1
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Patty BJ, Hainer SJ. Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589208. [PMID: 38659863 PMCID: PMC11042195 DOI: 10.1101/2024.04.12.589208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs), such as promoters and enhancers, that drive transcription of both mRNAs and CRE-associated non-coding RNAs (ncRNAs). Two classes of CRE-associated ncRNAs include upstream antisense RNAs (uaRNAs), which are transcribed divergently from a shared mRNA promoter, and enhancer RNAs (eRNAs), which are transcribed bidirectionally from active enhancers. The complicated network of CRE regulation by nucleosome remodelers remains only partially explored, with a focus on a select, limited number of remodelers. We endeavored to elucidate a remodeler-based regulatory network governing CRE-associated transcription (mRNA, eRNA, and uaRNA) in murine embryonic stem (ES) cells to test the hypothesis that many SNF2-family nucleosome remodelers collaborate to regulate the coding and non-coding transcriptome via alteration of underlying nucleosome architecture. Using depletion followed by transient transcriptome sequencing (TT-seq), we identified thousands of misregulated mRNAs and CRE-associated ncRNAs across the remodelers examined, identifying novel contributions by understudied remodelers in the regulation of coding and noncoding transcription. Our findings suggest that mRNA and eRNA transcription are coordinately co-regulated, while mRNA and uaRNAs sharing a common promoter are independently regulated. Subsequent mechanistic studies suggest that while remodelers SRCAP and CHD8 modulate transcription through classical mechanisms such as transcription factors and histone variants, a broad set of remodelers including SMARCAL1 indirectly contribute to transcriptional regulation through maintenance of genomic stability and proper Integrator complex localization. This study systematically examines the contribution of SNF2-remodelers to the CRE-associated transcriptome, identifying at least two classes for remodeler action.
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Affiliation(s)
- Benjamin J. Patty
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA USA
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2
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Shan Y, Yao L, Li L, Gao X, Jiang J. A novel CHD7 variant in a chinese family with CHARGE syndrome. Genes Genomics 2024; 46:379-387. [PMID: 37273125 DOI: 10.1007/s13258-023-01411-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/29/2023] [Indexed: 06/06/2023]
Abstract
OBJECTIVE CHARGE syndrome is a rare autosomal dominant (AD) multi-system disorder with a broad and variable clinical manifestation and occurs in approximately 1/10,000 newborns in the world. Mutations in the CHD7 gene are the genetic cause of over 90% of patients with typical CHARGE syndrome. The present study reported a novel variant in the CHD7 gene in a Chinese family with an abnormal fetus. METHODS Routine prenatal ultrasound screening showed fetal heart abnormality and left foot varus. Chromosomal microarray analysis (CMA) and fetus-parent whole-exome sequencing (trio-WES) were performed to determine the genetic cause of the fetus. The candidate variant was further verified using Sanger sequencing. RESULTS CMA analysis revealed normal results. However, WES analysis identified a de novo heterozygous variant of c.2919_2922del (NM_017780.4) on exon 11 of CHD7 gene, resulting in a premature truncation of the CHD7 protein (p.Gly975*). The variant was classified as Pathogenic (PVS1 + PS2_Moderate + PM2_Supporting) based on the ACMG guidelines. Combined with the clinical phenotype of fetal heart abnormalities, it was confirmed CHARGE syndrome. CONCLUSION We identified a novel heterozygous variant c.2919_2922del in CHD7 of a Chinese fetus with CHARGE syndrome, enriching the genotype-phenotype spectrum of CHD7. These results suggest that genetic testing could help facilitate prenatal diagnosis of CHARGE syndrome, thus promoting the appropriate genetic counseling.
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Affiliation(s)
- Yanhong Shan
- Department of Obstetrics, the First Hospital of Jilin University, Changchun, Jilin, 130061, China
| | - LingFang Yao
- Department of Obstetrics, Huangshi love and health hospital, Huangshi, Hubei, 435002, China.
| | - Linli Li
- Department of Obstetrics, the First Hospital of Jilin University, Changchun, Jilin, 130061, China
| | - Xueping Gao
- Yinfeng Gene Technology Co., Ltd, Jinan, Shandong, 250000, China
| | - Jinghan Jiang
- Yinfeng Gene Technology Co., Ltd, Jinan, Shandong, 250000, China
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3
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Gao Y, Wu Q, Wang G, Zhang S, Ma W, Shi X, Liu H, Wu L, Tian X, Li X, Ma X. Histomorphic analysis and expression of mRNA and miRNA in embryonic gonadal differentiation in Chinese soft-shelled turtle (Pelodiscus sinensis). Gene 2024; 893:147913. [PMID: 37866663 DOI: 10.1016/j.gene.2023.147913] [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: 06/27/2023] [Revised: 09/07/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
The Chinese soft-shelled turtle (Pelodiscus sinensis) is extensively cultured in Asia for its nutritional and medical value. Gonadal differentiation is fantastic in turtles, whereas morphologic, mRNA, and miRNA expressions were insufficient in the turtle. In this study, ovaries and testes histomorphology analysis of 14-23 stage embryos were performed, and mRNA and miRNA expression profiles were analyzed. Histomorphology analysis revealed that gonads were undifferentiated at embryonic stage 14. Ovarian morphological differentiation became evident from stage 15, which was characterized by the development of the cortical region and degeneration of the medullary region. Concurrently, testicular morphological differentiation was apparent from stage 15, marked by the development of the medullary region and degeneration of the cortical region. qRT-PCR results showed that Cyp19a1 and Foxl2 exhibited female-specific expression at stage 15 and the expression increased throughout most of the embryonic development. Dmrt1, Amh, and Sox9 displayed male-specific expression at stage 15 and tended to increase substantially at later developmental stages. The expression of miR-8356 and miR-3299 in ZZ gonads were significantly higher than that in ZW gonads at stage 15, 17 and 19, and they had the highest expression at stage 15. While the expression of miR-8085 and miR-7982 had the highest expression at stage 19. Furthermore, chromatin remodeler genes showed differential expression in female and male P. sinensis gonads. These results of master sex-differentiation genes and morphological characteristics would provide a reference for the research of sex differentiation and sex reversal in turtles. Additionally, the expression of chromatin remodeler genes indicated they might be involved in gonadal differentiation of P. sinensis.
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Affiliation(s)
- Yijie Gao
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Qisheng Wu
- Fisheries Research Institute of Fujian, Xiamen 361000, China.
| | - Guiyu Wang
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Shufang Zhang
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Wenge Ma
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Xi Shi
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Huifen Liu
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Limin Wu
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Xue Tian
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Xuejun Li
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Xiao Ma
- College of Fisheries, Henan Normal University, Xinxiang 453007, China.
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4
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Muhammad T, Pastore SF, Good K, Ausió J, Vincent JB. Chromatin gatekeeper and modifier CHD proteins in development, and in autism and other neurological disorders. Psychiatr Genet 2023; 33:213-232. [PMID: 37851134 DOI: 10.1097/ypg.0000000000000353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Chromatin, a protein-DNA complex, is a dynamic structure that stores genetic information within the nucleus and responds to molecular/cellular changes in its structure, providing conditional access to the genetic machinery. ATP-dependent chromatin modifiers regulate access of transcription factors and RNA polymerases to DNA by either "opening" or "closing" the structure of chromatin, and its aberrant regulation leads to a variety of neurodevelopmental disorders. The chromodomain helicase DNA-binding (CHD) proteins are ATP-dependent chromatin modifiers involved in the organization of chromatin structure, act as gatekeepers of genomic access, and deposit histone variants required for gene regulation. In this review, we first discuss the structural and functional domains of the CHD proteins, and their binding sites, and phosphorylation, acetylation, and methylation sites. The conservation of important amino acids in SWItch/sucrose non-fermenting (SWI/SNF) domains, and their protein and mRNA tissue expression profiles are discussed. Next, we convey the important binding partners of CHD proteins, their protein complexes and activities, and their involvements in epigenetic regulation. We also show the ChIP-seq binding dynamics for CHD1, CHD2, CHD4, and CHD7 proteins at promoter regions of histone genes, as well as several genes that are critical for neurodevelopment. The role of CHD proteins in development is also discussed. Finally, this review provides information about CHD protein mutations reported in autism and neurodevelopmental disorders, and their pathogenicity. Overall, this review provides information on the progress of research into CHD proteins, their structural and functional domains, epigenetics, and their role in stem cell, development, and neurological disorders.
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Affiliation(s)
- Tahir Muhammad
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Stephen F Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Katrina Good
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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5
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Shi L, Wang Z, Li Y, Song Z, Yin W, Hu B. Deletion of the chd7 Hinders Oligodendrocyte Progenitor Cell Development and Myelination in Zebrafish. Int J Mol Sci 2023; 24:13535. [PMID: 37686337 PMCID: PMC10488005 DOI: 10.3390/ijms241713535] [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: 08/04/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
CHD7, an encoding ATP-dependent chromodomain helicase DNA-binding protein 7, has been identified as the causative gene involved in CHARGE syndrome (Coloboma of the eye, Heart defects, Atresia choanae, Retardation of growth and/or development, Genital abnormalities and Ear abnormalities). Although studies in rodent models have expanded our understanding of CHD7, its role in oligodendrocyte (OL) differentiation and myelination in zebrafish is still unclear. In this study, we generated a chd7-knockout strain with CRISPR/Cas9 in zebrafish. We observed that knockout (KO) of chd7 intensely impeded the oligodendrocyte progenitor cells' (OPCs) migration and myelin formation due to massive expression of chd7 in oilg2+ cells, which might provoke upregulation of the MAPK signal pathway. Thus, our study demonstrates that chd7 is critical to oligodendrocyte migration and myelination during early development in zebrafish and describes a mechanism potentially associated with CHARGE syndrome.
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Affiliation(s)
- Lingyu Shi
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (L.S.)
| | - Zongyi Wang
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (L.S.)
| | - Yujiao Li
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (L.S.)
| | - Zheng Song
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (L.S.)
| | - Wu Yin
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Bing Hu
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (L.S.)
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
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6
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Bure IV, Nemtsova MV. Mutual Regulation of ncRNAs and Chromatin Remodeling Complexes in Normal and Pathological Conditions. Int J Mol Sci 2023; 24:ijms24097848. [PMID: 37175555 PMCID: PMC10178202 DOI: 10.3390/ijms24097848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Chromatin remodeling is the one of the main epigenetic mechanisms of gene expression regulation both in normal cells and in pathological conditions. In recent years, a growing number of investigations have confirmed that epigenetic regulators are tightly connected and form a comprehensive network of regulatory pathways and feedback loops. Genes encoding protein subunits of chromatin remodeling complexes are often mutated and change their expression in diseases, as well as non-coding RNAs (ncRNAs). Moreover, different mechanisms of their mutual regulation have already been described. Further understanding of these processes may help apply their clinical potential for establishment of the diagnosis, prognosis, and treatment of the diseases. The therapeutic targeting of the chromatin structure has many limitations because of the complexity of its regulation, with the involvement of a large number of genes, proteins, non-coding transcripts, and other intermediary molecules. However, several successful strategies have been proposed to target subunits of chromatin remodeling complexes and genes encoding them, as well as the ncRNAs that regulate the operation of these complexes and direct them to the target gene regions. In our review, we focus on chromatin remodeling complexes and ncRNAs, their mutual regulation, role in cellular processes and potential clinical application.
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Affiliation(s)
- Irina V Bure
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Marina V Nemtsova
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
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7
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Krueger LA, Bills JD, Lim ZY, Skidmore JM, Martin DM, Morris AC. Chromatin remodeler Chd7 regulates photoreceptor development and outer segment length. Exp Eye Res 2023; 226:109299. [PMID: 36343670 PMCID: PMC10354686 DOI: 10.1016/j.exer.2022.109299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/29/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
Mutations in the chromatin remodeling factor CHD7 are the predominant cause of CHARGE syndrome, a congenital disorder that frequently includes ocular coloboma. Although CHD7 is known to be required for proper ocular morphogenesis, its role in retinal development has not been thoroughly investigated. Given that individuals with CHARGE syndrome can experience visual impairment even in the absence of coloboma, a better understanding of CHD7 function in the retina is needed. In this study, we characterized the expression pattern of Chd7 in the developing zebrafish and mouse retina and documented ocular and retinal phenotypes in Chd7 loss-of-function mutants. Zebrafish Chd7 was expressed throughout the retinal neuroepithelium when retinal progenitor cells were actively proliferating, and later in subsets of newly post-mitotic retinal cells. At stages of retinal development when most retinal cell types had terminally differentiated, Chd7 expression remained strong in the ganglion cell layer and in some cells in the inner nuclear layer. Intriguingly, strong expression of Chd7 was also observed in the outer nuclear layer where it was co-expressed with markers of post-mitotic cone and rod photoreceptors. Expression of mouse CHD7 displayed a similar pattern, including expression in the ganglion cells, subsets of inner nuclear layer cells, and in the distal outer nuclear layer as late as P15. Two different mutant chd7 zebrafish lines were characterized for ocular and retinal defects. These mutants displayed microphthalmia, reduced numbers of cone photoreceptors, and truncated rod and cone photoreceptor outer segments. Reduced cone photoreceptor number and abnormal outer segments were also observed in heterozygous Chd7 mutant mice. Taken together, our results in zebrafish and mouse reveal a conserved, previously undescribed role for Chd7 in retinal development and photoreceptor outer segment morphogenesis. Moreover, our work suggests an avenue of future investigation into the pathogenesis of visual system defects in CHARGE syndrome.
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Affiliation(s)
- Laura A Krueger
- Department of Biology, University of Kentucky, Lexington, KY, 40506-0225, USA
| | - Jessica D Bills
- Department of Biology, University of Kentucky, Lexington, KY, 40506-0225, USA
| | - Zun Yi Lim
- Department of Biology, University of Kentucky, Lexington, KY, 40506-0225, USA
| | | | - Donna M Martin
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Ann C Morris
- Department of Biology, University of Kentucky, Lexington, KY, 40506-0225, USA.
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8
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Chromatin remodeler CHD7 targets active enhancer region to regulate cell type-specific gene expression in human neural crest cells. Sci Rep 2022; 12:22648. [PMID: 36587182 PMCID: PMC9805427 DOI: 10.1038/s41598-022-27293-6] [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: 09/13/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023] Open
Abstract
A mutation in the chromatin remodeler chromodomain helicase DNA-binding 7 (CHD7) gene causes the multiple congenital anomaly CHARGE syndrome. The craniofacial anomalies observed in CHARGE syndrome are caused by dysfunctions of neural crest cells (NCCs), which originate from the neural tube. However, the mechanism by which CHD7 regulates the function of human NCCs (hNCCs) remains unclear. We aimed to characterize the cis-regulatory elements governed by CHD7 in hNCCs by analyzing genome-wide ChIP-Seq data and identifying hNCC-specific CHD7-binding profiles. We compared CHD7-binding regions among cell types, including human induced pluripotent stem cells and human neuroepithelial cells, to determine the comprehensive properties of CHD7-binding in hNCCs. Importantly, analysis of the hNCC-specific CHD7-bound region revealed transcription factor AP-2α as a potential co-factor facilitating the cell type-specific transcriptional program in hNCCs. CHD7 was strongly associated with active enhancer regions, permitting the expression of hNCC-specific genes to sustain the function of hNCCs. Our findings reveal the regulatory mechanisms of CHD7 in hNCCs, thus providing additional information regarding the transcriptional programs in hNCCs.
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9
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Balendran V, Ritter KE, Martin DM. Epigenetic mechanisms of inner ear development. Hear Res 2022; 426:108440. [PMID: 35063312 PMCID: PMC9276839 DOI: 10.1016/j.heares.2022.108440] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/21/2021] [Accepted: 01/11/2022] [Indexed: 12/16/2022]
Abstract
Epigenetic factors are critically important for embryonic and postnatal development. Over the past decade, substantial technological advancements have occurred that now permit the study of epigenetic mechanisms that govern all aspects of inner ear development, from otocyst patterning to maturation and maintenance of hair cell stereocilia. In this review, we highlight how three major classes of epigenetic regulation (DNA methylation, histone modification, and chromatin remodeling) are essential for the development of the inner ear. We highlight open avenues for research and discuss how new tools enable the employment of epigenetic factors in regenerative and therapeutic approaches for hearing and balance disorders.
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Affiliation(s)
- Vinodh Balendran
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, United States
| | - K Elaine Ritter
- Department of Pediatrics, Medical Center Drive, University of Michigan Medical School, 8220C MSRB III, 1150 W, Ann Arbor, MI 48109-5652, United States
| | - Donna M Martin
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Pediatrics, Medical Center Drive, University of Michigan Medical School, 8220C MSRB III, 1150 W, Ann Arbor, MI 48109-5652, United States; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States.
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10
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Nie J, Ueda Y, Solivais AJ, Hashino E. CHD7 regulates otic lineage specification and hair cell differentiation in human inner ear organoids. Nat Commun 2022; 13:7053. [PMID: 36396635 PMCID: PMC9672366 DOI: 10.1038/s41467-022-34759-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 11/07/2022] [Indexed: 11/19/2022] Open
Abstract
Mutations in CHD7 cause CHARGE syndrome, affecting multiple organs including the inner ear in humans. We investigate how CHD7 mutations affect inner ear development using human pluripotent stem cell-derived organoids as a model system. We find that loss of CHD7 or its chromatin remodeling activity leads to complete absence of hair cells and supporting cells, which can be explained by dysregulation of key otic development-associated genes in mutant otic progenitors. Further analysis of the mutant otic progenitors suggests that CHD7 can regulate otic genes through a chromatin remodeling-independent mechanism. Results from transcriptome profiling of hair cells reveal disruption of deafness gene expression as a potential underlying mechanism of CHARGE-associated sensorineural hearing loss. Notably, co-differentiating CHD7 knockout and wild-type cells in chimeric organoids partially rescues mutant phenotypes by restoring otherwise severely dysregulated otic genes. Taken together, our results suggest that CHD7 plays a critical role in regulating human otic lineage specification and hair cell differentiation.
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Affiliation(s)
- Jing Nie
- grid.257413.60000 0001 2287 3919Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Yoshitomo Ueda
- grid.257413.60000 0001 2287 3919Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Alexander J. Solivais
- grid.257413.60000 0001 2287 3919Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Eri Hashino
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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11
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Krueger LA, Morris AC. Eyes on CHARGE syndrome: Roles of CHD7 in ocular development. Front Cell Dev Biol 2022; 10:994412. [PMID: 36172288 PMCID: PMC9512043 DOI: 10.3389/fcell.2022.994412] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
The development of the vertebrate visual system involves complex morphogenetic interactions of cells derived from multiple embryonic lineages. Disruptions in this process are associated with structural birth defects such as microphthalmia, anophthalmia, and coloboma (collectively referred to as MAC), and inherited retinal degenerative diseases such as retinitis pigmentosa and allied dystrophies. MAC and retinal degeneration are also observed in systemic congenital malformation syndromes. One important example is CHARGE syndrome, a genetic disorder characterized by coloboma, heart defects, choanal atresia, growth retardation, genital abnormalities, and ear abnormalities. Mutations in the gene encoding Chromodomain helicase DNA binding protein 7 (CHD7) cause the majority of CHARGE syndrome cases. However, the pathogenetic mechanisms that connect loss of CHD7 to the ocular complications observed in CHARGE syndrome have not been identified. In this review, we provide a general overview of ocular development and congenital disorders affecting the eye. This is followed by a comprehensive description of CHARGE syndrome, including discussion of the spectrum of ocular defects that have been described in this disorder. In addition, we discuss the current knowledge of CHD7 function and focus on its contributions to the development of ocular structures. Finally, we discuss outstanding gaps in our knowledge of the role of CHD7 in eye formation, and propose avenues of investigation to further our understanding of how CHD7 activity regulates ocular and retinal development.
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Affiliation(s)
| | - Ann C. Morris
- Department of Biology, University of Kentucky, Lexington, KY, United States
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12
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Jin Y, Liu T, Luo H, Liu Y, Liu D. Targeting Epigenetic Regulatory Enzymes for Cancer Therapeutics: Novel Small-Molecule Epidrug Development. Front Oncol 2022; 12:848221. [PMID: 35419278 PMCID: PMC8995554 DOI: 10.3389/fonc.2022.848221] [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: 01/10/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Dysregulation of the epigenetic enzyme-mediated transcription of oncogenes or tumor suppressor genes is closely associated with the occurrence, progression, and prognosis of tumors. Based on the reversibility of epigenetic mechanisms, small-molecule compounds that target epigenetic regulation have become promising therapeutics. These compounds target epigenetic regulatory enzymes, including DNA methylases, histone modifiers (methylation and acetylation), enzymes that specifically recognize post-translational modifications, chromatin-remodeling enzymes, and post-transcriptional regulators. Few compounds have been used in clinical trials and exhibit certain therapeutic effects. Herein, we summarize the classification and therapeutic roles of compounds that target epigenetic regulatory enzymes in cancer treatment. Finally, we highlight how the natural compounds berberine and ginsenosides can target epigenetic regulatory enzymes to treat cancer.
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Affiliation(s)
- Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Tianjia Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Haoming Luo
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yangyang Liu
- Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Da Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
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13
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Liu C, Xiong Q, Li Q, Lin W, Jiang S, Zhang D, Wang Y, Duan X, Gong P, Kang N. CHD7 regulates bone-fat balance by suppressing PPAR-γ signaling. Nat Commun 2022; 13:1989. [PMID: 35418650 PMCID: PMC9007978 DOI: 10.1038/s41467-022-29633-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 03/23/2022] [Indexed: 02/08/2023] Open
Abstract
Chromodomain helicase DNA-binding protein 7 (CHD7), an ATP-dependent eukaryotic chromatin remodeling enzyme, is essential for the development of organs. The mutation of CHD7 is the main cause of CHARGE syndrome, but its function and mechanism in skeletal system remain unclear. Here, we show conditional knockout of Chd7 in bone marrow mesenchymal stem cells (MSCs) and preosteoblasts leads to a pathological phenotype manifested as low bone mass and severely high marrow adiposity. Mechanistically, we identify enhancement of the peroxisome proliferator-activated receptor (PPAR) signaling in Chd7-deficient MSCs. Loss of Chd7 reduces the restriction of PPAR-γ and then PPAR-γ associates with trimethylated histone H3 at lysine 4 (H3K4me3), which subsequently activates the transcription of downstream adipogenic genes and disrupts the balance between osteogenic and adipogenic differentiation. Our data illustrate the pathological manifestations of Chd7 mutation in MSCs and reveal an epigenetic mechanism in skeletal health and diseases. CHD7 is chromatin remodeler and mutations of CHD7 are the main cause of CHARGE syndrome. Here the authors show that conditional knockout of Chd7 in bone marrow mesenchymal stem cells (MSCs) and pre-osteoblasts leads to a skeletal system development disorder in mice and upregulated PPAR signaling, disrupting the balance between osteogenic and adipogenic differentiation.
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Affiliation(s)
- Caojie Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Qiuchan Xiong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Qiwen Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Weimin Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Shuang Jiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Danting Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Yuan Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Xiaobo Duan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Ping Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China.
| | - Ning Kang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China.
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14
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Wu D, Tan H, Su W, Cheng D, Wang G, Wang J, Ma DA, Dong GM, Sun P. MZF1 mediates oncogene-induced senescence by promoting the transcription of p16 INK4A. Oncogene 2022; 41:414-426. [PMID: 34773072 PMCID: PMC8758531 DOI: 10.1038/s41388-021-02110-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 01/27/2023]
Abstract
Oncogene induced senescence is a tumor suppressing defense mechanism, in which the cell cycle-dependent protein kinase (CDK) inhibitor p16INK4A (encoded by the CDKN2A gene) plays a key role. We previously reported that a transcriptional co-activator chromodomain helicase DNA binding protein 7 (CHD7) mediates oncogenic ras-induced senescence by inducing transcription of the p16INK4A gene. In the current study, we identified myeloid zinc finger 1 (MZF1) as the transcriptional factor that recruits CHD7 to the p16INK4A promoter, where it mediates oncogenic ras-induced p16INK4A transcription and senescence through CHD7, in primary human cells from multiple origins. Moreover, the expression of MZF1 is induced by oncogenic ras in senescent cells through the c-Jun and Ets1 transcriptional factors upon their activation by the Ras-Raf-1-MEK-ERK signaling pathway. In non-small cell lung cancer (NSCLC) and pancreatic adenocarcinoma (PAAD) where activating ras mutations occur frequently, reduced MZF1 expression is observed in tumors, as compared to corresponding normal tissues, and correlates with poor patient survival. Analysis of single cell RNA-sequencing data from PAAD patients revealed that among the tumor cells with normal RB expression levels, those with reduced levels of MZF1 are more likely to express lower p16INK4A levels. These findings have identified novel signaling components in the pathway that mediates induction of the p16INK4A tumor suppressor and the senescence response, and suggested that MZF1 is a potential tumor suppressor in at least some cancer types, the loss of which contributes to the inactivation of the p16INK4A/RB pathway and disruption of senescence in tumor cells with intact RB.
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Affiliation(s)
- Dan Wu
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - Hua Tan
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Weijun Su
- Nankai University School of Medicine, Tianjin, China
| | - Dongmei Cheng
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - Guanwen Wang
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA,Nankai University School of Medicine, Tianjin, China
| | - Juan Wang
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA,Nankai University School of Medicine, Tianjin, China
| | - Ding A. Ma
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - George M. Dong
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - Peiqing Sun
- Department of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-, Salem, NC, 27157, USA.
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15
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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16
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Hsieh FK, Ji F, Damle M, Sadreyev RI, Kingston RE. HERVH-derived lncRNAs negatively regulate chromatin targeting and remodeling mediated by CHD7. Life Sci Alliance 2021; 5:5/1/e202101127. [PMID: 34663690 PMCID: PMC8548210 DOI: 10.26508/lsa.202101127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in CHD7 are diagnostic for human CHARGE syndrome. RNAs expressed from the HERVH repeats modulate CHD7 function providing one mechanism for regulation of differentiation of pluripotent cells. Chd7 encodes an ATP-dependent chromatin remodeler which has been shown to target specific genomic loci and alter local transcription potentially by remodeling chromatin structure. De novo mutations in CHD7 are the major cause of CHARGE syndrome which features multiple developmental defects. We examined whether nuclear RNAs might contribute to its targeting and function and identified a preferential interaction between CHD7 and lncRNAs derived from HERVH loci in pluripotent stem cells. Knockdown of HERVH family lncRNAs using LNAs or knockout of an individual copy of HERVH by CRISPR-Cas9 both resulted in increased binding of CHD7 and increased levels of H3K27ac at a subset of enhancers. Depletion of HERVH family RNAs led to the activation of multiple genes. CHD7 bound HERVH RNA with high affinity but low specificity and this interaction decreased the ability of CHD7 to bind and remodel nucleosomes. We present a model in which HERVH lncRNAs act as a decoy to modulate the dynamics of CHD7 binding to enhancers in pluripotent cells and the activation of numerous genes that might impact the differentiation process.
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Affiliation(s)
- Fu-Kai Hsieh
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Manashree Damle
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA .,Department of Genetics, Harvard Medical School, Boston, MA, USA
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17
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Liu C, Kang N, Guo Y, Gong P. Advances in Chromodomain Helicase DNA-Binding (CHD) Proteins Regulating Stem Cell Differentiation and Human Diseases. Front Cell Dev Biol 2021; 9:710203. [PMID: 34616726 PMCID: PMC8488160 DOI: 10.3389/fcell.2021.710203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Regulation of gene expression is critical for stem cell differentiation, tissue development, and human health maintenance. Recently, epigenetic modifications of histone and chromatin remodeling have been verified as key controllers of gene expression and human diseases. Objective: In this study, we review the role of chromodomain helicase DNA-binding (CHD) proteins in stem cell differentiation, cell fate decision, and several known human developmental disorders and cancers. Conclusion: CHD proteins play a crucial role in stem cell differentiation and human diseases.
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Affiliation(s)
- Caojie Liu
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Ning Kang
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Yuchen Guo
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Ping Gong
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
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18
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Kwan KY, White PM. Understanding the differentiation and epigenetics of cochlear sensory progenitors in pursuit of regeneration. Curr Opin Otolaryngol Head Neck Surg 2021; 29:366-372. [PMID: 34374667 PMCID: PMC8452321 DOI: 10.1097/moo.0000000000000741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PURPOSE OF REVIEW Sensory hair cells (HCs) of the inner ear are responsible for our ability to hear and balance. Loss of these cells results in hearing loss. Stem cell replacement and in situ regeneration have the potential to replace lost HCs. Newly discovered contributions of transcription factor regulatory networks and epigenetic mechanisms in regulating HC differentiation and regeneration are placed into context of the literature. RECENT FINDINGS A wealth of new data has helped to define cochlear sensory progenitors in their developmental trajectories. This includes transcription factor networks, epigenetic manipulations, and cochlear HC subtype specification. SUMMARY Understanding how sensory progenitors differ and how HC subtypes arise will substantially inform efforts in hearing restoration.
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Affiliation(s)
- Kelvin Y. Kwan
- Department of Cell Biology & Neuroscience, Rutgers University, Piscataway, New Jersey
| | - Patricia M. White
- Department of Neuroscience, Ernest J. Del Monte Institute of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
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19
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Reddy NC, Majidi SP, Kong L, Nemera M, Ferguson CJ, Moore M, Goncalves TM, Liu HK, Fitzpatrick JAJ, Zhao G, Yamada T, Bonni A, Gabel HW. CHARGE syndrome protein CHD7 regulates epigenomic activation of enhancers in granule cell precursors and gyrification of the cerebellum. Nat Commun 2021; 12:5702. [PMID: 34588434 PMCID: PMC8481233 DOI: 10.1038/s41467-021-25846-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/01/2021] [Indexed: 12/16/2022] Open
Abstract
Regulation of chromatin plays fundamental roles in the development of the brain. Haploinsufficiency of the chromatin remodeling enzyme CHD7 causes CHARGE syndrome, a genetic disorder that affects the development of the cerebellum. However, how CHD7 controls chromatin states in the cerebellum remains incompletely understood. Using conditional knockout of CHD7 in granule cell precursors in the mouse cerebellum, we find that CHD7 robustly promotes chromatin accessibility, active histone modifications, and RNA polymerase recruitment at enhancers. In vivo profiling of genome architecture reveals that CHD7 concordantly regulates epigenomic modifications associated with enhancer activation and gene expression of topologically-interacting genes. Genome and gene ontology studies show that CHD7-regulated enhancers are associated with genes that control brain tissue morphogenesis. Accordingly, conditional knockout of CHD7 triggers a striking phenotype of cerebellar polymicrogyria, which we have also found in a case of CHARGE syndrome. Finally, we uncover a CHD7-dependent switch in the preferred orientation of granule cell precursor division in the developing cerebellum, providing a potential cellular basis for the cerebellar polymicrogyria phenotype upon loss of CHD7. Collectively, our findings define epigenomic regulation by CHD7 in granule cell precursors and identify abnormal cerebellar patterning upon CHD7 depletion, with potential implications for our understanding of CHARGE syndrome. CHARGE syndrome that affects cerebellar development can be caused by haploinsufficiency of the chromatin remodeling enzyme CHD7; however the precise role of CHD7 remains unknown. Here the authors show CHD7 promotes chromatin accessibility and enhancer activity in granule cell precursors and regulates morphogenesis of the cerebellar cortex, where loss of CHD7 triggers cerebellar polymicrogyria.
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Affiliation(s)
- Naveen C Reddy
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Shahriyar P Majidi
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.,MD-PhD Program, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lingchun Kong
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Mati Nemera
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Cole J Ferguson
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michael Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tassia M Goncalves
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hai-Kun Liu
- Division of Molecular Neurogenetics, DKFZ-ZMBH Alliance, German Cancer Research Center Im Neunheimer Feld 280, 69120, Heidelberg, Germany
| | - James A J Fitzpatrick
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Guoyan Zhao
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tomoko Yamada
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Neurobiology, Northwestern University, Evanston, IL, 60201, USA
| | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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20
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Ufartes R, Grün R, Salinas G, Sitte M, Kahl F, Wong MTY, van Ravenswaaij-Arts CMA, Pauli S. CHARGE syndrome and related disorders: A mechanistic link. Hum Mol Genet 2021; 30:2215-2224. [PMID: 34230955 DOI: 10.1093/hmg/ddab183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
CHARGE syndrome is an autosomal dominant malformation disorder caused by pathogenic variants in the chromatin remodeler CHD7. Affected are craniofacial structures, cranial nerves and multiple organ systems. Depending on the combination of malformations present, its distinction from other congenital disorders can be challenging. To gain a better insight into the regulatory disturbances in CHARGE syndrome, we performed RNA-Seq analysis on blood samples of 19 children with CHARGE syndrome and a confirmed disease-causing CHD7 variant in comparison to healthy control children. Our analysis revealed a distinct CHARGE syndrome pattern with downregulation of genes that are linked to disorders described to mimic the CHARGE phenotype, i.e. KMT2D and KDM6A (Kabuki syndrome), EP300 and CREBBP (Rubinstein-Taybi syndrome) and ARID1A and ARID1B (Coffin-Siris syndrome). Furthermore, by performing protein-protein interaction studies using co-immunoprecipitation, direct yeast-two hybrid and in situ proximity ligation assays, we could demonstrate an interplay between CHD7, KMT2D, KDM6A and EP300. In summary, our data demonstrate a mechanistic and regulatory link between the developmental disorders CHARGE-, Kabuki- and Rubinstein Taybi-syndrome providing an explanation for the overlapping phenotypes.
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Affiliation(s)
- Roser Ufartes
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073 Göttingen, Germany
| | - Regina Grün
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073 Göttingen, Germany
| | - Gabriela Salinas
- NGS Integrative Genomics Core Unit, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Maren Sitte
- NGS Integrative Genomics Core Unit, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Fritz Kahl
- Department of General-, Visceral- and Pediatric Surgery, University Medical Center Goettingen, UMG, Göttingen, Germany
| | - Monica T Y Wong
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
| | - Conny M A van Ravenswaaij-Arts
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
| | - Silke Pauli
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073 Göttingen, Germany
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21
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Lettieri A, Oleari R, Paganoni AJJ, Gervasini C, Massa V, Fantin A, Cariboni A. Semaphorin Regulation by the Chromatin Remodeler CHD7: An Emerging Genetic Interaction Shaping Neural Cells and Neural Crest in Development and Cancer. Front Cell Dev Biol 2021; 9:638674. [PMID: 33869187 PMCID: PMC8047133 DOI: 10.3389/fcell.2021.638674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
CHD7 is a chromatin remodeler protein that controls gene expression via the formation of multi-protein complexes with specific transcription factors. During development, CHD7 controls several differentiation programs, mainly by acting on neural progenitors and neural crest (NC) cells. Thus, its roles range from the central nervous system to the peripheral nervous system and the organs colonized by NC cells, including the heart. Accordingly, mutated CHD7 is linked to CHARGE syndrome, which is characterized by several neuronal dysfunctions and by malformations of NC-derived/populated organs. Altered CHD7 has also been associated with different neoplastic transformations. Interestingly, recent evidence revealed that semaphorins, a class of molecules involved in developmental and pathological processes similar to those controlled by CHD7, are regulated by CHD7 in a context-specific manner. In this article, we will review the recent insights that support the existence of genetic interactions between these pathways, both during developmental processes and cancer progression.
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Affiliation(s)
- Antonella Lettieri
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Roberto Oleari
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Alyssa J J Paganoni
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Cristina Gervasini
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valentina Massa
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Fantin
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Anna Cariboni
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
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22
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Camacho-Ordonez N, Ballestar E, Timmers HTM, Grimbacher B. What can clinical immunology learn from inborn errors of epigenetic regulators? J Allergy Clin Immunol 2021; 147:1602-1618. [PMID: 33609625 DOI: 10.1016/j.jaci.2021.01.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/20/2022]
Abstract
The epigenome is at the interface between environmental factors and the genome, regulating gene transcription, DNA repair, and replication. Epigenetic modifications play a crucial role in establishing and maintaining cell identity and are especially crucial for neurology, musculoskeletal integrity, and the function of the immune system. Mutations in genes encoding for the components of the epigenetic machinery lead to the development of distinct disorders, especially involving the central nervous system and host defense. In this review, we focus on the role of epigenetic modifications for the function of the immune system. By studying the immune phenotype of patients with monogenic mutations in components of the epigenetic machinery (inborn errors of epigenetic regulators), we demonstrate the importance of DNA methylation, histone modifications, chromatin remodeling, noncoding RNAs, and mRNA processing for immunity. Moreover, we give a short overview on therapeutic strategies targeting the epigenome.
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Affiliation(s)
- Nadezhda Camacho-Ordonez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
| | - H Th Marc Timmers
- German Cancer Consortium (DKTK), partner site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Urology, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST- Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany.
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23
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Boyd NH, Tran AN, Bernstock JD, Etminan T, Jones AB, Gillespie GY, Friedman GK, Hjelmeland AB. Glioma stem cells and their roles within the hypoxic tumor microenvironment. Theranostics 2021; 11:665-683. [PMID: 33391498 PMCID: PMC7738846 DOI: 10.7150/thno.41692] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Tumor microenvironments are the result of cellular alterations in cancer that support unrestricted growth and proliferation and result in further modifications in cell behavior, which are critical for tumor progression. Angiogenesis and therapeutic resistance are known to be modulated by hypoxia and other tumor microenvironments, such as acidic stress, both of which are core features of the glioblastoma microenvironment. Hypoxia has also been shown to promote a stem-like state in both non-neoplastic and tumor cells. In glial tumors, glioma stem cells (GSCs) are central in tumor growth, angiogenesis, and therapeutic resistance, and further investigation of the interplay between tumor microenvironments and GSCs is critical to the search for better treatment options for glioblastoma. Accordingly, we summarize the impact of hypoxia and acidic stress on GSC signaling and biologic phenotypes, and potential methods to inhibit these pathways.
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24
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Simpson BN, Khattar D, Saal H, Prada CE, Choo D, Marcheschi L, Wiley S, Hopkin RJ. CHARGE syndrome in the era of molecular diagnosis: Similar outcomes in those without coloboma or choanal atresia. Eur J Med Genet 2020; 64:104103. [PMID: 33189935 DOI: 10.1016/j.ejmg.2020.104103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 11/17/2022]
Abstract
CHARGE syndrome (OMIM 214800) is a condition characterized by multisystem involvement with CHD7 pathogenic mutations leading to disease in the majority of patients. Discovery of the molecular cause of CHARGE unmasked a larger phenotypic spectrum than was previously appreciated. Within our interdisciplinary CHARGE syndrome program, we sought to characterize our CHD7-positive CHARGE cohort without coloboma or choanal atresia, highlighting complications and outcomes. We describe 18 individuals with CHD7-confirmed diagnosis from 15 families. The most sensitive finding in the cohort was temporal bone malformations, present in 13/15 individuals. Individuals had an average of 1.6 major features and 3.3 minor features defined by the Blake et al. guidelines. Despite lack of major features or major malformations, the majority of individuals continued to have difficulties with pneumonia, aspiration, secretion management and motility issues that greatly impacted their lives. Our findings illustrate the need for molecular testing and timely recognition given that the major co-morbidities are frequently experienced by patients with the mildest clinical spectrum of CHARGE syndrome.
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Affiliation(s)
- Brittany N Simpson
- Cincinnati Children's Hospital Medical Center: Division of Human Genetics, United States; Cincinnati Children's Hospital Medical Center: Department of Pediatrics, University of Cincinnati College of Medicine, United States.
| | - Divya Khattar
- Cincinnati Children's Hospital Medical Center: Division of Human Genetics, United States; Cincinnati Children's Hospital Medical Center: Department of Pediatrics, University of Cincinnati College of Medicine, United States
| | - Howard Saal
- Cincinnati Children's Hospital Medical Center: Division of Human Genetics, United States; Cincinnati Children's Hospital Medical Center: Department of Pediatrics, University of Cincinnati College of Medicine, United States
| | - Carlos E Prada
- Cincinnati Children's Hospital Medical Center: Division of Human Genetics, United States; Cincinnati Children's Hospital Medical Center: Department of Pediatrics, University of Cincinnati College of Medicine, United States
| | - Daniel Choo
- Cincinnati Children's Hospital Medical Center, Division of Pediatric Otolaryngology, University of Cincinnati College of Medicine, Department of Otolaryngology Head and Neck Surgery, United States
| | - Lucy Marcheschi
- Cincinnati Children's Hospital Medical Center: Division of Pediatric Otolaryngology, United States
| | - Susan Wiley
- Cincinnati Children's Hospital Medical Center: Division of Developmental and Behavioral Pediatrics, United States
| | - Robert J Hopkin
- Cincinnati Children's Hospital Medical Center: Division of Human Genetics, United States; Cincinnati Children's Hospital Medical Center: Department of Pediatrics, University of Cincinnati College of Medicine, United States
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CHD7 regulates cardiovascular development through ATP-dependent and -independent activities. Proc Natl Acad Sci U S A 2020; 117:28847-28858. [PMID: 33127760 DOI: 10.1073/pnas.2005222117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
CHD7 encodes an ATP-dependent chromatin remodeling factor. Mutation of this gene causes multiple developmental disorders, including CHARGE (Coloboma of the eye, Heart defects, Atresia of the choanae, Retardation of growth/development, Genital abnormalities, and Ear anomalies) syndrome, in which conotruncal anomalies are the most prevalent form of heart defects. How CHD7 regulates conotruncal development remains unclear. In this study, we establish that deletion of Chd7 in neural crest cells (NCCs) causes severe conotruncal defects and perinatal lethality, thus providing mouse genetic evidence demonstrating that CHD7 cell-autonomously regulates cardiac NCC development, thereby clarifying a long-standing controversy in the literature. Using transcriptomic analyses, we show that CHD7 fine-tunes the expression of a gene network that is critical for cardiac NCC development. To gain further molecular insights into gene regulation by CHD7, we performed a protein-protein interaction screen by incubating recombinant CHD7 on a protein array. We find that CHD7 directly interacts with several developmental disorder-mutated proteins including WDR5, a core component of H3K4 methyltransferase complexes. This direct interaction suggested that CHD7 may recruit histone-modifying enzymes to target loci independently of its remodeling functions. We therefore generated a mouse model that harbors an ATPase-deficient allele and demonstrates that mutant CHD7 retains the ability to recruit H3K4 methyltransferase activity to its targets. Thus, our data uncover that CHD7 regulates cardiovascular development through ATP-dependent and -independent activities, shedding light on the etiology of CHD7-related congenital disorders. Importantly, our data also imply that patients carrying a premature stop codon versus missense mutations will likely display different molecular alterations; these patients might therefore require personalized therapeutic interventions.
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Yao H, Hannum DF, Zhai Y, Hill SF, Albanus RD'O, Lou W, Skidmore JM, Sanchez G, Saiakhova A, Bielas SL, Scacheri P, Ljungman M, Parker SCJ, Martin DM. CHD7 promotes neural progenitor differentiation in embryonic stem cells via altered chromatin accessibility and nascent gene expression. Sci Rep 2020; 10:17445. [PMID: 33060836 PMCID: PMC7562747 DOI: 10.1038/s41598-020-74537-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/30/2020] [Indexed: 01/09/2023] Open
Abstract
CHARGE syndrome, a rare multiple congenital anomaly condition, is caused by haploinsufficiency of the chromatin remodeling protein gene CHD7 (Chromodomain helicase DNA binding protein 7). Brain abnormalities and intellectual disability are commonly observed in individuals with CHARGE, and neuronal differentiation is reduced in CHARGE patient-derived iPSCs and conditional knockout mouse brains. However, the mechanisms of CHD7 function in nervous system development are not well understood. In this study, we asked whether CHD7 promotes gene transcription in neural progenitor cells via changes in chromatin accessibility. We used Chd7 null embryonic stem cells (ESCs) derived from Chd7 mutant mouse blastocysts as a tool to investigate roles of CHD7 in neuronal and glial differentiation. Loss of Chd7 significantly reduced neuronal and glial differentiation. Sholl analysis showed that loss of Chd7 impaired neuronal complexity and neurite length in differentiated neurons. Genome-wide studies demonstrated that loss of Chd7 leads to modified chromatin accessibility (ATAC-seq) and differential nascent expression (Bru-Seq) of neural-specific genes. These results suggest that CHD7 acts preferentially to alter chromatin accessibility of key genes during the transition of NPCs to neurons to promote differentiation. Our results form a basis for understanding the cell stage-specific roles for CHD7-mediated chromatin remodeling during cell lineage acquisition.
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Affiliation(s)
- Hui Yao
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA
| | - Douglas F Hannum
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Yiwen Zhai
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA.,Center of Genetic and Prenatal Diagnosis, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sophie F Hill
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA
| | | | - Wenjia Lou
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA
| | - Jennifer M Skidmore
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA
| | - Gilson Sanchez
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Donna M Martin
- Department of Pediatrics, University of Michigan, 8220C MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5652, USA. .,Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
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CHD7 Regulates Osteogenic Differentiation of Human Dental Follicle Cells via PTH1R Signaling. Stem Cells Int 2020; 2020:8882857. [PMID: 33014071 PMCID: PMC7525296 DOI: 10.1155/2020/8882857] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/16/2020] [Accepted: 08/28/2020] [Indexed: 02/05/2023] Open
Abstract
Chromodomain helicase DNA-binding protein 7 (CHD7) is an ATP-dependent chromatin remodeling enzyme, functioning as chromatin reader to conduct epigenetic modification. Its effect on osteogenic differentiation of human dental follicle cells (hDFCs) remains unclear. Here, we show the CHD7 expression increases with osteogenic differentiation. The knockdown of CHD7 impairs the osteogenic ability of hDFCs, characterized by reduced alkaline phosphatase activity and mineralization, and the decreased expression of osteogenesis-related genes. Conversely, the CHD7 overexpression enhances the osteogenic differentiation of hDFCs. Mechanically, RNA-seq analyses revealed the downregulated enrichment of PTH (parathyroid hormone)/PTH1R (parathyroid hormone receptor-1) signaling pathway after CHD7 knockdown. We found the expression of PTH1R positively correlates with CHD7. Importantly, the overexpression of PTH1R in CHD7-knockdown hDFCs partially rescued the impaired osteogenic differentiation. Our research demonstrates that CHD7 regulates the osteogenic differentiation of hDFCs by regulating the transcription of PTH1R.
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28
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Evsen L, Li X, Zhang S, Razin S, Doetzlhofer A. let-7 miRNAs inhibit CHD7 expression and control auditory-sensory progenitor cell behavior in the developing inner ear. Development 2020; 147:147/15/dev183384. [PMID: 32816902 DOI: 10.1242/dev.183384] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 07/07/2020] [Indexed: 11/20/2022]
Abstract
The evolutionarily conserved lethal-7 (let-7) microRNAs (miRNAs) are well-known activators of proliferative quiescence and terminal differentiation. However, in the murine auditory organ, let-7g overexpression delays the differentiation of mechano-sensory hair cells (HCs). To address whether the role of let-7 in auditory-sensory differentiation is conserved among vertebrates, we manipulated let-7 levels within the chicken auditory organ: the basilar papilla. Using a let-7 sponge construct to sequester let-7 miRNAs, we found that endogenous let-7 miRNAs are essential for limiting the self-renewal of HC progenitor cells. Furthermore, let-7b overexpression experiments revealed that, similar to mice, higher than normal let-7 levels slow/delay HC differentiation. Finally, we identify CHD7, a chromatin remodeler, as a candidate for mediating the repressive function of let-7 in HC differentiation and inner ear morphogenesis. Our analysis uncovered an evolutionarily conserved let-7-5p-binding site within the chicken Chd7 gene and its human and murine homologs, and we show that let-7g overexpression in mice limits CHD7 expression in the developing inner ear, retina and brain. Haploinsufficiency of CHD7 in humans causes CHARGE syndrome and attenuation of let-7 function may be an effective method for treating CHD7 deficiency.
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Affiliation(s)
- Lale Evsen
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xiaojun Li
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shuran Zhang
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sharjil Razin
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Angelika Doetzlhofer
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA .,Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Patty BJ, Hainer SJ. Non-Coding RNAs and Nucleosome Remodeling Complexes: An Intricate Regulatory Relationship. BIOLOGY 2020; 9:E213. [PMID: 32784701 PMCID: PMC7465399 DOI: 10.3390/biology9080213] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
Abstract
Eukaryotic genomes are pervasively transcribed, producing both coding and non-coding RNAs (ncRNAs). ncRNAs are diverse and a critical family of biological molecules, yet much remains unknown regarding their functions and mechanisms of regulation. ATP-dependent nucleosome remodeling complexes, in modifying chromatin structure, play an important role in transcriptional regulation. Recent findings show that ncRNAs regulate nucleosome remodeler activities at many levels and that ncRNAs are regulatory targets of nucleosome remodelers. Further, a series of recent screens indicate this network of regulatory interactions is more expansive than previously appreciated. Here, we discuss currently described regulatory interactions between ncRNAs and nucleosome remodelers and contextualize their biological functions.
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Affiliation(s)
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA;
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30
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Xie Y, Chen L. Epigenetic Regulation of Gibberellin Metabolism and Signaling. ACTA ACUST UNITED AC 2020; 61:1912-1918. [DOI: 10.1093/pcp/pcaa101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/08/2020] [Indexed: 12/24/2022]
Abstract
Abstract
The precise regulation of gibberellin (GA) metabolism and signaling is essential for plant development and environmental responses. Epigenetic regulatory mechanisms, such as histone modification, noncoding RNA-mediated regulation, chromatin remodeling and DNA methylation, are emerging as important means of fine-tuning gene expression. Recent studies have significantly improved our understanding of the relationships between epigenetic regulation and GA metabolism and signaling. Here, we summarize the molecular mechanisms by which epigenetic modifications affect GA metabolism and signaling pathways and provide new insight into an unfolding avenue of research related to the epigenetic regulation of GA pathways.
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Affiliation(s)
- Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China
- Department of Genetics, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China
- Department of Genetics, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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31
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Li L, Wang R, Yu Y, Zhang H, Jiang Y, Yang X, Liu R. CHD7 missense variants and clinical characteristics of Chinese males with infertility. Mol Genet Genomic Med 2020; 8:e1372. [PMID: 32573075 PMCID: PMC7503206 DOI: 10.1002/mgg3.1372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 04/30/2020] [Accepted: 05/28/2020] [Indexed: 11/19/2022] Open
Abstract
Background Isolated hypogonadotropic hypogonadism (IHH) and Kallmann syndrome (KS) are rare genetic diseases that cause male infertility. The chromodomain helicase DNA‐binding protein 7 (CHD7) gene is commonly associated with KS and IHH. We speculated that CHD7 variants may be associated with male infertility. Methods Two hundred males with azoospermia and 120 with oligozoospermia were recruited. The patients underwent clinical examination and reproductive hormone testing. A panel of genes including CHD7 and others related to spermatogenic failure was sequenced by targeted‐gene exome sequencing. Results Three patients with severe oligozoospermia had CHD7 variants (a detection rate of 0.94% (3/320)). After prediction software analysis, two of the variants c.3464G>A (p.R1155H) and c.4516G>A (p.G1506S) were predicted to be likely pathogenic. Although predicted to be benign, the variants of c.2824A>G (p.T942A) located in the chromodomain 2 could not be excluded as disease causing. The patients with variants had small testicular volumes. In particular, the testes of the patient with a p.G1506S variant varied in size (left, 8 ml; right, 4.5 ml). Two patients (patients 31 and 120) had low E2 levels and two (patients 83 and 120) had low T levels. Ultimately, these variants were classified as “variants of unknown significant” that may be associated with male infertility. Conclusions There may be a relationship between the CHD7 gene missense variants and male infertility. These variants are easier to find in patients with azoospermia and severe oligospermia whose testosterone levels are decreased.
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Affiliation(s)
- Leilei Li
- Centre for Reproductive Medicine and Prenatal DiagnosisFirst Hospital of Jilin UniversityChangchunChina
| | - Ruixue Wang
- Centre for Reproductive Medicine and Prenatal DiagnosisFirst Hospital of Jilin UniversityChangchunChina
| | - Yang Yu
- Centre for Reproductive Medicine and Prenatal DiagnosisFirst Hospital of Jilin UniversityChangchunChina
| | - Hongguo Zhang
- Centre for Reproductive Medicine and Prenatal DiagnosisFirst Hospital of Jilin UniversityChangchunChina
| | - Yuting Jiang
- Centre for Reproductive Medicine and Prenatal DiagnosisFirst Hospital of Jilin UniversityChangchunChina
| | - Xiao Yang
- Centre for Reproductive Medicine and Prenatal DiagnosisFirst Hospital of Jilin UniversityChangchunChina
| | - Ruizhi Liu
- Centre for Reproductive Medicine and Prenatal DiagnosisFirst Hospital of Jilin UniversityChangchunChina
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32
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Srivastava D, Mahony S. Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194443. [PMID: 31639474 PMCID: PMC7166147 DOI: 10.1016/j.bbagrm.2019.194443] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/21/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022]
Abstract
Transcription factors (TFs) selectively bind distinct sets of sites in different cell types. Such cell type-specific binding specificity is expected to result from interplay between the TF's intrinsic sequence preferences, cooperative interactions with other regulatory proteins, and cell type-specific chromatin landscapes. Cell type-specific TF binding events are highly correlated with patterns of chromatin accessibility and active histone modifications in the same cell type. However, since concurrent chromatin may itself be a consequence of TF binding, chromatin landscapes measured prior to TF activation provide more useful insights into how cell type-specific TF binding events became established in the first place. Here, we review the various sequence and chromatin determinants of cell type-specific TF binding specificity. We identify the current challenges and opportunities associated with computational approaches to characterizing, imputing, and predicting cell type-specific TF binding patterns. We further focus on studies that characterize TF binding in dynamic regulatory settings, and we discuss how these studies are leading to a more complex and nuanced understanding of dynamic protein-DNA binding activities. We propose that TF binding activities at individual sites can be viewed along a two-dimensional continuum of local sequence and chromatin context. Under this view, cell type-specific TF binding activities may result from either strongly favorable sequence features or strongly favorable chromatin context.
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Affiliation(s)
- Divyanshi Srivastava
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America.
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33
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Parras C, Marie C, Zhao C, Lu QR. Chromatin remodelers in oligodendroglia. Glia 2020; 68:1604-1618. [PMID: 32460418 DOI: 10.1002/glia.23837] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 04/09/2020] [Accepted: 04/16/2020] [Indexed: 01/09/2023]
Abstract
Oligodendrocytes, the myelinating cells in the vertebrate central nervous system, produce myelin sheaths to enable saltatory propagation of action potentials. The process of oligodendrocyte myelination entails a stepwise progression from precursor specification to differentiation, which is coordinated by a series of transcriptional and chromatin remodeling events. ATP-dependent chromatin remodeling enzymes, which utilize ATP as an energy source to control chromatin dynamics and regulate the accessibility of chromatin to transcriptional regulators, are critical for oligodendrocyte lineage development and regeneration. In this review, we focus on the latest insights into the spatial and temporal specificity of chromatin remodelers during oligodendrocyte development, myelinogenesis, and regeneration. We will also bring together various plausible mechanisms by which lineage specific transcriptional regulators coordinate with chromatin remodeling factors for programming genomic landscapes to specifically modulate these different processes during developmental myelination and remyelination upon injury.
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Affiliation(s)
- Carlos Parras
- Sorbonne Université, UPMC University Paris 06, Inserm U1127, CNRS UMR 7225, GH Pitié-Salpêtrière, Institut du Cerveau et de la Moelle Épinière, ICM, Paris, France
| | - Corentine Marie
- Sorbonne Université, UPMC University Paris 06, Inserm U1127, CNRS UMR 7225, GH Pitié-Salpêtrière, Institut du Cerveau et de la Moelle Épinière, ICM, Paris, France
| | - Chuntao Zhao
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Qing Richard Lu
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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George A, Cogliati T, Brooks BP. Genetics of syndromic ocular coloboma: CHARGE and COACH syndromes. Exp Eye Res 2020; 193:107940. [PMID: 32032630 DOI: 10.1016/j.exer.2020.107940] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 02/07/2023]
Abstract
Optic fissure closure defects result in uveal coloboma, a potentially blinding condition affecting between 0.5 and 2.6 per 10,000 births that may cause up to 10% of childhood blindness. Uveal coloboma is on a phenotypic continuum with microphthalmia (small eye) and anophthalmia (primordial/no ocular tissue), the so-called MAC spectrum. This review gives a brief overview of the developmental biology behind coloboma and its clinical presentation/spectrum. Special attention will be given to two prominent, syndromic forms of coloboma, namely, CHARGE (Coloboma, Heart defect, Atresia choanae, Retarded growth and development, Genital hypoplasia, and Ear anomalies/deafness) and COACH (Cerebellar vermis hypoplasia, Oligophrenia, Ataxia, Coloboma, and Hepatic fibrosis) syndromes. Approaches employed to identify genes involved in optic fissure closure in animal models and recent advances in live imaging of zebrafish eye development are also discussed.
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Affiliation(s)
- Aman George
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA
| | - Tiziana Cogliati
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA.
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Small Molecules Targeting the Specific Domains of Histone-Mark Readers in Cancer Therapy. Molecules 2020; 25:molecules25030578. [PMID: 32013155 PMCID: PMC7037402 DOI: 10.3390/molecules25030578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
Epigenetic modifications (or epigenetic tags) on DNA and histones not only alter the chromatin structure, but also provide a recognition platform for subsequent protein recruitment and enable them to acquire executive instructions to carry out specific intracellular biological processes. In cells, different epigenetic-tags on DNA and histones are often recognized by the specific domains in proteins (readers), such as bromodomain (BRD), chromodomain (CHD), plant homeodomain (PHD), Tudor domain, Pro-Trp-Trp-Pro (PWWP) domain and malignant brain tumor (MBT) domain. Recent accumulating data reveal that abnormal intracellular histone modifications (histone marks) caused by tumors can be modulated by small molecule-mediated changes in the activity of the above domains, suggesting that small molecules targeting histone-mark reader domains may be the trend of new anticancer drug development. Here, we summarize the protein domains involved in histone-mark recognition, and introduce recent research findings about small molecules targeting histone-mark readers in cancer therapy.
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Gervais L, van den Beek M, Josserand M, Sallé J, Stefanutti M, Perdigoto CN, Skorski P, Mazouni K, Marshall OJ, Brand AH, Schweisguth F, Bardin AJ. Stem Cell Proliferation Is Kept in Check by the Chromatin Regulators Kismet/CHD7/CHD8 and Trr/MLL3/4. Dev Cell 2020; 49:556-573.e6. [PMID: 31112698 PMCID: PMC6547167 DOI: 10.1016/j.devcel.2019.04.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/15/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022]
Abstract
Chromatin remodeling accompanies differentiation, however, its role in self-renewal is less well understood. We report that in Drosophila, the chromatin remodeler Kismet/CHD7/CHD8 limits intestinal stem cell (ISC) number and proliferation without affecting differentiation. Stem-cell-specific whole-genome profiling of Kismet revealed its enrichment at transcriptionally active regions bound by RNA polymerase II and Brahma, its recruitment to the transcription start site of activated genes and developmental enhancers and its depletion from regions bound by Polycomb, Histone H1, and heterochromatin Protein 1. We demonstrate that the Trithorax-related/MLL3/4 chromatin modifier regulates ISC proliferation, colocalizes extensively with Kismet throughout the ISC genome, and co-regulates genes in ISCs, including Cbl, a negative regulator of Epidermal Growth Factor Receptor (EGFR). Loss of kismet or trr leads to elevated levels of EGFR protein and signaling, thereby promoting ISC self-renewal. We propose that Kismet with Trr establishes a chromatin state that limits EGFR proliferative signaling, preventing tumor-like stem cell overgrowths. Chromatin modifiers Kismet and Trr limit intestinal stem cell proliferation Kismet and Trr colocalize at transcriptionally active regions and co-regulate genes EGFR negative regulator Cbl is a target gene of Kismet and Trr Kismet and Trr limit EGFR signaling in ISCs, preventing tumor-like ISC accumulation
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Affiliation(s)
- Louis Gervais
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, Paris, France; Sorbonne Universités, UPMC Univ Paris 6, Paris, France.
| | - Marius van den Beek
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, Paris, France; Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - Manon Josserand
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, Paris, France; Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - Jérémy Sallé
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, Paris, France; Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - Marine Stefanutti
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, Paris, France; Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - Carolina N Perdigoto
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, Paris, France; Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - Patricia Skorski
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, Paris, France; Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - Khallil Mazouni
- Institut Pasteur, Department of Developmental and Stem Cell Biology, Paris 75015, France; CNRS, URA2578, Rue du Dr Roux, Paris 75015, France
| | - Owen J Marshall
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 1QN, UK; Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street Hobart, Tasmania, 7000, Australia
| | - Andrea H Brand
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 1QN, UK
| | - François Schweisguth
- Institut Pasteur, Department of Developmental and Stem Cell Biology, Paris 75015, France; CNRS, URA2578, Rue du Dr Roux, Paris 75015, France
| | - Allison J Bardin
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, Paris, France; Sorbonne Universités, UPMC Univ Paris 6, Paris, France.
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Meisner JK, Martin DM. Congenital heart defects in CHARGE: The molecular role of CHD7 and effects on cardiac phenotype and clinical outcomes. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 184:81-89. [PMID: 31833191 DOI: 10.1002/ajmg.c.31761] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023]
Abstract
CHARGE syndrome is characterized by a pattern of congenital anomalies (Coloboma of the eye, Heart defects, Atresia of the choanae, Retardation of growth, Genital abnormalities, and Ear abnormalities). De novo mutations of chromodomain helicase DNA binding protein 7 (CHD7) are the primary cause of CHARGE syndrome. The clinical phenotype is highly variable including a wide spectrum of congenital heart defects. Here, we review the range of congenital heart defects and the molecular effects of CHD7 on cardiovascular development that lead to an over-representation of atrioventricular septal, conotruncal, and aortic arch defects in CHARGE syndrome. Further, we review the overlap of cardiovascular and noncardiovascular comorbidities present in CHARGE and their impact on the peri-operative morbidity and mortality in individuals with CHARGE syndrome.
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Affiliation(s)
- Joshua K Meisner
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Donna M Martin
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
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A functional assay to study the pathogenicity of CHD7 protein variants encountered in CHARGE syndrome patients. Eur J Hum Genet 2019; 27:1683-1691. [PMID: 31289371 DOI: 10.1038/s41431-019-0465-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 06/04/2019] [Accepted: 06/25/2019] [Indexed: 11/08/2022] Open
Abstract
CHARGE syndrome is a rare genetic disease characterized by numerous congenital abnormalities, mainly caused by de novo alterations of the CHD7 gene. It encodes a chromodomain protein, involved in the ATP-dependent remodeling of chromatin. The vast majority of CHD7 alterations consists in null alleles like deletions, nonsense substitutions or frameshift-causing variations. The aim of this study was to develop a biological test of CHD7 protein, to study the impact upon protein functionality of rare allelic variants in the CHD7 gene that elicits changes in the amino acid sequence. Using an expression vector encoding CHD7, three amino acid substitutions and one five-amino acid insertion were generated via site-directed mutagenesis. Then CHD7 proteins, either wild-type (WT) or variants, were overexpressed in HeLa cell line. Protein expression was highlighted by western blot and immunofluorescence. We then used real-time RT-PCR to study CHD7 functionality by evaluating the transcript amounts of five genes whose expression is regulated by CHD7 according to the literature. These reporter genes are 45S rDNA, SOX4, SOX10, ID2, and MYRF. We observed that, upon WT-CHD7 expression, the reporter gene transcriptions were downregulated, whereas the four variant alleles of CHD7 had no impact. This suggests that these alleles are not polymorphisms because the variant proteins appeared nonfunctional. Therefore, these variations can be considered as disease-causing of CHARGE syndrome.
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Investigating the structural features of chromodomain proteins in the human genome and predictive impacts of their mutations in cancers. Int J Biol Macromol 2019; 131:1101-1116. [PMID: 30917913 DOI: 10.1016/j.ijbiomac.2019.03.162] [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: 01/15/2019] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 11/22/2022]
Abstract
Epigenetic readers are specific proteins which recognize histone marks and represents the underlying mechanism for chromatin regulation. Histone H3 lysine methylation is a potential epigenetic code for the chromatin organization and transcriptional control. Recognition of histone methylation is achieved by evolutionary conserved reader modules known as chromodomain, identified in several proteins, and is involved in transcriptional silencing and chromatin remodelling. Genetic perturbations within the structurally conserved chromodomain could potentially mistarget the reader protein and impair their regulatory pathways, ultimately leading to cellular chaos by setting the stage for tumor development and progression. Here, we report the structural conservations associated with diverse functions, prognostic significance and functional consequences of mutations within chromodomain of human proteins in distinct cancers. We have extensively analysed chromodomain containing human proteins in terms of their structural-functional ability to act as a molecular switch in the recognition of methyl-lysine recognition. We further investigated the combinatorial potential, target promiscuity and binding specificity associated with their underlying mechanisms. Indeed, the molecular mechanism of epigenetic silencing significantly underlies a newer cancer therapy approach. We hope that a critical understanding of chromodomains will pave the way for novel paths of research providing newer insights into the designing of effective anti-cancer therapies.
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Chen X, Yan K, Gao Y, Wang H, Chen G, Wu B, Qin Q, Yang L, Zhou W. Feeding difficulty is the dominant feature in 12 Chinese newborns with CHD7 pathogenic variants. BMC MEDICAL GENETICS 2019; 20:93. [PMID: 31146700 PMCID: PMC6543684 DOI: 10.1186/s12881-019-0813-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/23/2019] [Indexed: 11/10/2022]
Abstract
Background CHARGE syndrome is characterized by coloboma, heart defects, choanal atresia, growth retardation, genitourinary malformation and ear abnormalities. The chromodomain helicase DNA-binding protein 7 (CHD7) gene is the major cause of CHARGE syndrome and is inherited in an autosomal dominant manner. Currently, the phenotype spectrum of CHARGE syndrome in neonatal population remain elusive. We aimed to investigate the phenotype spectrum of neonatal patients suspected to have CHARGE syndrome with pathogenic or likely pathogenic variants in the CHD7 gene. Methods We pooled next-generation sequencing data from the Neonatal Birth Defects Cohort (NBDC, ClinicalTrials.gov Identifier: NCT02551081) in Children’s Hospital of Fudan University. The pathogenicity of novel variants was analyzed by bioinformatic and genetic analyses. Clinical information collection, Sanger sequencing and follow-up interviews were performed when possible. Cranial MRI of these patients was performed, the volumes of different regions of the brain were analyzed. Results A total of 12 unrelated patients in our cohort were found with CHD7 variants. Eight patients received a firm clinical diagnosis of CHARGE syndrome (Bergmann criteria, Blake criteria, Verloes criteria and Hale criteria). Three patients did not match any diagnostic criteria, and no patients matched the Verloes criteria. Phenotype spectrum analysis found that feeding difficulty was the dominant feature among this neonatal cohort. Six novel variants in the CHD7 gene (Glu2408*, Lys651*, c.5607 + 1G > T, Leu373Val, Lys2005Asnfs*37 and Gln1991*) were identified, expanding the variant database of the CHD7 gene. Cranial MRI analysis revealed significant volume loss in cingulate gyrus, occipital lobe, and cerebellum and volume gain in the left medial and inferior temporal gyri anterior white matter parts. Conclusions Based on a relatively unbiased neonatal cohort, we concluded that CHARGE syndrome and CHD7 gene variants should be suspected in newborns who have feeding difficulty, and one or more malformations. Trial registration Neonatal Birth Defects Cohort (NBDC, ClinicalTrials.gov identifier: NCT02551081). Electronic supplementary material The online version of this article (10.1186/s12881-019-0813-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiang Chen
- Departments of Neonatology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Kai Yan
- Departments of Neonatology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yanyan Gao
- Ultrasonography Unit, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Huijun Wang
- Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Guoqiang Chen
- Departments of Neonatology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Bingbing Wu
- Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Qian Qin
- Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China.
| | - Lin Yang
- Departments of Endocrinology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China.
| | - Wenhao Zhou
- Departments of Neonatology, Children's Hospital of Fudan University, Shanghai, 201102, China.,Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
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41
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Goodman JV, Bonni A. Regulation of neuronal connectivity in the mammalian brain by chromatin remodeling. Curr Opin Neurobiol 2019; 59:59-68. [PMID: 31146125 DOI: 10.1016/j.conb.2019.04.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/22/2019] [Indexed: 10/26/2022]
Abstract
Precise temporal and spatial control of gene expression is essential for brain development. Besides DNA sequence-specific transcription factors, epigenetic factors play an integral role in the control of gene expression in neurons. Among epigenetic mechanisms, chromatin remodeling enzymes have emerged as essential to the control of neural circuit assembly and function in the brain. Here, we review recent studies on the roles and mechanisms of the chromodomain-helicase-DNA-binding (Chd) family of chromatin remodeling enzymes in the regulation of neuronal morphogenesis and connectivity in the mammalian brain. We explore the field through the lens of Chd3, Chd4, and Chd5 proteins, which incorporate into the nucleosome remodeling and deacetylase (NuRD) complex, and the related proteins Chd7 and Chd8, implicated in the pathogenesis of intellectual disability and autism spectrum disorders. These studies have advanced our understanding of the mechanisms that regulate neuronal connectivity in brain development and neurodevelopmental disorders of cognition.
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Affiliation(s)
- Jared V Goodman
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA; Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, USA
| | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA.
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The Drosophila Chromodomain Protein Kismet Activates Steroid Hormone Receptor Transcription to Govern Axon Pruning and Memory In Vivo. iScience 2019; 16:79-93. [PMID: 31153043 PMCID: PMC6543131 DOI: 10.1016/j.isci.2019.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/08/2019] [Accepted: 05/13/2019] [Indexed: 11/23/2022] Open
Abstract
Axon pruning is critical for sculpting precise neural circuits. Although axon pruning has been described in the literature for decades, relatively little is known about the molecular and cellular mechanisms that govern axon pruning in vivo. Here, we show that the epigenetic reader Kismet (Kis) is required for developmental axon pruning in Drosophila mushroom bodies. Kis binds to cis-regulatory elements of the steroid hormone receptor ecdysone receptor (ecr) gene and is necessary for activating expression of EcR-B1. Kis promotes the active H3K36 di- and tri-methylation and H4K16 acetylation histone marks at the ecr locus. We show that transgenic EcR-B1 can rescue axon pruning and memory defects associated with loss of Kis and that the histone deacetylase inhibitor SAHA also rescues these phenotypes. EcR protein abundance is the cell-autonomous, rate-limiting step required to initiate axon pruning in Drosophila, and our data suggest this step is under the epigenetic control of Kis.
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43
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Asad Z, Sachidanandan C. Chemical screens in a zebrafish model of CHARGE syndrome identifies small molecules that ameliorate disease-like phenotypes in embryo. Eur J Med Genet 2019; 63:103661. [PMID: 31051269 DOI: 10.1016/j.ejmg.2019.04.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/09/2019] [Accepted: 04/28/2019] [Indexed: 01/03/2023]
Abstract
CHARGE syndrome is an autosomal dominant congenital disorder caused primarily by mutations in the CHD7 gene. Using a small molecule screen in a zebrafish model of CHARGE syndrome, we identified 4 compounds that rescue embryos from disease-like phenotypes. Our screen yielded DAPT, a Notch signaling inhibitor that could ameliorate the craniofacial, cranial neuronal and myelination defects in chd7 morphant zebrafish embryos. We discovered that Procainamide, an inhibitor of DNA methyltransferase 1, was able to recover the pattern of expression of isl2a, a cranial neuronal marker while also reducing the effect on craniofacial cartilage and myelination. M344, an inhibitor of Histone deacetylases had a strong recovery effect on craniofacial cartilage defects and could also modestly revert the myelination defects in zebrafish embryos. CHIC-35, a SIRT1 inhibitor partially restored the expression of isl2a in cranial neurons while causing a partial reversion of myelination and craniofacial cartilage defects. Our results suggest that a modular approach to phenotypic rescue in multi-organ syndromes might be a more successful approach to treat these disorders. Our findings also open up the possibility of using these compounds for other disorders with shared phenotypes.
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Affiliation(s)
- Zainab Asad
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Chetana Sachidanandan
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
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Machado RAC, Schneider H, DeOcesano-Pereira C, Lichtenstein F, Andrade F, Fujita A, Trombetta-Lima M, Weller M, Bowman-Colin C, Sogayar MC. CHD7 promotes glioblastoma cell motility and invasiveness through transcriptional modulation of an invasion signature. Sci Rep 2019; 9:3952. [PMID: 30850678 PMCID: PMC6408455 DOI: 10.1038/s41598-019-39564-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/10/2019] [Indexed: 01/21/2023] Open
Abstract
Chromatin remodeler proteins exert an important function in promoting dynamic modifications in the chromatin architecture, performing a central role in regulating gene transcription. Deregulation of these molecular machines may lead to striking perturbations in normal cell function. The CHD7 gene is a member of the chromodomain helicase DNA-binding family and, when mutated, has been shown to be the cause of the CHARGE syndrome, a severe developmental human disorder. Moreover, CHD7 has been described to be essential for neural stem cells and it is also highly expressed or mutated in a number of human cancers. However, its potential role in glioblastoma has not yet been tested. Here, we show that CHD7 is up-regulated in human glioma tissues and we demonstrate that CHD7 knockout (KO) in LN-229 glioblastoma cells suppresses anchorage-independent growth and spheroid invasion in vitro. Additionally, CHD7 KO impairs tumor growth and increases overall survival in an orthotopic mouse xenograft model. Conversely, ectopic overexpression of CHD7 in LN-428 and A172 glioblastoma cell lines increases cell motility and invasiveness in vitro and promotes LN-428 tumor growth in vivo. Finally, RNA-seq analysis revealed that CHD7 modulates a specific transcriptional signature of invasion-related target genes. Further studies should explore clinical-translational implications for glioblastoma treatment.
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Affiliation(s)
- Raquel A C Machado
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo 05508-000 SP, Brazil.,Cell and Molecular Therapy Center (NUCEL), Internal Medicine Department, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil
| | - Hannah Schneider
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Carlos DeOcesano-Pereira
- Cell and Molecular Therapy Center (NUCEL), Internal Medicine Department, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil.,Centre of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, SP, Brazil
| | - Flavio Lichtenstein
- Centre of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, SP, Brazil
| | - Fernando Andrade
- Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | - André Fujita
- Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | - Marina Trombetta-Lima
- Cell and Molecular Therapy Center (NUCEL), Internal Medicine Department, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil
| | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Christian Bowman-Colin
- Cell and Molecular Therapy Center (NUCEL), Internal Medicine Department, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil. .,Dana Farber Cancer Institute, Harvard Medical School, 1 Jimmi Fund Way - SM808, Boston, MA, USA.
| | - Mari Cleide Sogayar
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo 05508-000 SP, Brazil. .,Cell and Molecular Therapy Center (NUCEL), Internal Medicine Department, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil.
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45
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Boyd NH, Walker K, Ayokanmbi A, Gordon ER, Whetsel J, Smith CM, Sanchez RG, Lubin FD, Chakraborty A, Tran AN, Herting C, Hambardzumyan D, Yancey Gillespie G, Hackney JR, Cooper SJ, Jiao K, Hjelmeland AB. Chromodomain Helicase DNA-Binding Protein 7 Is Suppressed in the Perinecrotic/Ischemic Microenvironment and Is a Novel Regulator of Glioblastoma Angiogenesis. Stem Cells 2019; 37:453-462. [PMID: 30629778 DOI: 10.1002/stem.2969] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 09/20/2018] [Accepted: 09/30/2018] [Indexed: 11/11/2022]
Abstract
Tumorigenic and non-neoplastic tissue injury occurs via the ischemic microenvironment defined by low oxygen, pH, and nutrients due to blood supply malfunction. Ischemic conditions exist within regions of pseudopalisading necrosis, a pathological hallmark of glioblastoma (GBM), the most common primary malignant brain tumor in adults. To recapitulate the physiologic microenvironment found in GBM tumors and tissue injury, we developed an in vitro ischemic model and identified chromodomain helicase DNA-binding protein 7 (CHD7) as a novel ischemia-regulated gene. Point mutations in the CHD7 gene are causal in CHARGE syndrome (a developmental disorder causing coloboma, heart defects, atresia choanae, retardation of growth, and genital and ear anomalies) and interrupt the epigenetic functions of CHD7 in regulating neural stem cell maintenance and development. Using our ischemic system, we observed microenvironment-mediated decreases in CHD7 expression in brain tumor-initiating cells and neural stem cells. Validating our approach, CHD7 was suppressed in the perinecrotic niche of GBM patient and xenograft sections, and an interrogation of patient gene expression datasets determined correlations of low CHD7 with increasing glioma grade and worse patient outcomes. Segregation of GBM by molecular subtype revealed a novel observation that CHD7 expression is elevated in proneural versus mesenchymal GBM. Genetic targeting of CHD7 and subsequent gene ontology analysis of RNA sequencing data indicated angiogenesis as a primary biological function affected by CHD7 expression changes. We validated this finding in tube-formation assays and vessel formation in orthotopic GBM models. Together, our data provide further understanding of molecular responses to ischemia and a novel function of CHD7 in regulating angiogenesis in both neoplastic and non-neoplastic systems. Stem Cells 2019;37:453-462.
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Affiliation(s)
- Nathaniel H Boyd
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kiera Walker
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Adetokunbo Ayokanmbi
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Emily R Gordon
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Julia Whetsel
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Cynthia M Smith
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Richard G Sanchez
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Asmi Chakraborty
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Anh Nhat Tran
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Cameron Herting
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | | | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - James R Hackney
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Kai Jiao
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Anita B Hjelmeland
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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46
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Moore-Morris T, van Vliet PP, Andelfinger G, Puceat M. Role of Epigenetics in Cardiac Development and Congenital Diseases. Physiol Rev 2019; 98:2453-2475. [PMID: 30156497 DOI: 10.1152/physrev.00048.2017] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The heart is the first organ to be functional in the fetus. Heart formation is a complex morphogenetic process regulated by both genetic and epigenetic mechanisms. Congenital heart diseases (CHD) are the most prominent congenital diseases. Genetics is not sufficient to explain these diseases or the impact of them on patients. Epigenetics is more and more emerging as a basis for cardiac malformations. This review brings the essential knowledge on cardiac biology of development. It further provides a broad background on epigenetics with a focus on three-dimensional conformation of chromatin. Then, we summarize the current knowledge of the impact of epigenetics on cardiac cell fate decision. We further provide an update on the epigenetic anomalies in the genesis of CHD.
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Affiliation(s)
- Thomas Moore-Morris
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Patrick Piet van Vliet
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Gregor Andelfinger
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Michel Puceat
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
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47
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The Role of Nucleosomes in Epigenetic Gene Regulation. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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48
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Khatua S, Song A, Citla Sridhar D, Mack SC. Childhood Medulloblastoma: Current Therapies, Emerging Molecular Landscape and Newer Therapeutic Insights. Curr Neuropharmacol 2018; 16:1045-1058. [PMID: 29189165 PMCID: PMC6120114 DOI: 10.2174/1570159x15666171129111324] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 11/06/2017] [Accepted: 11/27/2017] [Indexed: 12/21/2022] Open
Abstract
Background: Medulloblastoma is the most common malignant brain tumor in children, currently treated uniformly based on histopathology and clinico-radiological risk stratification leading to unpredictable relapses and therapeutic failures. Identification of molecular subgroups have thrown light on the reasons for these and now reveals clues to profile molecularly based personalized therapy against these tumors. Methods: Research and online contents were evaluated for pediatric medulloblastoma which included latest information on the molecular subgroups and their clinical relevance and update on efforts to translate them into clinics. Results: Scientific endeavors over the last decade have clearly identified four molecular variants (WNT, SHH, Group 3, and Group 4) and their demographic, genomic, and epigenetic profile. Latest revelations include significant heterogeneity within these subgroups and 12 different subtypes of MB are now identified with disparate outcomes and biology. These findings have important implications for stratification and profiling future clinical trials against these formidable tumors. Conclusion: With the continued outpouring of genomic/epigenomic data of these molecular subgroups and evolution of further subtypes in each subgroup, the challenge lies in comprehensive evaluation of these informations. Current and future endeavors are now needed to profile personalized therapy for each child based on the molecular risk stratification of medulloblastoma, with a hope to improve survival outcome and reduce relapses.
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Affiliation(s)
- Soumen Khatua
- Department of Pediatrics, MD Anderson Cancer Center, The University of Texas Health Science Center at Houston, Pediatrics Houston, Texas, United States
| | - Anne Song
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, The University of Texas Health Science Center at Houston, Pediatrics Houston, Texas, United States
| | - Divyaswathi Citla Sridhar
- Department of Pediatrics, The University of Texas Health Science Center at Houston, Pediatrics Houston, Texas, United States
| | - Stephen C Mack
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, The University of Texas Health Science Center at Houston, Pediatrics Houston, Texas, United States
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49
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Oligodendrocyte precursor survival and differentiation requires chromatin remodeling by Chd7 and Chd8. Proc Natl Acad Sci U S A 2018; 115:E8246-E8255. [PMID: 30108144 PMCID: PMC6126750 DOI: 10.1073/pnas.1802620115] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Oligodendrocyte precursor cells (OPCs) constitute the main proliferative cells in the adult brain and deregulation of OPC proliferation-differentiation balance results in either glioma formation or defective (re)myelination. Mutations in chromatin remodelers CHD7 and CHD8 are the cause of CHARGE syndrome and some autism spectrum disorders (ASD). Here we show that Chd7 protects OPCs from apoptosis by chromatin closing and gene repression of p53, while Chd7 induces chromatin opening and gene activation of OPC-differentiation regulators. Chd7 is, however, dispensable for oligodendrocyte stage progression, consistent with Chd8 compensatory function, as suggested by their common chromatin-binding profiles, including ASD-risk–associated genes. Our results thus involve oligodendroglia in ASD and CHARGE and offer new avenues to understand and modulate CHD7/CHD8 functions in normal and pathological brain development. Oligodendrocyte precursor cells (OPCs) constitute the main proliferative cells in the adult brain, and deregulation of OPC proliferation-differentiation balance results in either glioma formation or defective adaptive (re)myelination. OPC differentiation requires significant genetic reprogramming, implicating chromatin remodeling. Mounting evidence indicates that chromatin remodelers play important roles during normal development and their mutations are associated with neurodevelopmental defects, with CHD7 haploinsuficiency being the cause of CHARGE syndrome and CHD8 being one of the strongest autism spectrum disorder (ASD) high-risk–associated genes. Herein, we report on uncharacterized functions of the chromatin remodelers Chd7 and Chd8 in OPCs. Their OPC-chromatin binding profile, combined with transcriptome and chromatin accessibility analyses of Chd7-deleted OPCs, demonstrates that Chd7 protects nonproliferative OPCs from apoptosis by chromatin closing and transcriptional repression of p53. Furthermore, Chd7 controls OPC differentiation through chromatin opening and transcriptional activation of key regulators, including Sox10, Nkx2.2, and Gpr17. However, Chd7 is dispensable for oligodendrocyte stage progression, consistent with Chd8 compensatory function, as suggested by their common chromatin-binding profiles and genetic interaction. Finally, CHD7 and CHD8 bind in OPCs to a majority of ASD risk-associated genes, suggesting an implication of oligodendrocyte lineage cells in ASD neurological defects. Our results thus offer new avenues to understand and modulate the CHD7 and CHD8 functions in normal development and disease.
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Su W, Hong L, Xu X, Huang S, Herpai D, Li L, Xu Y, Truong L, Hu WY, Wu X, Xiao C, Zhang W, Han J, Debinski W, Xiang R, Sun P. miR-30 disrupts senescence and promotes cancer by targeting both p16 INK4A and DNA damage pathways. Oncogene 2018; 37:5618-5632. [PMID: 29907771 PMCID: PMC6195819 DOI: 10.1038/s41388-018-0358-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/07/2018] [Accepted: 05/21/2018] [Indexed: 11/12/2022]
Abstract
miR-30 is a microRNA frequently overexpressed in human cancers. However, the biological consequence of miR-30 overexpression in cancer has been unclear. In a genetic screen, miR-30 was found to abrogate oncogenic-induced senescence, a key tumor-suppressing mechanism that involves DNA damage responses, activation of p53 and induction of p16INK4A. In cells and mouse models, miR-30 disrupts senescence and promotes cancer by suppressing 2 targets, CHD7 and TNRC6A. We show that while CHD7 is a transcriptional coactivator essential for induction of p16INK4A in senescent cells, TNRC6A, a miRNA machinery component, is required for expression and functionality of DNA damage response RNAs (DDRNAs) that mediate DNA damage responses and p53 activation by orchestrating histone modifications, chromatin remodeling and recruitment of DNA damage factors at damaged sites. Thus, miR-30 inhibits both p16INK4A and p53, 2 key senescence effectors, leading to efficient senescence disruption. These findings have identified novel signaling pathways mediating oncogene-induced senescence and tumor-suppression, and revealed the molecular and cellular mechanisms underlying the oncogenic activity of miR-30. Thus, the miR-30/CHD7/TNRC6A pathway is potentially a novel diagnostic biomarker and therapeutic target for cancer.
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Affiliation(s)
- Weijun Su
- Department of Cancer Biology, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA.,School of Medicine, Nankai University, Tianjin, China
| | - Lixin Hong
- Departments of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xin Xu
- No 2 People's Hospital of Wuxi City, Wuxi, China
| | - Shan Huang
- Department of Cancer Biology, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Denise Herpai
- Department of Cancer Biology, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Brain Tumor Center of Excellence, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Lisheng Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yingxi Xu
- School of Medicine, Nankai University, Tianjin, China.,Departments of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Lan Truong
- Departments of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Xiaohua Wu
- Departments of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Changchun Xiao
- Departments of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | - Wei Zhang
- Department of Cancer Biology, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Cancer Genomics and Precision Oncology, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Waldemar Debinski
- Department of Cancer Biology, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Brain Tumor Center of Excellence, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Rong Xiang
- School of Medicine, Nankai University, Tianjin, China
| | - Peiqing Sun
- Department of Cancer Biology, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA. .,Departments of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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