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Lukin J, Smith CM, De Rubeis S. Emerging X-linked genes associated with neurodevelopmental disorders in females. Curr Opin Neurobiol 2024; 88:102902. [PMID: 39167997 PMCID: PMC11392613 DOI: 10.1016/j.conb.2024.102902] [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: 04/16/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 08/23/2024]
Abstract
A significant source of risk for neurodevelopmental disorders (NDDs), including intellectual disability (ID) and autism spectrum disorder (ASD), lies in genes located on the X chromosome. Males can be particularly vulnerable to X-linked variation because of hemizygosity, and male-specific segregation in pedigrees has guided earlier gene discovery for X-linked recessive conditions. More recently, X-linked disorders disproportionally affecting females, with complex inheritance patterns and/or presenting with sex differences, have surfaced. Here, we discuss the genetics and neurobiology of X-linked genes that are paradigmatic to understand NDDs in females. Integrating genetic, clinical, and functional data will be key to understand how X-linked variation contributes to the risk architecture of NDDs.
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Affiliation(s)
- Jeronimo Lukin
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Corinne M Smith
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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2
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Nakamura T, Yoshihara T, Tanegashima C, Kadota M, Kobayashi Y, Honda K, Ishiwata M, Ueda J, Hara T, Nakanishi M, Takumi T, Itohara S, Kuraku S, Asano M, Kasahara T, Nakajima K, Tsuboi T, Takata A, Kato T. Transcriptomic dysregulation and autistic-like behaviors in Kmt2c haploinsufficient mice rescued by an LSD1 inhibitor. Mol Psychiatry 2024; 29:2888-2904. [PMID: 38528071 PMCID: PMC11420081 DOI: 10.1038/s41380-024-02479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 03/27/2024]
Abstract
Recent studies have consistently demonstrated that the regulation of chromatin and gene transcription plays a pivotal role in the pathogenesis of neurodevelopmental disorders. Among many genes involved in these pathways, KMT2C, encoding one of the six known histone H3 lysine 4 (H3K4) methyltransferases in humans and rodents, was identified as a gene whose heterozygous loss-of-function variants are causally associated with autism spectrum disorder (ASD) and the Kleefstra syndrome phenotypic spectrum. However, little is known about how KMT2C haploinsufficiency causes neurodevelopmental deficits and how these conditions can be treated. To address this, we developed and analyzed genetically engineered mice with a heterozygous frameshift mutation of Kmt2c (Kmt2c+/fs mice) as a disease model with high etiological validity. In a series of behavioral analyses, the mutant mice exhibit autistic-like behaviors such as impairments in sociality, flexibility, and working memory, demonstrating their face validity as an ASD model. To investigate the molecular basis of the observed abnormalities, we performed a transcriptomic analysis of their bulk adult brains and found that ASD risk genes were specifically enriched in the upregulated differentially expressed genes (DEGs), whereas KMT2C peaks detected by ChIP-seq were significantly co-localized with the downregulated genes, suggesting an important role of putative indirect effects of Kmt2c haploinsufficiency. We further performed single-cell RNA sequencing of newborn mouse brains to obtain cell type-resolved insights at an earlier stage. By integrating findings from ASD exome sequencing, genome-wide association, and postmortem brain studies to characterize DEGs in each cell cluster, we found strong ASD-associated transcriptomic changes in radial glia and immature neurons with no obvious bias toward upregulated or downregulated DEGs. On the other hand, there was no significant gross change in the cellular composition. Lastly, we explored potential therapeutic agents and demonstrate that vafidemstat, a lysine-specific histone demethylase 1 (LSD1) inhibitor that was effective in other models of neuropsychiatric/neurodevelopmental disorders, ameliorates impairments in sociality but not working memory in adult Kmt2c+/fs mice. Intriguingly, the administration of vafidemstat was shown to alter the vast majority of DEGs in the direction to normalize the transcriptomic abnormalities in the mutant mice (94.3 and 82.5% of the significant upregulated and downregulated DEGs, respectively, P < 2.2 × 10-16, binomial test), which could be the molecular mechanism underlying the behavioral rescuing. In summary, our study expands the repertoire of ASD models with high etiological and face validity, elucidates the cell-type resolved molecular alterations due to Kmt2c haploinsufficiency, and demonstrates the efficacy of an LSD1 inhibitor that might be generalizable to multiple categories of psychiatric disorders along with a better understanding of its presumed mechanisms of action.
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Affiliation(s)
- Takumi Nakamura
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Toru Yoshihara
- Institute of Laboratory Animals, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Yuki Kobayashi
- Laboratory for Behavioral Genetics, RIKEN Center for Brain Science, Saitama, Japan
| | - Kurara Honda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Mizuho Ishiwata
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Junko Ueda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Tomonori Hara
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Organ Anatomy, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Moe Nakanishi
- Laboratory for Mental Biology, RIKEN Center for Brain Science, Saitama, Japan
- Laboratory for Molecular Mechanism of Brain Development, RIKEN Center for Brain Science, Saitama, Japan
| | - Toru Takumi
- Laboratory for Mental Biology, RIKEN Center for Brain Science, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Hyogo, Japan
| | - Shigeyoshi Itohara
- Laboratory for Behavioral Genetics, RIKEN Center for Brain Science, Saitama, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan
| | - Masahide Asano
- Institute of Laboratory Animals, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takaoki Kasahara
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Kazuo Nakajima
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Physiology, Teikyo University School of Medicine, Tokyo, Japan
| | - Takashi Tsuboi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan.
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan.
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan.
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3
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Oliver BG, Huang X, Yarak R, Bai X, Wang Q, Zakarya R, Reddy KD, Donovan C, Kim RY, Morkaya J, Wang B, Lung Chan Y, Saad S, Faiz A, Reyk DV, Verkhratsky A, Yi C, Chen H. Chronic maternal exposure to low-dose PM 2.5 impacts cognitive outcomes in a sex-dependent manner. ENVIRONMENT INTERNATIONAL 2024; 191:108971. [PMID: 39180775 DOI: 10.1016/j.envint.2024.108971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/29/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
There is no safe level of air pollution for human health. Traffic-related particulate matter (PM2.5) is a major in-utero toxin, mechanisms of action of which are not fully understood. BALB/c dams were exposed to an Australian level of traffic PM2.5 (5 µg/mouse/day, intranasal, 6 weeks before mating, during gestation and lactation). Male offspring had reduced memory in adulthood, whereas memory was normal in female littermates, similar to human responses. Maternal PM2.5 exposure resulted in oxidative stress and abnormal mitochondria in male, but not female, brains. RNA-sequencing analysis showed unique sex-related changes in newborn brains. Two X-chromosome-linked histone lysine demethylases, Kdm6a and Kdm5c, demonstrated higher expression in female compared to male littermates, in addition to upregulated genes with known functions to support mitochondrial function, synapse growth and maturation, cognitive function, and neuroprotection. No significant changes in Kdm6a and Kdm5c were found in male littermates, nor other genes, albeit significantly impaired memory function after birth. In primary foetal cortical neurons, PM2.5 exposure suppressed neuron and synaptic numbers and induced oxidative stress, which was prevented by upregulation of Kdm6a or Kdm5c. Therefore, timely epigenetic adaptation by histone demethylation to open DNA for translation before birth may be the key to protecting females against prenatal PM2.5 exposure-induced neurological disorders, which fail to occur in males associated with their poor cognitive outcomes.
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Affiliation(s)
- Brian G Oliver
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia; Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Xiaomin Huang
- Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Rochelle Yarak
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia
| | - Xu Bai
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia
| | - Qi Wang
- Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Razia Zakarya
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia; Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Karosham D Reddy
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia; Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Chantal Donovan
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia; Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Richard Y Kim
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia; Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - James Morkaya
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia
| | - Baoming Wang
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia
| | - Yik Lung Chan
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia
| | - Sonia Saad
- Renal Group, Kolling Institute of Medical Research, University of Sydney, NSW 2065, Australia
| | - Alen Faiz
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia
| | - David van Reyk
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia
| | - Alexei Verkhratsky
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK; Department of Neurosciences, University of the Basque Country, Leioa 48940, Bizkaia, Spain; IKERBASQUE Basque Foundation for Science, Bilbao, Spain; Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania; Department of Forensic Analytical Toxicology, School of Forensic Medicine, China Medical University, Shenyang, China
| | - Chenju Yi
- Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China; Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, China; Shenzhen Key Laboratory of Chinese Medicine Active Substance Screening and Translational Research, Shenzhen 518107, China.
| | - Hui Chen
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia
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4
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Guak H, Weiland M, Ark AV, Zhai L, Lau K, Corrado M, Davidson P, Asiedu E, Mabvakure B, Compton S, DeCamp L, Scullion CA, Jones RG, Nowinski SM, Krawczyk CM. Transcriptional programming mediated by the histone demethylase KDM5C regulates dendritic cell population heterogeneity and function. Cell Rep 2024; 43:114506. [PMID: 39052479 DOI: 10.1016/j.celrep.2024.114506] [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: 11/06/2023] [Revised: 03/30/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Functional and phenotypic heterogeneity of dendritic cells (DCs) play crucial roles in facilitating the development of diverse immune responses essential for host protection. Here, we report that KDM5C, a histone lysine demethylase, regulates conventional or classical DC (cDC) and plasmacytoid DC (pDC) population heterogeneity and function. Mice deficient in KDM5C in DCs have increased proportions of cDC2Bs and cDC1s, which is partly dependent on type I interferon (IFN) and pDCs. Loss of KDM5C results in an increase in Ly6C- pDCs, which, compared to Ly6C+ pDCs, have limited ability to produce type I IFN and more efficiently stimulate antigen-specific CD8 T cells. KDM5C-deficient DCs have increased expression of inflammatory genes, altered expression of lineage-specific genes, and decreased function. In response to Listeria infection, KDM5C-deficient mice mount reduced CD8 T cell responses due to decreased antigen presentation by cDC1s. Thus, KDM5C is a key regulator of DC heterogeneity and critical driver of the functional properties of DCs.
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Affiliation(s)
- Hannah Guak
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA; Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew Weiland
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Alexandra Vander Ark
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Lukai Zhai
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kin Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Mario Corrado
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA; Department of Internal Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Paula Davidson
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ebenezer Asiedu
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Batsirai Mabvakure
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA; Department of Oncology, Georgetown University School of Medicine, Washington, DC 20057, USA; Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Shelby Compton
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Lisa DeCamp
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Catherine A Scullion
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA; Department of Experimental Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Russell G Jones
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Sara M Nowinski
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Connie M Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA.
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Lavorando E, Owens MC, Liu KF. Comparing the roles of sex chromosome-encoded protein homologs in gene regulation. Genes Dev 2024; 38:585-596. [PMID: 39048311 PMCID: PMC11368246 DOI: 10.1101/gad.351890.124] [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] [Indexed: 07/27/2024]
Abstract
The X and Y chromosomes play important roles outside of human reproduction; namely, their potential contribution to human sex biases in physiology and disease. While sex biases are often thought to be an effect of hormones and environmental exposures, genes encoded on the sex chromosomes also play a role. Seventeen homologous gene pairs exist on the X and Y chromosomes whose proteins have critical functions in biology, from direct regulation of transcription and translation to intercellular signaling and formation of extracellular structures. In this review, we cover the current understanding of several of these sex chromosome-encoded protein homologs that are involved in transcription and chromatin regulation: SRY/SOX3, ZFX/ZFY, KDM5C/KDM5D, UTX/UTY, and TBL1X/TBL1Y. Their mechanisms of gene regulation are discussed, including any redundancies or divergent roles of the X- and Y-chromosome homologs. Additionally, we discuss associated diseases related to these proteins and any sex biases that exist therein in an effort to drive further research into how these pairs contribute to sexually dimorphic gene regulation in health and disease.
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Affiliation(s)
- Ellen Lavorando
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael C Owens
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Penn Institute for RNA Innovation, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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6
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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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7
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Del Blanco B, Niñerola S, Martín-González AM, Paraíso-Luna J, Kim M, Muñoz-Viana R, Racovac C, Sanchez-Mut JV, Ruan Y, Barco Á. Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons. Nat Commun 2024; 15:1781. [PMID: 38453932 PMCID: PMC10920760 DOI: 10.1038/s41467-024-45773-3] [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: 07/27/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Kdm1a is a histone demethylase linked to intellectual disability with essential roles during gastrulation and the terminal differentiation of specialized cell types, including neurons, that remains highly expressed in the adult brain. To explore Kdm1a's function in adult neurons, we develop inducible and forebrain-restricted Kdm1a knockouts. By applying multi-omic transcriptome, epigenome and chromatin conformation data, combined with super-resolution microscopy, we find that Kdm1a elimination causes the neuronal activation of nonneuronal genes that are silenced by the polycomb repressor complex and interspersed with active genes. Functional assays demonstrate that the N-terminus of Kdm1a contains an intrinsically disordered region that is essential to segregate Kdm1a-repressed genes from the neighboring active chromatin environment. Finally, we show that the segregation of Kdm1a-target genes is weakened in neurons during natural aging, underscoring the role of Kdm1a safeguarding neuronal genome organization and gene silencing throughout life.
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Affiliation(s)
- Beatriz Del Blanco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain.
| | - Sergio Niñerola
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Ana M Martín-González
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Juan Paraíso-Luna
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
- Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Minji Kim
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Rafael Muñoz-Viana
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
- Bioinformatics Unit, Hospital universitario Puerta de Hierro Majadahonda, 28220, Majadahonda, Spain
| | - Carina Racovac
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Jose V Sanchez-Mut
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Yijun Ruan
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China
| | - Ángel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain.
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8
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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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9
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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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10
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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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11
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Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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12
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Lin X, Chen JD, Wang CY, Cai Z, Zhan R, Yang C, Zhang LY, Li LY, Xiao Y, Chen MK, Wu M. Cooperation of MLL1 and Jun in controlling H3K4me3 on enhancers in colorectal cancer. Genome Biol 2023; 24:268. [PMID: 38012744 PMCID: PMC10680327 DOI: 10.1186/s13059-023-03108-3] [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: 04/24/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Enhancer dysregulation is one of the important features for cancer cells. Enhancers enriched with H3K4me3 have been implicated to play important roles in cancer. However, their detailed features and regulatory mechanisms have not been well characterized. RESULTS Here, we profile the landscape of H3K4me3-enriched enhancers (m3Es) in 43 pairs of colorectal cancer (CRC) samples. M3Es are widely distributed in CRC and averagely possess around 10% of total active enhancers. We identify 1322 gain variant m3Es and 367 lost variant m3Es in CRC. The target genes of the gain m3Es are enriched in immune response pathways. We experimentally prove that repression of CBX8 and RPS6KA5 m3Es inhibits target gene expression in CRC. Furthermore, we find histone methyltransferase MLL1 is responsible for depositing H3K4me3 on the identified Vm3Es. We demonstrate that the transcription factor AP1/JUN interacts with MLL1 and regulates m3E activity. Application of a small chemical inhibitor for MLL1 activity, OICR-9429, represses target gene expression of the identified Vm3Es, enhances anti-tumor immunity and inhibits CRC growth in an animal model. CONCLUSIONS Taken together, our study illustrates the genome-wide landscape and the regulatory mechanisms of m3Es in CRC, and reveals potential novel strategies for cancer treatment.
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Affiliation(s)
- Xiang Lin
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Ji-Dong Chen
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Chen-Yu Wang
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Zhen Cai
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Rui Zhan
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Chen Yang
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - La-Ying Zhang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Lian-Yun Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Yong Xiao
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China.
| | - Ming-Kai Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China.
| | - Min Wu
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Taikang Center for Life and Medical Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China.
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13
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Cording KR, Bateup HS. Altered motor learning and coordination in mouse models of autism spectrum disorder. Front Cell Neurosci 2023; 17:1270489. [PMID: 38026686 PMCID: PMC10663323 DOI: 10.3389/fncel.2023.1270489] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with increasing prevalence. Over 1,000 risk genes have now been implicated in ASD, suggesting diverse etiology. However, the diagnostic criteria for the disorder still comprise two major behavioral domains - deficits in social communication and interaction, and the presence of restricted and repetitive patterns of behavior (RRBs). The RRBs associated with ASD include both stereotyped repetitive movements and other motor manifestations including changes in gait, balance, coordination, and motor skill learning. In recent years, the striatum, the primary input center of the basal ganglia, has been implicated in these ASD-associated motor behaviors, due to the striatum's role in action selection, motor learning, and habit formation. Numerous mouse models with mutations in ASD risk genes have been developed and shown to have alterations in ASD-relevant behaviors. One commonly used assay, the accelerating rotarod, allows for assessment of both basic motor coordination and motor skill learning. In this corticostriatal-dependent task, mice walk on a rotating rod that gradually increases in speed. In the extended version of this task, mice engage striatal-dependent learning mechanisms to optimize their motor routine and stay on the rod for longer periods. This review summarizes the findings of studies examining rotarod performance across a range of ASD mouse models, and the resulting implications for the involvement of striatal circuits in ASD-related motor behaviors. While performance in this task is not uniform across mouse models, there is a cohort of models that show increased rotarod performance. A growing number of studies suggest that this increased propensity to learn a fixed motor routine may reflect a common enhancement of corticostriatal drive across a subset of mice with mutations in ASD-risk genes.
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Affiliation(s)
- Katherine R. Cording
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Helen S. Bateup
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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14
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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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15
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Gupta N, Yakhou L, Albert JR, Azogui A, Ferry L, Kirsh O, Miura F, Battault S, Yamaguchi K, Laisné M, Domrane C, Bonhomme F, Sarkar A, Delagrange M, Ducos B, Cristofari G, Ito T, Greenberg MVC, Defossez PA. A genome-wide screen reveals new regulators of the 2-cell-like cell state. Nat Struct Mol Biol 2023; 30:1105-1118. [PMID: 37488355 DOI: 10.1038/s41594-023-01038-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/19/2023] [Indexed: 07/26/2023]
Abstract
In mammals, only the zygote and blastomeres of the early embryo are totipotent. This totipotency is mirrored in vitro by mouse '2-cell-like cells' (2CLCs), which appear at low frequency in cultures of embryonic stem cells (ESCs). Because totipotency is not completely understood, we carried out a genome-wide CRISPR knockout screen in mouse ESCs, searching for mutants that reactivate the expression of Dazl, a gene expressed in 2CLCs. Here we report the identification of four mutants that reactivate Dazl and a broader 2-cell-like signature: the E3 ubiquitin ligase adaptor SPOP, the Zinc-Finger transcription factor ZBTB14, MCM3AP, a component of the RNA processing complex TREX-2, and the lysine demethylase KDM5C. All four factors function upstream of DPPA2 and DUX, but not via p53. In addition, SPOP binds DPPA2, and KDM5C interacts with ncPRC1.6 and inhibits 2CLC gene expression in a catalytic-independent manner. These results extend our knowledge of totipotency, a key phase of organismal life.
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Affiliation(s)
- Nikhil Gupta
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France.
- Joint AZ CRUK Functional Genomics Centre, The Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
| | - Lounis Yakhou
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | | | - Anaelle Azogui
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Laure Ferry
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Olivier Kirsh
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, Japan
| | - Sarah Battault
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Kosuke Yamaguchi
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Marthe Laisné
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Cécilia Domrane
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Frédéric Bonhomme
- Epigenetic Chemical Biology, UMR3523, Institut Pasteur, Université Paris Cité, CNRS, Paris, France
| | - Arpita Sarkar
- IRCAN, Université Côte d'Azur, Inserm, CNRS, Nice, France
| | - Marine Delagrange
- High Throughput qPCR Facility, Institut de Biologie de l'École Normale Supérieure (IBENS), Laboratoire de Physique de l'ENS CNRS UMR8023, PSL Research University, Paris, France
| | - Bertrand Ducos
- High Throughput qPCR Facility, Institut de Biologie de l'École Normale Supérieure (IBENS), Laboratoire de Physique de l'ENS CNRS UMR8023, PSL Research University, Paris, France
| | | | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, Japan
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16
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Aughey GN. Maintenance of neuronal fate and transcriptional identity. Biol Open 2023; 12:bio059953. [PMID: 37272626 PMCID: PMC10259840 DOI: 10.1242/bio.059953] [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] [Indexed: 06/06/2023] Open
Abstract
The processes that drive naive multipotent stem cells towards fully differentiated fates are increasingly well understood. However, once differentiated, the mechanisms and molecular factors involved in maintaining differentiated states and associated transcriptomes are less well studied. Neurons are a post-mitotic cell-type with highly specialised functions that largely lack the capacity for renewal. Therefore, neuronal cell identities and the transcriptional states that underpin them are locked into place by active mechanisms that prevent lineage reversion/dedifferentiation and repress cell cycling. Furthermore, individual neurons may be very long-lived, so these mechanisms must be sufficient to ensure the fidelity of neuronal transcriptomes over long time periods. This Review aims to provide an overview of recent progress in understanding how neuronal cell fate and associated gene expression are maintained and the transcriptional regulators that are involved. Maintenance of neuronal fate and subtype specification are discussed, as well as the activating and repressive mechanisms involved. The relevance of these processes to disease states, such as brain cancers and neurodegeneration is outlined. Finally, outstanding questions and hypotheses in this field are proposed.
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Affiliation(s)
- Gabriel N. Aughey
- Queen Square Institute of Neurology, Department of Clinical and Experimental Epilepsy, University College London, London WC1N 3BG, UK
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17
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Davis DL, Metzger DB, Vann PH, Wong JM, Shetty RA, Forster MJ, Sumien N. Effects of chronic methamphetamine exposure on rewarding behavior and neurodegeneration markers in adult mice. Psychopharmacology (Berl) 2023; 240:1343-1358. [PMID: 37127834 DOI: 10.1007/s00213-023-06374-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 04/27/2023] [Indexed: 05/03/2023]
Abstract
Recreational and medical use of stimulants among young adults have gained popularity in the United States over the last decade and their use may increase vulnerability to brain biochemical changes and addictive behaviors. The long-term effects of chronic stimulant exposure in later adulthood have not been fully elucidated.Our study investigated whether chronic exposure to methamphetamine (METH), at a dose designed to emulate human therapeutic dosing for ADHD, would promote biochemical alterations and affect sensitivity to the rewarding effects of subsequent METH dosing.Groups of 3.5-month-old male and female C57BL/6J mice were administered non-contingent intraperitoneal injections of either saline or METH (1.4 mg/kg) twice a day for 1 month (5 days/week). METH (0.5 mg/kg)-induced conditioned place preference (CPP) was tested in mice to determine the effects of previous METH exposure on reward-related behavior. Mice were randomly assigned to Experiment I (males and females) or Experiment II (females only) in which CPP testing was respectively performed either 0.5 or 5 months after the end of METH injections, at ~5 or 10 months old respectively. The midbrain and striatum, regions involved in reward circuit, were assessed for markers associated with neurotoxicity, dopaminergic function, neuroinflammation and epigenetic changes after behavioral testing.Previous exposure to chronic METH did not have significant short-term effects on CPP response but led to a decreased CPP response in 10-month-old females. Previous exposure to METH induced some short-term changes to biochemical markers measured in a brain region and sex-dependent manner, while long-term changes were only observed with GFAP and KDM5C.In conclusion, our data suggest sex- and post-exposure duration-dependent outcomes and warrant further exploration of the long-term neurobehavioral consequences of psychostimulant use in both sexes.
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Affiliation(s)
- Delaney L Davis
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, Texas, USA
| | - Daniel B Metzger
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, Texas, USA
| | - Philip H Vann
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, Texas, USA
| | - Jessica M Wong
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, Texas, USA
| | - Ritu A Shetty
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, Texas, USA
| | - Michael J Forster
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, Texas, USA
| | - Nathalie Sumien
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, Texas, USA.
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18
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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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19
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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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20
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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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21
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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; 12:637. [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
| | - 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
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22
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Al Adhami H, Vallet J, Schaal C, Schumacher P, Bardet AF, Dumas M, Chicher J, Hammann P, Daujat S, Weber M. Systematic identification of factors involved in the silencing of germline genes in mouse embryonic stem cells. Nucleic Acids Res 2023; 51:3130-3149. [PMID: 36772830 PMCID: PMC10123117 DOI: 10.1093/nar/gkad071] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 12/29/2022] [Accepted: 01/23/2023] [Indexed: 02/12/2023] Open
Abstract
In mammals, many germline genes are epigenetically repressed to prevent their illegitimate expression in somatic cells. To advance our understanding of the mechanisms restricting the expression of germline genes, we analyzed their chromatin signature and performed a CRISPR-Cas9 knock-out screen for genes involved in germline gene repression using a Dazl-GFP reporter system in mouse embryonic stem cells (mESCs). We show that the repression of germline genes mainly depends on the polycomb complex PRC1.6 and DNA methylation, which function additively in mESCs. Furthermore, we validated novel genes involved in the repression of germline genes and characterized three of them: Usp7, Shfm1 (also known as Sem1) and Erh. Inactivation of Usp7, Shfm1 or Erh led to the upregulation of germline genes, as well as retrotransposons for Shfm1, in mESCs. Mechanistically, USP7 interacts with PRC1.6 components, promotes PRC1.6 stability and presence at germline genes, and facilitates DNA methylation deposition at germline gene promoters for long term repression. Our study provides a global view of the mechanisms and novel factors required for silencing germline genes in embryonic stem cells.
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Affiliation(s)
- Hala Al Adhami
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Judith Vallet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Celia Schaal
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Paul Schumacher
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France.,Karlsruhe Institute of Technology (KIT), IAB, Department of Food Chemistry and Toxicology, 76131 Karlsruhe, Germany
| | - Anaïs Flore Bardet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, 67000 Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, 67000 Strasbourg, France
| | - Sylvain Daujat
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Michael Weber
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
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23
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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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24
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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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25
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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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26
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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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27
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Shang D, Lan T, Wang Y, Li X, Liu Q, Dong H, Xu B, Cheng H, Zhou R. PGCLCs of human 45,XO reveal pathogenetic pathways of neurocognitive and psychosocial disorders. Cell Biosci 2022; 12:194. [DOI: 10.1186/s13578-022-00925-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/03/2022] [Indexed: 12/03/2022] Open
Abstract
Abstract
Background
Neurocognitive disorders and psychosocial difficulties are common in patients with Turner syndrome and multiple neurodegenerative diseases, yet there is no effective cure. Human primordial germ cells (hPGCs) are pluripotent germline stem cells in early embryo, which pass genetic information from one generation to the next, whereas all somatic cells will die along with the end of life. However, it is not known whether patient hPGCs with Turner syndrome contain information of neurocognitive and psychosocial illness.
Results
In this report, we used a high-density of culture system of embryoids derived from iPSCs of a patient with Turner syndrome to ask how pathogenetic pathways are associated with onset of neurocognitive and psychosocial disorders. The hPGC-Like Cells (hPGCLCs) were in vitro specified from iPSCs of 45,XO, 46,XX and 46,XY by the high-density induction of embryoids. Amazingly, we found that the specification process of the hPGCLCs in 45,XO, compared to those in 46,XX and 46,XY, enriched several common pathogenetic pathways regulating neurocognitive and psychosocial disorders, that shared among multiple neurodegenerative diseases and Turner syndrome. The downregulated chemical synaptic transmission pathways, including glutamatergic, GABAergic, and nicotine cholinergic synapses, indicated synaptic dysfunctions, while upregulated pathways that were associated with imbalance of mitochondrial respiratory chain complexes and apoptosis, may contribute to neuronal dysfunctions. Notably, downregulation of three types of ubiquitin ligases E1-E2-E3 and lysosome-associated sulfatases and RAB9A, owing to haploinsufficiency and parental preference of the X chromosome expression, indicated that two pathways of cellular degradation, lysosome and ubiquitin–proteasome, were impaired in the specification process of 45,XO hPGCLCs. This would lead to accumulation of undesired proteins and aggregates, which is a typically pathological hallmark in neurodegenerative diseases.
Conclusions
Our data suggest that the specification process of the hPGCLCs in 45,XO, compared to those in 46,XX and 46,XY, enriched pathogenetic pathways that are associated with the onset of neurocognitive and psychosocial disorders.
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28
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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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Lipinski M, Niñerola S, Fuentes-Ramos M, Valor LM, Del Blanco B, López-Atalaya JP, Barco A. CBP Is Required for Establishing Adaptive Gene Programs in the Adult Mouse Brain. J Neurosci 2022; 42:7984-8001. [PMID: 36109165 PMCID: PMC9617619 DOI: 10.1523/jneurosci.0970-22.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/03/2022] [Accepted: 08/26/2022] [Indexed: 11/21/2022] Open
Abstract
Environmental factors and life experiences impinge on brain circuits triggering adaptive changes. Epigenetic regulators contribute to this neuroadaptation by enhancing or suppressing specific gene programs. The paralogous transcriptional coactivators and lysine acetyltransferases CREB binding protein (CBP) and p300 are involved in brain plasticity and stimulus-dependent transcription, but their specific roles in neuroadaptation are not fully understood. Here we investigated the impact of eliminating either CBP or p300 in excitatory neurons of the adult forebrain of mice from both sexes using inducible and cell type-restricted knock-out strains. The elimination of CBP, but not p300, reduced the expression and chromatin acetylation of plasticity genes, dampened activity-driven transcription, and caused memory deficits. The defects became more prominent in elderly mice and in paradigms that involved enduring changes in transcription, such as kindling and environmental enrichment, in which CBP loss interfered with the establishment of activity-induced transcriptional and epigenetic changes in response to stimulus or experience. These findings further strengthen the link between CBP deficiency in excitatory neurons and etiopathology in the nervous system.SIGNIFICANCE STATEMENT How environmental conditions and life experiences impinge on mature brain circuits to elicit adaptive responses that favor the survival of the organism remains an outstanding question in neurosciences. Epigenetic regulators are thought to contribute to neuroadaptation by initiating or enhancing adaptive gene programs. In this article, we examined the role of CREB binding protein (CBP) and p300, two paralogous transcriptional coactivators and histone acetyltransferases involved in cognitive processes and intellectual disability, in neuroadaptation in adult hippocampal circuits. Our experiments demonstrate that CBP, but not its paralog p300, plays a highly specific role in the epigenetic regulation of neuronal plasticity gene programs in response to stimulus and provide unprecedented insight into the molecular mechanisms underlying neuroadaptation.
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Affiliation(s)
- Michal Lipinski
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Sergio Niñerola
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Miguel Fuentes-Ramos
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Luis M Valor
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Beatriz Del Blanco
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Jose P López-Atalaya
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Angel Barco
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
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Regulation of KDM5C stability and enhancer reprogramming in breast cancer. Cell Death Dis 2022; 13:843. [PMID: 36192394 PMCID: PMC9530161 DOI: 10.1038/s41419-022-05296-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/10/2022] [Accepted: 09/23/2022] [Indexed: 01/23/2023]
Abstract
Abnormality of enhancer regulation has emerged as one of the critical features for cancer cells. KDM5C is a histone H3K4 demethylase and frequently mutated in several types of cancer. It is critical for H3K4me3 and activity of enhancers, but its regulatory mechanisms remain elusive. Here, we identify TRIM11 as one ubiquitin E3 ligase for KDM5C. TRIM11 interacts with KDM5C, catalyzes K48-linked ubiquitin chain on KDM5C, and promotes KDM5C degradation through proteasome. TRIM11 deficiency in an animal model represses the growth of breast tumor and stabilizes KDM5C. In breast cancer patient tissues, TRIM11 is highly expressed and KDM5C is lower expressed, and their expression is negatively correlated. Mechanistically, TRIM11 regulates the enhancer activity of genes involved in cell migration and immune response by targeting KDM5C. TRIM11 and KDM5C regulate MCAM expression and cell migration through targeting H3K4me3 on MCAM enhancer. Taken together, our study reveals novel mechanisms for enhancer regulation during breast cancer tumorigenesis and development.
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Sánchez-Luquez KY, Carpena MX, Karam SM, Tovo-Rodrigues L. The contribution of whole-exome sequencing to intellectual disability diagnosis and knowledge of underlying molecular mechanisms: A systematic review and meta-analysis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108428. [PMID: 35905832 DOI: 10.1016/j.mrrev.2022.108428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 01/01/2023]
Abstract
Whole-exome sequencing (WES) is useful for molecular diagnosis, family genetic counseling, and prognosis of intellectual disability (ID). However, ID molecular diagnosis ascertainment based on WES is highly dependent on de novo mutations (DNMs) and variants of uncertain significance (VUS). The quantification of DNM frequency in ID molecular diagnosis ascertainment and the biological mechanisms common to genes with VUS may provide objective information about WES use in ID diagnosis and etiology. We aimed to investigate and estimate the rate of ID molecular diagnostic assessment by WES, quantify the contribution of DNMs to this rate, and biologically and functionally characterize the genes whose mutations were identified through WES. A PubMed/Medline, Web of Science, Scopus, Science Direct, BIREME, and PsycINFO systematic review and meta-analysis was performed, including studies published between 2010 and 2022. Thirty-seven articles with data on ID molecular diagnostic yield using the WES approach were included in the review. WES testing accounted for an overall diagnostic rate of 42% (Confidence interval (CI): 35-50%), while the estimate restricted to DNMs was 11% (CI: 6-18%). Genetic information on mutations and genes was extracted and split into two groups: (1) genes whose mutation was used for positive molecular diagnosis, and (2) genes whose mutation led to uncertain molecular diagnosis. After functional enrichment analysis, in addition to their expected roles in neurodevelopment, genes from the first group were enriched in epigenetic regulatory mechanisms, immune system regulation, and circadian rhythm control. Genes from uncertain diagnosis cases were enriched in the renin angiotensin pathway. Taken together, our results support WES as an important approach to the molecular diagnosis of ID. The results also indicated relevant pathways that may underlie the pathogenesis of ID with the renin-angiotensin pathway being suggested to be a potential pathway underlying the pathogenesis of ID.
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Affiliation(s)
| | - Marina Xavier Carpena
- Postgraduate Program in Epidemiology, Universidade Federal de Pelotas, Pelotas, Brazil.
| | - Simone M Karam
- Postgraduate Program in Public Health, Universidade Federal do Rio Grande, Rio Grande, Brazil.
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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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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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Chiang MH, Ho SM, Wu HY, Lin YC, Tsai WH, Wu T, Lai CH, Wu CL. Drosophila Model for Studying Gut Microbiota in Behaviors and Neurodegenerative Diseases. Biomedicines 2022; 10:596. [PMID: 35327401 PMCID: PMC8945323 DOI: 10.3390/biomedicines10030596] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [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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Affiliation(s)
- Meng-Hsuan Chiang
- Graduate Institute of Biomedical Sciences, Department of Biochemistry, Department of Microbiology, Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (M.-H.C.); (S.-M.H.); (H.-Y.W.); (Y.-C.L.)
| | - Shuk-Man Ho
- Graduate Institute of Biomedical Sciences, Department of Biochemistry, Department of Microbiology, Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (M.-H.C.); (S.-M.H.); (H.-Y.W.); (Y.-C.L.)
| | - Hui-Yu Wu
- Graduate Institute of Biomedical Sciences, Department of Biochemistry, Department of Microbiology, Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (M.-H.C.); (S.-M.H.); (H.-Y.W.); (Y.-C.L.)
| | - Yu-Chun Lin
- Graduate Institute of Biomedical Sciences, Department of Biochemistry, Department of Microbiology, Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (M.-H.C.); (S.-M.H.); (H.-Y.W.); (Y.-C.L.)
| | - Wan-Hua Tsai
- Research and Development Department, GenMont Biotech Incorporation, Tainan 74144, Taiwan;
| | - Tony Wu
- Department of Neurology, Molecular Infectious Disease Research Center, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
- Department of Neurology, New Taipei Municipal Tucheng Hospital, Tucheng 23652, Taiwan
- Department of Neurology, Xiamen Chang Gung Hospital, Xiamen 361028, China
| | - Chih-Ho Lai
- Graduate Institute of Biomedical Sciences, Department of Biochemistry, Department of Microbiology, Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (M.-H.C.); (S.-M.H.); (H.-Y.W.); (Y.-C.L.)
- Department of Neurology, Molecular Infectious Disease Research Center, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
- Department of Medical Research, Graduate Institute of Biomedical Sciences, China Medical University and Hospital, Taichung 40402, Taiwan
- Department of Nursing, Asia University, Taichung 41354, Taiwan
| | - Chia-Lin Wu
- Graduate Institute of Biomedical Sciences, Department of Biochemistry, Department of Microbiology, Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (M.-H.C.); (S.-M.H.); (H.-Y.W.); (Y.-C.L.)
- Department of Neurology, Molecular Infectious Disease Research Center, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan;
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
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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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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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Gzielo K, Nikiforuk A. Astroglia in Autism Spectrum Disorder. Int J Mol Sci 2021; 22:11544. [PMID: 34768975 PMCID: PMC8583956 DOI: 10.3390/ijms222111544] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/13/2021] [Accepted: 10/21/2021] [Indexed: 01/12/2023] Open
Abstract
Autism spectrum disorder (ASD) is an umbrella term encompassing several neurodevelopmental disorders such as Asperger syndrome or autism. It is characterised by the occurrence of distinct deficits in social behaviour and communication and repetitive patterns of behaviour. The symptoms may be of different intensity and may vary in types. Risk factors for ASD include disturbed brain homeostasis, genetic predispositions, or inflammation during the prenatal period caused by viruses or bacteria. The number of diagnosed cases is growing, but the main cause and mechanism leading to ASD is still uncertain. Recent findings from animal models and human cases highlight the contribution of glia to the ASD pathophysiology. It is known that glia cells are not only "gluing" neurons together but are key players participating in different processes crucial for proper brain functioning, including neurogenesis, synaptogenesis, inflammation, myelination, proper glutamate processing and many others. Despite the prerequisites for the involvement of glia in the processes related to the onset of autism, there are far too little data regarding the engagement of these cells in the development of ASD.
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Affiliation(s)
- Kinga Gzielo
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Behavioral Neuroscience and Drug Development, 12 Smętna Street, 31-343 Kraków, Poland;
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Ciptasari U, van Bokhoven H. The phenomenal epigenome in neurodevelopmental disorders. Hum Mol Genet 2021; 29:R42-R50. [PMID: 32766754 PMCID: PMC7530535 DOI: 10.1093/hmg/ddaa175] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Disruption of chromatin structure due to epimutations is a leading genetic etiology of neurodevelopmental disorders, collectively known as chromatinopathies. We show that there is an increasing level of convergence from the high diversity of genes that are affected by mutations to the molecular networks and pathways involving the respective proteins, the disrupted cellular and subcellular processes, and their consequence for higher order cellular network function. This convergence is ultimately reflected by specific phenotypic features shared across the various chromatinopathies. Based on these observations, we propose that the commonly disrupted molecular and cellular anomalies might provide a rational target for the development of symptomatic interventions for defined groups of genetically distinct neurodevelopmental disorders.
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Affiliation(s)
- Ummi Ciptasari
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands.,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
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Poeta L, Padula A, Lioi MB, van Bokhoven H, Miano MG. Analysis of a Set of KDM5C Regulatory Genes Mutated in Neurodevelopmental Disorders Identifies Temporal Coexpression Brain Signatures. Genes (Basel) 2021; 12:genes12071088. [PMID: 34356104 PMCID: PMC8305412 DOI: 10.3390/genes12071088] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/22/2022] Open
Abstract
Dysregulation of transcriptional pathways is observed in multiple forms of neurodevelopmental disorders (NDDs), such as intellectual disability (ID), epilepsy and autism spectrum disorder (ASD). We previously demonstrated that the NDD genes encoding lysine-specific demethylase 5C (KDM5C) and its transcriptional regulators Aristaless related-homeobox (ARX), PHD Finger Protein 8 (PHF8) and Zinc Finger Protein 711 (ZNF711) are functionally connected. Here, we show their relation to each other with respect to the expression levels in human and mouse datasets and in vivo mouse analysis indicating that the coexpression of these syntenic X-chromosomal genes is temporally regulated in brain areas and cellular sub-types. In co-immunoprecipitation assays, we found that the homeotic transcription factor ARX interacts with the histone demethylase PHF8, indicating that this transcriptional axis is highly intersected. Furthermore, the functional impact of pathogenic mutations of ARX, KDM5C, PHF8 and ZNF711 was tested in lymphoblastoid cell lines (LCLs) derived from children with varying levels of syndromic ID establishing the direct correlation between defects in the KDM5C-H3K4me3 pathway and ID severity. These findings reveal novel insights into epigenetic processes underpinning NDD pathogenesis and provide new avenues for assessing developmental timing and critical windows for potential treatments.
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Affiliation(s)
- Loredana Poeta
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy;
- Department of Science, University of Basilicata, 85100 Potenza, Italy;
- Correspondence: (L.P.); (M.G.M.); Tel.: +39-(0)-816132261/445 (M.G.M.)
| | - Agnese Padula
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy;
| | | | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, 6525 GA Nijmegen, The Netherlands;
| | - Maria Giuseppina Miano
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy;
- Correspondence: (L.P.); (M.G.M.); Tel.: +39-(0)-816132261/445 (M.G.M.)
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40
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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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Cid E, Marquez-Galera A, Valero M, Gal B, Medeiros DC, Navarron CM, Ballesteros-Esteban L, Reig-Viader R, Morales AV, Fernandez-Lamo I, Gomez-Dominguez D, Sato M, Hayashi Y, Bayés À, Barco A, Lopez-Atalaya JP, de la Prida LM. Sublayer- and cell-type-specific neurodegenerative transcriptional trajectories in hippocampal sclerosis. Cell Rep 2021; 35:109229. [PMID: 34107264 DOI: 10.1016/j.celrep.2021.109229] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 03/18/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Hippocampal sclerosis, the major neuropathological hallmark of temporal lobe epilepsy, is characterized by different patterns of neuronal loss. The mechanisms of cell-type-specific vulnerability and their progression and histopathological classification remain controversial. Using single-cell electrophysiology in vivo and immediate-early gene expression, we reveal that superficial CA1 pyramidal neurons are overactive in epileptic rodents. Bulk tissue and single-nucleus expression profiling disclose sublayer-specific transcriptomic signatures and robust microglial pro-inflammatory responses. Transcripts regulating neuronal processes such as voltage channels, synaptic signaling, and cell adhesion are deregulated differently by epilepsy across sublayers, whereas neurodegenerative signatures primarily involve superficial cells. Pseudotime analysis of gene expression in single nuclei and in situ validation reveal separated trajectories from health to epilepsy across cell types and identify a subset of superficial cells undergoing a later stage in neurodegeneration. Our findings indicate that sublayer- and cell-type-specific changes associated with selective CA1 neuronal damage contribute to progression of hippocampal sclerosis.
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Affiliation(s)
- Elena Cid
- Instituto Cajal, CSIC, 28002 Madrid, Spain
| | - Angel Marquez-Galera
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550 Sant Joan d'Alacant, Alicante, Spain
| | | | - Beatriz Gal
- Instituto Cajal, CSIC, 28002 Madrid, Spain; Universidad Europea de Madrid, 28670 Villaviciosa de Odón, Madrid, Spain
| | | | - Carmen M Navarron
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550 Sant Joan d'Alacant, Alicante, Spain
| | | | - Rita Reig-Viader
- Institut d'Investigació Biomèdica San Pau, 08041 Barcelona, Spain; Universitat Autònoma de Barcelona, 08193 Bellaterra, Cerdanyola del Vallès, Spain
| | | | | | | | - Masaaki Sato
- RIKEN Brain Science Institute, Wako, 351-0198 Saitama, Japan
| | - Yasunori Hayashi
- RIKEN Brain Science Institute, Wako, 351-0198 Saitama, Japan; Department of Pharmacology, Kyoto University Graduate School of Medicine, 606-8501 Kyoto, Japan
| | - Àlex Bayés
- Institut d'Investigació Biomèdica San Pau, 08041 Barcelona, Spain; Universitat Autònoma de Barcelona, 08193 Bellaterra, Cerdanyola del Vallès, Spain
| | - Angel Barco
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550 Sant Joan d'Alacant, Alicante, Spain
| | - Jose P Lopez-Atalaya
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550 Sant Joan d'Alacant, Alicante, Spain.
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42
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Petrillo F, Iervolino A, Angrisano T, Jelen S, Costanzo V, D’Acierno M, Cheng L, Wu Q, Guerriero I, Mazzarella MC, De Falco A, D’Angelo F, Ceccarelli M, Caraglia M, Capasso G, Fenton RA, Trepiccione F. Dysregulation of Principal Cell miRNAs Facilitates Epigenetic Regulation of AQP2 and Results in Nephrogenic Diabetes Insipidus. J Am Soc Nephrol 2021; 32:1339-1354. [PMID: 33727367 PMCID: PMC8259636 DOI: 10.1681/asn.2020010031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/02/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs), formed by cleavage of pre-microRNA by the endoribonuclease Dicer, are critical modulators of cell function by post-transcriptionally regulating gene expression. METHODS Selective ablation of Dicer in AQP2-expressing cells (DicerAQP2Cre+ mice) was used to investigate the role of miRNAs in the kidney collecting duct of mice. RESULTS The mice had severe polyuria and nephrogenic diabetes insipidus, potentially due to greatly reduced AQP2 and AQP4 levels. Although epithelial sodium channel levels were decreased in cortex and increased in inner medulla, amiloride-sensitive sodium reabsorption was equivalent in DicerAQP2Cre+ mice and controls. Small-RNA sequencing and proteomic analysis revealed 31 and 178 significantly regulated miRNAs and proteins, respectively. Integrated bioinformatic analysis of the miRNAome and proteome suggested alterations in the epigenetic machinery and various transcription factors regulating AQP2 expression in DicerAQP2Cre+ mice. The expression profile and function of three miRNAs (miR-7688-5p, miR-8114, and miR-409-3p) whose predicted targets were involved in epigenetic control (Phf2, Kdm5c, and Kdm4a) or transcriptional regulation (GATA3, GATA2, and ELF3) of AQP2 were validated. Luciferase assays could not demonstrate direct interaction of AQP2 or the three potential transcription factors with miR-7688-5p, miR-8114, and miR-409-3p. However, transfection of respective miRNA mimics reduced AQP2 expression. Chromatin immunoprecipitation assays demonstrated decreased Phf2 and significantly increased Kdm5c interactions at the Aqp2 gene promoter in DicerAQP2Cre+ mice, resulting in decreased RNA Pol II association. CONCLUSIONS Novel evidence indicates miRNA-mediated epigenetic regulation of AQP2 expression.
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Affiliation(s)
- Federica Petrillo
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Anna Iervolino
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | - Tiziana Angrisano
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Sabina Jelen
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | - Vincenzo Costanzo
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | | | - Lei Cheng
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Qi Wu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Ilaria Guerriero
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | | | - Alfonso De Falco
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | - Fulvio D’Angelo
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy
| | - Michele Ceccarelli
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy,Department of Electrical Engineering and Information Technology (DIETI) University of Naples “Federico II”, Naples, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Giovambattista Capasso
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy,Department of Translational Medical Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Francesco Trepiccione
- Biogem, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino, Italy,Department of Translational Medical Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
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43
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Herrero-Navarro Á, Puche-Aroca L, Moreno-Juan V, Sempere-Ferràndez A, Espinosa A, Susín R, Torres-Masjoan L, Leyva-Díaz E, Karow M, Figueres-Oñate M, López-Mascaraque L, López-Atalaya JP, Berninger B, López-Bendito G. Astrocytes and neurons share region-specific transcriptional signatures that confer regional identity to neuronal reprogramming. SCIENCE ADVANCES 2021; 7:7/15/eabe8978. [PMID: 33827819 PMCID: PMC8026135 DOI: 10.1126/sciadv.abe8978] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/18/2021] [Indexed: 05/15/2023]
Abstract
Neural cell diversity is essential to endow distinct brain regions with specific functions. During development, progenitors within these regions are characterized by specific gene expression programs, contributing to the generation of diversity in postmitotic neurons and astrocytes. While the region-specific molecular diversity of neurons and astrocytes is increasingly understood, whether these cells share region-specific programs remains unknown. Here, we show that in the neocortex and thalamus, neurons and astrocytes express shared region-specific transcriptional and epigenetic signatures. These signatures not only distinguish cells across these two brain regions but are also detected across substructures within regions, such as distinct thalamic nuclei, where clonal analysis reveals the existence of common nucleus-specific progenitors for neurons and astrocytes. Consistent with their shared molecular signature, regional specificity is maintained following astrocyte-to-neuron reprogramming. A detailed understanding of these regional-specific signatures may thus inform strategies for future cell-based brain repair.
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Affiliation(s)
- Álvaro Herrero-Navarro
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Lorenzo Puche-Aroca
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Verónica Moreno-Juan
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Alejandro Sempere-Ferràndez
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Ana Espinosa
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Rafael Susín
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Laia Torres-Masjoan
- Institute of Psychiatry, Psychology, and Neuroscience, Centre for Developmental Neurobiology, and MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL London, UK
| | - Eduardo Leyva-Díaz
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Marisa Karow
- Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany
- Physiological Genomics, Biomedical Center, Ludwig Maximilians University Munich, 82152 Planegg/Munich, Germany
| | | | | | - José P López-Atalaya
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Benedikt Berninger
- Institute of Psychiatry, Psychology, and Neuroscience, Centre for Developmental Neurobiology, and MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL London, UK
- Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Guillermina López-Bendito
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain.
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44
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Sas-Nowosielska H, Magalska A. Long Noncoding RNAs-Crucial Players Organizing the Landscape of the Neuronal Nucleus. Int J Mol Sci 2021; 22:ijms22073478. [PMID: 33801737 PMCID: PMC8037058 DOI: 10.3390/ijms22073478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
The ability to regulate chromatin organization is particularly important in neurons, which dynamically respond to external stimuli. Accumulating evidence shows that lncRNAs play important architectural roles in organizing different nuclear domains like inactive chromosome X, splicing speckles, paraspeckles, and Gomafu nuclear bodies. LncRNAs are abundantly expressed in the nervous system where they may play important roles in compartmentalization of the cell nucleus. In this review we will describe the architectural role of lncRNAs in the nuclei of neuronal cells.
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45
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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: 12] [Impact Index Per Article: 4.0] [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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46
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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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47
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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: 15] [Impact Index Per Article: 5.0] [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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48
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Raznahan A, Disteche CM. X-chromosome regulation and sex differences in brain anatomy. Neurosci Biobehav Rev 2021; 120:28-47. [PMID: 33171144 PMCID: PMC7855816 DOI: 10.1016/j.neubiorev.2020.10.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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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Affiliation(s)
- Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health, Bethesda, MD, 20892, USA.
| | - Christine M Disteche
- Department of Pathology and Medicine, University of Washington, Seattle, WA 98195, USA.
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Pottmeier P, Doszyn O, Peuckert C, Jazin E. Increased Expression of Y-Encoded Demethylases During Differentiation of Human Male Neural Stem Cells. Stem Cells Dev 2020; 29:1497-1509. [PMID: 33040644 DOI: 10.1089/scd.2020.0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human neural stem cells (hNSCs) have long been used as an in vitro model to study neurogenesis and as candidates for nervous system therapy. Many parameters have been considered when evaluating the success of transplantation, but sex of donor and recipients is often not discussed. We investigated two commercial NSC lines, the female hNSC-H9 and male hNSC-H14, and we observed faster growth rates in the male cells. At 4 days of differentiation, male cells presented a significant increase in expression of DCX, an immature neuronal marker, while female cells showed a significant increase in RMST, a long noncoding RNA, which is indispensable during neurogenesis. In addition, expression of neural markers MAP2, PSD95, SYP, DCX, and TUJ1 at day 14 of differentiation suggested a similar differentiation potential in both lines. The most significant differences at day 14 of differentiation were the expression levels of RELN, with almost 100-fold difference between the sexes, and MASH1, with more than 1,000-fold increase in male cells. To evaluate whether some of the observed differences may be sex related, we measured the expression of gametologous genes located on the X- and Y-chromosome. Most noticeable was the increase of Y-encoded demethylases KDM6C (UTY) and KDM5D during differentiation of male cells. Our results indicate that attention should be paid to sex when planning neurogenesis and transplantation experiments.
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Affiliation(s)
- Philipp Pottmeier
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Olga Doszyn
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Christiane Peuckert
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden.,Department of Molecular Biology, Stockholm University, Stockholm, Sweden
| | - Elena Jazin
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
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The PWWP2A Histone Deacetylase Complex Represses Intragenic Spurious Transcription Initiation in mESCs. iScience 2020; 23:101741. [PMID: 33235983 PMCID: PMC7670215 DOI: 10.1016/j.isci.2020.101741] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/22/2020] [Accepted: 10/23/2020] [Indexed: 12/26/2022] Open
Abstract
Transcriptional fidelity depends on accurate promoter selection and initiation from the correct sites. In yeast, H3K36me3-mediated recruitment of the Rpd3S HDAC complex to gene bodies suppresses spurious transcription initiation. Here we describe an equivalent pathway in metazoans. PWWP2A/B is an H3K36me3 reader that forms a stable complex with HDAC1/2. We used CAGE-seq to profile all transcription initiation sites in wild-type mESCs and cells lacking PWWP2A/B. Loss of PWWP2A/B enhances spurious initiation from intragenic sites present in wild-type mESCs, and this effect is associated with increased levels of initiating Pol-II and histone acetylation. Spurious initiation events in Pwwp2a/b DKO mESCs do not overlap in genomic location or chromatin features with spurious sites that arise in Dnmt3b KO mESCs, previously reported to function in the suppression of intragenic transcriptional initiation, suggesting these pathways function cooperatively in maintaining the fidelity of transcription initiation in metazoans. Loss of PWWP2A/B leads to increased levels of spurious transcription initiation Spurious TSS sites are predominantly in the gene bodies of highly expressed genes Spurious sites are marked with increased histone acetylation and initiating Pol II PWWP2-spurious TSSs are distinct from those caused by DNMT3B loss
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