022]
Abstract
Transcriptional enhancers enable exquisite spatiotemporal control of gene expression in metazoans. Enrichment of monomethylation of histone H3 lysine 4 (H3K4me1) is a major chromatin signature of transcriptional enhancers. Lysine (K)-specific demethylase 1A (KDM1A, also known as LSD1), an H3K4me2/me1 demethylase, inactivates stem-cell enhancers during the differentiation of mouse embryonic stem cells (mESCs). However, its role in undifferentiated mESCs remains obscure. Here, we show that KDM1A actively maintains the optimal enhancer status in both undifferentiated and lineage-committed cells. KDM1A occupies a majority of enhancers in undifferentiated mESCs. KDM1A levels at enhancers exhibit clear positive correlations with its substrate H3K4me2, H3K27ac, and transcription at enhancers. In Kdm1a-deficient mESCs, a large fraction of these enhancers gains additional H3K4 methylation, which is accompanied by increases in H3K27 acetylation and increased expression of both enhancer RNAs (eRNAs) and target genes. In postmitotic neurons, loss of KDM1A leads to premature activation of neuronal activity-dependent enhancers and genes. Taken together, these results suggest that KDM1A is a versatile regulator of enhancers and acts as a rheostat to maintain optimal enhancer activity by counterbalancing H3K4 methylation at enhancers.
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Affiliation(s)
- Saurabh Agarwal
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California 92093-0653, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Katherine M Bonefas
- Neuroscience Graduate Program, The University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Patricia M Garay
- Neuroscience Graduate Program, The University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Emily Brookes
- Division of Newborn Medicine, Boston Children's Hospital, and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yumie Murata-Nakamura
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Robert S Porter
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Todd S Macfarlan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California 92093-0653, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
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41
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Roles of HIF and 2-Oxoglutarate-Dependent Dioxygenases in Controlling Gene Expression in Hypoxia. Cancers (Basel) 2021; 13:cancers13020350. [PMID: 33477877 PMCID: PMC7832865 DOI: 10.3390/cancers13020350] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that such dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. Abstract Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. We highlight the relevance of HIF and 2-OGDs in the control of gene expression in response to hypoxia and their relevance to human biology and health.
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Fallah MS, Szarics D, Robson CM, Eubanks JH. Impaired Regulation of Histone Methylation and Acetylation Underlies Specific Neurodevelopmental Disorders. Front Genet 2021; 11:613098. [PMID: 33488679 PMCID: PMC7820808 DOI: 10.3389/fgene.2020.613098] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
Epigenetic processes are critical for governing the complex spatiotemporal patterns of gene expression in neurodevelopment. One such mechanism is the dynamic network of post-translational histone modifications that facilitate recruitment of transcription factors or even directly alter chromatin structure to modulate gene expression. This is a tightly regulated system, and mutations affecting the function of a single histone-modifying enzyme can shift the normal epigenetic balance and cause detrimental developmental consequences. In this review, we will examine select neurodevelopmental conditions that arise from mutations in genes encoding enzymes that regulate histone methylation and acetylation. The methylation-related conditions discussed include Wiedemann-Steiner, Kabuki, and Sotos syndromes, and the acetylation-related conditions include Rubinstein-Taybi, KAT6A, genitopatellar/Say-Barber-Biesecker-Young-Simpson, and brachydactyly mental retardation syndromes. In particular, we will discuss the clinical/phenotypic and genetic basis of these conditions and the model systems that have been developed to better elucidate cellular and systemic pathological mechanisms.
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Affiliation(s)
- Merrick S Fallah
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Dora Szarics
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Clara M Robson
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - James H Eubanks
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.,Department of Surgery (Neurosurgery), University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada.,Department of Physiology, University of Toronto, Toronto, ON, Canada
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AlSiraj Y, Thatcher SE, Blalock E, Saintilnord WN, Daugherty A, Lu HS, Luo W, Shen YH, LeMaire SA, Arnold AP, Cassis LA. Monosomy X in Female Mice Influences the Regional Formation and Augments the Severity of Angiotensin II-Induced Aortopathies. Arterioscler Thromb Vasc Biol 2021; 41:269-283. [PMID: 33054396 PMCID: PMC8259710 DOI: 10.1161/atvbaha.120.314407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
OBJECTIVE Turner syndrome women (monosomy X) have high risk of aortopathies consistent with a role for sex chromosomes in disease development. We demonstrated that sex chromosomes influence regional development of Ang II (angiotensin II)-induced aortopathies in mice. In this study, we determined if the number of X chromosomes regulates regional development of Ang II-induced aortopathies. Approach and Results: We used females with varying numbers of X chromosomes (XX female mice [XXF] or XO female mice [XOF]) on an C57BL/6J (ascending aortopathies) or low-density lipoprotein receptor deficient (Ldlr-/-) background (descending and abdominal aortopathies) compared with XY males (XYM). To induce aortopathies, mice were infused with Ang II. XOF (C57BL/6J) exhibited larger percent increases in ascending aortic lumen diameters than Ang II-infused XXF or XYM. Ang II-infused XOF (Ldlr-/-) exhibited similar incidences of thoracic (XOF, 50%; XYM, 71%) and abdominal aortopathies (XOF, 83%; XYM, 71%) as XYM, which were greater than XXF (XXF, 0%). Abdominal aortic lumen diameters and maximal external diameters were similar between XOF and XYM but greater than XXF, and these effects persisted with extended Ang II infusions. Larger aortic lumen diameters, abdominal aortopathy incidence (XXF, 20%; XOF, 75%), and maximal aneurysm diameters (XXF, 1.02±0.17; XOF, 1.96±0.32 mm; P=0.027) persisted in ovariectomized Ang II-infused XOF mice. Data from RNA-seq demonstrated that X chromosome genes that escape X-inactivation (histone lysine demethylases Kdm5c and Kdm6a) exhibited lower mRNA abundance in aortas of XOF than XXF (P=0.033 and 0.024, respectively). Conversely, DNA methylation was higher in aortas of XOF than XXF (P=0.038). CONCLUSIONS The absence of a second X chromosome promotes diffuse Ang II-induced aortopathies in females.
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MESH Headings
- Angiotensin II
- Animals
- Aorta, Abdominal/metabolism
- Aorta, Abdominal/pathology
- Aorta, Thoracic/metabolism
- Aorta, Thoracic/pathology
- Aortic Aneurysm, Abdominal/chemically induced
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/metabolism
- Aortic Aneurysm, Abdominal/pathology
- Aortic Aneurysm, Thoracic/chemically induced
- Aortic Aneurysm, Thoracic/genetics
- Aortic Aneurysm, Thoracic/metabolism
- Aortic Aneurysm, Thoracic/pathology
- DNA Methylation
- Disease Models, Animal
- Female
- Histone Demethylases/genetics
- Histone Demethylases/metabolism
- Mice, Inbred C57BL
- Mice, Knockout
- Ovariectomy
- Receptors, LDL/deficiency
- Receptors, LDL/genetics
- Severity of Illness Index
- Turner Syndrome/complications
- Turner Syndrome/genetics
- Mice
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Affiliation(s)
- Yasir AlSiraj
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington KY
| | - Sean E. Thatcher
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington KY
| | - Eric Blalock
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington KY
| | - Wesley N. Saintilnord
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY
| | - Alan Daugherty
- Department of Physiology, University of Kentucky, Lexington KY
- Saha Cardiovascular Research Center, University of Kentucky, Lexington KY
| | - Hong S. Lu
- Department of Physiology, University of Kentucky, Lexington KY
- Saha Cardiovascular Research Center, University of Kentucky, Lexington KY
| | - Wei Luo
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, and Department of Cardiovascular Surgery, Texas Heart Institute, Houston TX
| | - Ying H. Shen
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, and Department of Cardiovascular Surgery, Texas Heart Institute, Houston TX
| | - Scott A. LeMaire
- Division of Cardiothoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, and Department of Cardiovascular Surgery, Texas Heart Institute, Houston TX
| | - Arthur P. Arnold
- Integrative Biology and Physiology, University of California, Los Angeles CA
| | - Lisa A. Cassis
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington KY
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El Hayek L, Tuncay IO, Nijem N, Russell J, Ludwig S, Kaur K, Li X, Anderton P, Tang M, Gerard A, Heinze A, Zacher P, Alsaif HS, Rad A, Hassanpour K, Abbaszadegan MR, Washington C, DuPont BR, Louie RJ, Couse M, Faden M, Rogers RC, Abou Jamra R, Elias ER, Maroofian R, Houlden H, Lehman A, Beutler B, Chahrour MH. KDM5A mutations identified in autism spectrum disorder using forward genetics. eLife 2020; 9:56883. [PMID: 33350388 PMCID: PMC7755391 DOI: 10.7554/elife.56883] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/06/2020] [Indexed: 12/29/2022] Open
Abstract
Autism spectrum disorder (ASD) is a constellation of neurodevelopmental disorders with high phenotypic and genetic heterogeneity, complicating the discovery of causative genes. Through a forward genetics approach selecting for defective vocalization in mice, we identified Kdm5a as a candidate ASD gene. To validate our discovery, we generated a Kdm5a knockout mouse model (Kdm5a-/-) and confirmed that inactivating Kdm5a disrupts vocalization. In addition, Kdm5a-/- mice displayed repetitive behaviors, sociability deficits, cognitive dysfunction, and abnormal dendritic morphogenesis. Loss of KDM5A also resulted in dysregulation of the hippocampal transcriptome. To determine if KDM5A mutations cause ASD in humans, we screened whole exome sequencing and microarray data from a clinical cohort. We identified pathogenic KDM5A variants in nine patients with ASD and lack of speech. Our findings illustrate the power and efficacy of forward genetics in identifying ASD genes and highlight the importance of KDM5A in normal brain development and function.
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Affiliation(s)
- Lauretta El Hayek
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Islam Oguz Tuncay
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nadine Nijem
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kiran Kaur
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Priscilla Anderton
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Texas Children's Hospital, Houston, United States
| | - Anja Heinze
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Pia Zacher
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.,The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Aboulfazl Rad
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Islamic Republic of Iran
| | - Kazem Hassanpour
- Non-Communicable Diseases Research Center, Sabzevar University of Medical Sciences, Sabzevar, Islamic Republic of Iran
| | - Mohammad Reza Abbaszadegan
- Pardis Clinical and Genetics Laboratory, Mashhad, Islamic Republic of Iran.,Division of Human Genetics, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Islamic Republic of Iran
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- Department of Medical Genetics, University of British Columbia, British Columbia Children's and Women's Hospital Research Institute, Vancouver, Canada
| | - Madeline Couse
- Department of Medical Genetics, University of British Columbia, British Columbia Children's and Women's Hospital Research Institute, Vancouver, Canada
| | - Maha Faden
- Department of Genetics, King Saud Medical City, Riyadh, Saudi Arabia
| | | | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Ellen R Elias
- Department of Pediatrics and Genetics, University of Colorado School of Medicine, Aurora, United States
| | - Reza Maroofian
- Department of Neuromuscular Diseases, University College London, Queen Square Institute of Neurology, London, United Kingdom
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London, Queen Square Institute of Neurology, London, United Kingdom
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, British Columbia Children's and Women's Hospital Research Institute, Vancouver, Canada
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Maria H Chahrour
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States.,Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, United States.,Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
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45
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X-chromosome regulation and sex differences in brain anatomy. Neurosci Biobehav Rev 2020; 120:28-47. [PMID: 33171144 DOI: 10.1016/j.neubiorev.2020.10.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 01/08/2023]
Abstract
Humans show reproducible sex-differences in cognition and psychopathology that may be contributed to by influences of gonadal sex-steroids and/or sex-chromosomes on regional brain development. Gonadal sex-steroids are well known to play a major role in sexual differentiation of the vertebrate brain, but far less is known regarding the role of sex-chromosomes. Our review focuses on this latter issue by bridging together two literatures that have to date been largely disconnected. We first consider "bottom-up" genetic and molecular studies focused on sex-chromosome gene content and regulation. This literature nominates specific sex-chromosome genes that could drive developmental sex-differences by virtue of their sex-biased expression and their functions within the brain. We then consider the complementary "top down" view, from magnetic resonance imaging studies that map sex- and sex chromosome effects on regional brain anatomy, and link these maps to regional gene-expression within the brain. By connecting these top-down and bottom-up approaches, we emphasize the potential role of X-linked genes in driving sex-biased brain development and outline key goals for future work in this field.
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46
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Loss of PHF6 leads to aberrant development of human neuron-like cells. Sci Rep 2020; 10:19030. [PMID: 33149206 PMCID: PMC7642390 DOI: 10.1038/s41598-020-75999-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/22/2020] [Indexed: 11/09/2022] Open
Abstract
Pathogenic variants in PHD finger protein 6 (PHF6) cause Borjeson-Forssman-Lehmann syndrome (BFLS), a rare X-linked neurodevelopmental disorder, which manifests variably in both males and females. To investigate the mechanisms behind overlapping but distinct clinical aspects between genders, we assessed the consequences of individual variants with structural modelling and molecular techniques. We found evidence that de novo variants occurring in females are more severe and result in loss of PHF6, while inherited variants identified in males might be hypomorph or have weaker effects on protein stability. This might contribute to the different phenotypes in male versus female individuals with BFLS. Furthermore, we used CRISPR/Cas9 to induce knockout of PHF6 in SK-N-BE (2) cells which were then differentiated to neuron-like cells in order to model nervous system related consequences of PHF6 loss. Transcriptome analysis revealed a broad deregulation of genes involved in chromatin and transcriptional regulation as well as in axon and neuron development. Subsequently, we could demonstrate that PHF6 is indeed required for proper neuron proliferation, neurite outgrowth and migration. Impairment of these processes might therefore contribute to the neurodevelopmental and cognitive dysfunction in BFLS.
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47
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Link JC, Wiese CB, Chen X, Avetisyan R, Ronquillo E, Ma F, Guo X, Yao J, Allison M, Chen YDI, Rotter JI, El -Sayed Moustafa JS, Small KS, Iwase S, Pellegrini M, Vergnes L, Arnold AP, Reue K. X chromosome dosage of histone demethylase KDM5C determines sex differences in adiposity. J Clin Invest 2020; 130:5688-5702. [PMID: 32701509 PMCID: PMC7598065 DOI: 10.1172/jci140223] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/16/2020] [Indexed: 12/29/2022] Open
Abstract
Males and females differ in body composition and fat distribution. Using a mouse model that segregates gonadal sex (ovaries and testes) from chromosomal sex (XX and XY), we showed that XX chromosome complement in combination with a high-fat diet led to enhanced weight gain in the presence of male or female gonads. We identified the genomic dosage of Kdm5c, an X chromosome gene that escapes X chromosome inactivation, as a determinant of the X chromosome effect on adiposity. Modulating Kdm5c gene dosage in XX female mice to levels that are normally present in males resulted in reduced body weight, fat content, and food intake to a degree similar to that seen with altering the entire X chromosome dosage. In cultured preadipocytes, the levels of KDM5C histone demethylase influenced chromatin accessibility (ATAC-Seq), gene expression (RNA-Seq), and adipocyte differentiation. Both in vitro and in vivo, Kdm5c dosage influenced gene expression involved in extracellular matrix remodeling, which is critical for adipocyte differentiation and adipose tissue expansion. In humans, adipose tissue KDM5C mRNA levels and KDM5C genetic variants were associated with body mass. These studies demonstrate that the sex-dependent dosage of Kdm5c contributes to male/female differences in adipocyte biology and highlight X-escape genes as a critical component of female physiology.
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Affiliation(s)
| | | | - Xuqi Chen
- Integrative Biology and Physiology, and
| | | | | | - Feiyang Ma
- Molecular, Cellular and Developmental Biology, UCLA, Los Angeles, California, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Matthew Allison
- Division of Preventive Medicine, School of Medicine, UCSD, San Diego, California, USA
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | | | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Shigeki Iwase
- Human Genetics, Medical School, University of Michigan, Ann Arbor, Michigan, USA
| | - Matteo Pellegrini
- Molecular, Cellular and Developmental Biology, UCLA, Los Angeles, California, USA
| | | | | | - Karen Reue
- Molecular Biology Institute
- Human Genetics, David Geffen School of Medicine
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48
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Mu MD, Qian ZM, Yang SX, Rong KL, Yung WH, Ke Y. Therapeutic effect of a histone demethylase inhibitor in Parkinson's disease. Cell Death Dis 2020; 11:927. [PMID: 33116116 PMCID: PMC7595123 DOI: 10.1038/s41419-020-03105-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 12/30/2022]
Abstract
Iron accumulation in the substantia nigra is recognized as a hallmark of Parkinson's disease (PD). Therefore, reducing accumulated iron and associated oxidative stress is considered a promising therapeutic strategy for PD. However, current iron chelators have poor membrane permeability and lack cell-type specificity. Here we identified GSK-J4, a histone demethylase inhibitor with the ability to cross blood brain barrier, as a potent iron suppressor. Only a trace amount of GSK-J4 significantly and selectively reduced intracellular labile iron in dopaminergic neurons, and suppressed H2O2 and 6-OHDA-induced cell death in vitro. The iron-suppressive effect was mainly mediated by inducing an increase in the expression of the iron exporter ferroportin-1. In parallel, GSK-J4 rescued dopaminergic neuron loss and motor defects in 6-OHDA-induced PD rats, which was accompanied by reduction of oxidative stress. Importantly, GSK-J4 rescued the abnormal changes of histone methylation, H3K4me3 and H3K27me3 during 6-OHDA treatment although the iron-suppressive and neuroprotective effects were sensitive to H3K4me3 inhibition only. Also, upregulating H3K4me3 increased ferroportin-1 expression and neuroprotection. Taken together, we demonstrate a previously unappreciated action of GSK-J4 on cell-specific iron suppression and neuroprotection via epigenetic mechanism. Compared with conventional iron chelators, this compound has a stronger therapeutic potential for PD.
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Affiliation(s)
- Ming-Dao Mu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Zhong-Ming Qian
- Institute of Translational and Precision Medicine, Nantong University, Nantong 226001, China
| | - Sheng-Xi Yang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Kang-Lin Rong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Wing-Ho Yung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China. .,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.
| | - Ya Ke
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China. .,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.
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49
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Poeta L, Padula A, Attianese B, Valentino M, Verrillo L, Filosa S, Shoubridge C, Barra A, Schwartz CE, Christensen J, van Bokhoven H, Helin K, Lioi MB, Collombat P, Gecz J, Altucci L, Di Schiavi E, Miano MG. Histone demethylase KDM5C is a SAHA-sensitive central hub at the crossroads of transcriptional axes involved in multiple neurodevelopmental disorders. Hum Mol Genet 2020; 28:4089-4102. [PMID: 31691806 DOI: 10.1093/hmg/ddz254] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 12/26/2022] Open
Abstract
A disproportional large number of neurodevelopmental disorders (NDDs) is caused by variants in genes encoding transcription factors and chromatin modifiers. However, the functional interactions between the corresponding proteins are only partly known. Here, we show that KDM5C, encoding a H3K4 demethylase, is at the intersection of transcriptional axes under the control of three regulatory proteins ARX, ZNF711 and PHF8. Interestingly, mutations in all four genes (KDM5C, ARX, ZNF711 and PHF8) are associated with X-linked NDDs comprising intellectual disability as a core feature. in vitro analysis of the KDM5C promoter revealed that ARX and ZNF711 function as antagonist transcription factors that activate KDM5C expression and compete for the recruitment of PHF8. Functional analysis of mutations in these genes showed a correlation between phenotype severity and the reduction in KDM5C transcriptional activity. The KDM5C decrease was associated with a lack of repression of downstream target genes Scn2a, Syn1 and Bdnf in the embryonic brain of Arx-null mice. Aiming to correct the faulty expression of KDM5C, we studied the effect of the FDA-approved histone deacetylase inhibitor suberanilohydroxamic acid (SAHA). In Arx-KO murine ES-derived neurons, SAHA was able to rescue KDM5C depletion, recover H3K4me3 signalling and improve neuronal differentiation. Indeed, in ARX/alr-1-deficient Caenorhabditis elegans animals, SAHA was shown to counteract the defective KDM5C/rbr-2-H3K4me3 signalling, recover abnormal behavioural phenotype and ameliorate neuronal maturation. Overall, our studies indicate that KDM5C is a conserved and druggable effector molecule across a number of NDDs for whom the use of SAHA may be considered a potential therapeutic strategy.
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Affiliation(s)
- Loredana Poeta
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy
| | - Agnese Padula
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy.,University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Benedetta Attianese
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy
| | - Mariaelena Valentino
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy
| | - Lucia Verrillo
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy.,University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Stefania Filosa
- Institute of Biosciences and BioResources, National Research Council (CNR), Naples, Italy.,Istituto Neurologico Mediterraneo (Neuromed), Pozzilli, Isernia, Italy
| | - Cheryl Shoubridge
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.,Robinson Research Institute, Department of Paediatrics, University of Adelaide, Adelaide, South Australia, Australia
| | - Adriano Barra
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy
| | | | - Jesper Christensen
- University of Copenhagen, Biotech Research and Innovation Centre (BRIC), Copenhagen, Denmark.,University of Copenhagen, The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Copenhagen, Denmark
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Behaviour and Cognition, Radboudumc, Nijmegen, The Netherlands
| | - Kristian Helin
- University of Copenhagen, Biotech Research and Innovation Centre (BRIC), Copenhagen, Denmark.,University of Copenhagen, The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Copenhagen, Denmark
| | | | | | - Jozef Gecz
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
| | - Lucia Altucci
- University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Elia Di Schiavi
- Institute of Biosciences and BioResources, National Research Council (CNR), Naples, Italy
| | - Maria Giuseppina Miano
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy
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Vallianatos CN, Raines B, Porter RS, Bonefas KM, Wu MC, Garay PM, Collette KM, Seo YA, Dou Y, Keegan CE, Tronson NC, Iwase S. Mutually suppressive roles of KMT2A and KDM5C in behaviour, neuronal structure, and histone H3K4 methylation. Commun Biol 2020; 3:278. [PMID: 32483278 PMCID: PMC7264178 DOI: 10.1038/s42003-020-1001-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/09/2020] [Indexed: 12/17/2022] Open
Abstract
Histone H3 lysine 4 methylation (H3K4me) is extensively regulated by numerous writer and eraser enzymes in mammals. Nine H3K4me enzymes are associated with neurodevelopmental disorders to date, indicating their important roles in the brain. However, interplay among H3K4me enzymes during brain development remains largely unknown. Here, we show functional interactions of a writer-eraser duo, KMT2A and KDM5C, which are responsible for Wiedemann-Steiner Syndrome (WDSTS), and mental retardation X-linked syndromic Claes-Jensen type (MRXSCJ), respectively. Despite opposite enzymatic activities, the two mouse models deficient for either Kmt2a or Kdm5c shared reduced dendritic spines and increased aggression. Double mutation of Kmt2a and Kdm5c clearly reversed dendritic morphology, key behavioral traits including aggression, and partially corrected altered transcriptomes and H3K4me landscapes. Thus, our study uncovers common yet mutually suppressive aspects of the WDSTS and MRXSCJ models and provides a proof of principle for balancing a single writer-eraser pair to ameliorate their associated disorders.
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Affiliation(s)
- Christina N Vallianatos
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Genetics and Genomics Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Brynne Raines
- Department of Psychology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Robert S Porter
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Genetics and Genomics Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Katherine M Bonefas
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,The University of Michigan Neuroscience Graduate Program, Ann Arbor, MI, USA
| | | | - Patricia M Garay
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,The University of Michigan Neuroscience Graduate Program, Ann Arbor, MI, USA
| | - Katie M Collette
- Department of Psychology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Young Ah Seo
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yali Dou
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Catherine E Keegan
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Natalie C Tronson
- Department of Psychology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Shigeki Iwase
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
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