151
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Histone 4 Lysine 20 Methylation: A Case for Neurodevelopmental Disease. BIOLOGY 2019; 8:biology8010011. [PMID: 30832413 PMCID: PMC6466304 DOI: 10.3390/biology8010011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
Neurogenesis is an elegantly coordinated developmental process that must maintain a careful balance of proliferation and differentiation programs to be compatible with life. Due to the fine-tuning required for these processes, epigenetic mechanisms (e.g., DNA methylation and histone modifications) are employed, in addition to changes in mRNA transcription, to regulate gene expression. The purpose of this review is to highlight what we currently know about histone 4 lysine 20 (H4K20) methylation and its role in the developing brain. Utilizing publicly-available RNA-Sequencing data and published literature, we highlight the versatility of H4K20 methyl modifications in mediating diverse cellular events from gene silencing/chromatin compaction to DNA double-stranded break repair. From large-scale human DNA sequencing studies, we further propose that the lysine methyltransferase gene, KMT5B (OMIM: 610881), may fit into a category of epigenetic modifier genes that are critical for typical neurodevelopment, such as EHMT1 and ARID1B, which are associated with Kleefstra syndrome (OMIM: 610253) and Coffin-Siris syndrome (OMIM: 135900), respectively. Based on our current knowledge of the H4K20 methyl modification, we discuss emerging themes and interesting questions on how this histone modification, and particularly KMT5B expression, might impact neurodevelopment along with current challenges and potential avenues for future research.
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152
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Scandaglia M, Barco A. Contribution of spurious transcription to intellectual disability disorders. J Med Genet 2019; 56:491-498. [PMID: 30745423 DOI: 10.1136/jmedgenet-2018-105668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/17/2018] [Accepted: 01/18/2019] [Indexed: 12/31/2022]
Abstract
During the development of multicellular organisms, chromatin-modifying enzymes orchestrate the establishment of gene expression programmes that characterise each differentiated cell type. These enzymes also contribute to the maintenance of cell type-specific transcription profiles throughout life. But what happens when epigenomic regulation goes awry? Genomic screens in experimental models of intellectual disability disorders (IDDs) caused by mutations in epigenetic machinery-encoding genes have shown that transcriptional dysregulation constitutes a hallmark of these conditions. Here, we underscore the connections between a subset of chromatin-linked IDDs and spurious transcription in brain cells. We also propose that aberrant gene expression in neurons, including both the ectopic transcription of non-neuronal genes and the activation of cryptic promoters, may importantly contribute to the pathoaetiology of these disorders.
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Affiliation(s)
- Marilyn Scandaglia
- Molecular Neurobiology and Neuropathology Unit, Instituto de Neurociencias (UMH-CSIC), San Juan de Alicante, Alicante, Spain
| | - Angel Barco
- Molecular Neurobiology and Neuropathology Unit, Instituto de Neurociencias (UMH-CSIC), San Juan de Alicante, Alicante, Spain
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153
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Spatially clustering de novo variants in CYFIP2, encoding the cytoplasmic FMRP interacting protein 2, cause intellectual disability and seizures. Eur J Hum Genet 2019; 27:747-759. [PMID: 30664714 DOI: 10.1038/s41431-018-0331-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022] Open
Abstract
CYFIP2, encoding the evolutionary highly conserved cytoplasmic FMRP interacting protein 2, has previously been proposed as a candidate gene for intellectual disability and autism because of its important role linking FMRP-dependent transcription regulation and actin polymerization via the WAVE regulatory complex (WRC). Recently, de novo variants affecting the amino acid p.Arg87 of CYFIP2 were reported in four individuals with epileptic encephalopathy. We here report 12 independent patients harboring a variety of de novo variants in CYFIP2 broadening the molecular and clinical spectrum of a novel CYFIP2-related neurodevelopmental disorder. Using trio whole-exome or -genome sequencing, we identified 12 independent patients carrying a total of eight distinct de novo variants in CYFIP2 with a shared phenotype of intellectual disability, seizures, and muscular hypotonia. We detected seven different missense variants, of which two occurred recurrently (p.(Arg87Cys) and p.(Ile664Met)), and a splice donor variant in the last intron for which we showed exon skipping in the transcript. The latter is expected to escape nonsense-mediated mRNA decay resulting in a truncated protein. Despite the large spacing in the primary structure, the variants spatially cluster in the tertiary structure and are all predicted to weaken the interaction with WAVE1 or NCKAP1 of the actin polymerization regulating WRC-complex. Preliminary genotype-phenotype correlation indicates a profound phenotype in p.Arg87 substitutions and a more variable phenotype in other alterations. This study evidenced a variety of de novo variants in CYFIP2 as a novel cause of mostly severe intellectual disability with seizures and muscular hypotonia.
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154
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Xu WH, Liang DY, Wang Q, Shen J, Liu QH, Peng YB. Knockdown of KDM2A inhibits proliferation associated with TGF-β expression in HEK293T cell. Mol Cell Biochem 2019; 456:95-104. [PMID: 30604066 DOI: 10.1007/s11010-018-03493-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/22/2018] [Indexed: 02/08/2023]
Abstract
Lysine-specific demethylase 2A (KDM2A, also known as JHDM1A or FBXL11) plays an important role in regulating cell proliferation. However, the mechanisms on KDM2A controlling cell proliferation are varied among cell types, even controversial conclusions have been drawn. In order to elucidate the functions and underlying mechanisms for KDM2A controlling cell proliferation and apoptosis, we screened a KDM2A knockout HEK293T cell lines by CRISPR-Cas9 to illustrate the effects of KDM2A on both biological process. The results indicate that knocking down expression of KDM2A can significantly weaken HEK293T cell proliferation. The cell cycle analysis via flow cytometry demonstrate that knockdown expression of KDM2A will lead more cells arrested at G2/M phase. Through the RNA-seq analysis of the differential expressed genes between KDM2A knockdown HEK293T cells and wild type, we screened out that TGF-β pathway was significantly downregulated in KDM2A knockdown cells, which indicates that TGF-β signaling pathway might be the downstream target of KDM2A to regulate cell proliferation. When the KDM2A knockdown HEK293T cells were transient-transfected with KDM2A overexpression plasmid or treated by TGF-β agonist hydrochloride, the cell proliferation levels can be partial or completely rescued. However, the TGF-β inhibitor LY2109761 can significantly inhibit the KDM2A WT cells proliferation, but not the KDM2A knockdown HEK293T cells. Taken together, these findings suggested that KDM2A might be a key regulator of cell proliferation and cell cycle via impacting TGF-β signaling pathway.
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Affiliation(s)
- Wen-Hao Xu
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, 82 MinZu Ave., Wuhan, 430074, Hubei, People's Republic of China
| | - Da-Yan Liang
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, 82 MinZu Ave., Wuhan, 430074, Hubei, People's Republic of China
| | - Qi Wang
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, 82 MinZu Ave., Wuhan, 430074, Hubei, People's Republic of China
| | - Jinhua Shen
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, 82 MinZu Ave., Wuhan, 430074, Hubei, People's Republic of China
| | - Qing-Hua Liu
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, 82 MinZu Ave., Wuhan, 430074, Hubei, People's Republic of China
| | - Yong-Bo Peng
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, 82 MinZu Ave., Wuhan, 430074, Hubei, People's Republic of China.
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155
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Vevera J, Zarrei M, Hartmannová H, Jedličková I, Mušálková D, Přistoupilová A, Oliveriusová P, Trešlová H, Nosková L, Hodaňová K, Stránecký V, Jiřička V, Preiss M, Příhodová K, Šaligová J, Wei J, Woodbury-Smith M, Bleyer AJ, Scherer SW, Kmoch S. Rare copy number variation in extremely impulsively violent males. GENES BRAIN AND BEHAVIOR 2018; 18:e12536. [DOI: 10.1111/gbb.12536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Jan Vevera
- Department of Psychiatry; Faculty of Medicine and University Hospital in Pilsen, Charles University; Prague Czech Republic
- Department of Psychiatry, First Faculty of Medicine; Charles University and General University Hospital in Prague; Prague Czech Republic
- Institute for Postgraduate Medical Education; Prague Czech Republic
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Petra Oliveriusová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Helena Trešlová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Václav Jiřička
- Prison Service of the Czech Republic, Directorate General; Department of Psychology; Prague Czech Republic
| | - Marek Preiss
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
- Psychology Department; University of New York in Prague; Prague Czech Republic
| | - Kateřina Příhodová
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
| | - Jana Šaligová
- Children's Faculty Hospital; Department of Pediatrics and Adolescent Medicine; Kosice Slovakia
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine of Pavel Jozef Šafárik University Kosice; Kosice Slovakia
| | - John Wei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - Marc Woodbury-Smith
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
- Institute of Neuroscience, Newcastle University, Sir James Spence Institute, Royal Victoria Infirmary; Newcastle upon Tyne UK
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
- Section on Nephrology, Wake Forest School of Medicine; Medical Center Blvd.; Winston-Salem North Carolina USA
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
- Department of Molecular Genetics and McLaughlin Centre; University of Toronto; Toronto Ontario Canada
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
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156
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Lu DH, Yang J, Gao LK, Min J, Tang JM, Hu M, Li Y, Li ST, Chen J, Hong L. Lysine demethylase 2A promotes the progression of ovarian cancer by regulating the PI3K pathway and reversing epithelial‑mesenchymal transition. Oncol Rep 2018; 41:917-927. [PMID: 30483796 PMCID: PMC6313075 DOI: 10.3892/or.2018.6888] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/21/2018] [Indexed: 12/11/2022] Open
Abstract
Metastasis is the most common cause of death in ovarian cancer patients but remains largely untreated. Epithelial‑mesenchymal transition (EMT) is critical for the conversion of early‑stage ovarian tumors into metastatic malignancies. Thus, investigating the signaling pathways promoting EMT may identify potential targets for the treatment of metastatic ovarian cancer. Lysine demethylase 2A (KDM2A), also known as FBXL11 and JHDM1A, is a histone H3 lysine 36 (H3K36) demethylase that regulates EMT and the metastasis of ovarian cancer. However, the function and underlying mechanisms of EMT suppression in ovarian cancer have not been thoroughly elucidated to date. In the present study, we used Gene Expression Omnibus (GEO) databases to determine that KDM2A is significantly upregulated in human ovarian cancers. KDM2A expression was assessed by immunohistochemistry of epithelial ovarian cancer (EOC) borderline ovarian tumors and normal ovary tissues. Seven fresh EOC tissues and 3 fresh normal ovary tissues were collected for western blot analysis. Kaplan‑Meier survival curves were constructed to identify genes related to EOC prognosis from the TCGA data portal. Stable KDM2A‑knockdown cell lines were established to study the biological functions and underlying mechanisms of KDM2A in EMT in vitro. GEO database analysis revealed that KDM2A was highly upregulated in EOC tissues; this analysis was accompanied by immunochemistry and western blot analysis using samples of human tissues. High expression of KDM2A was associated with poor survival in EOC patients. KDM2A knockdown promoted apoptosis and suppressed the proliferation, migration and invasion of tumor cells in vitro. EMT and the PI3K/AKT/mTOR signaling pathway were suppressed in KDM2A‑silenced cells. Inactivation of the PI3K/AKT/mTOR signaling pathway in A2780 cells induced EMT inhibition. Our data revealed that KDM2A functions as a tumor oncogene, and the downregulation of KDM2A expression regulates EMT and EOC progression, providing a valuable prognostic marker and potential target for the treatment of EOC patients.
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Affiliation(s)
- Dan-Hua Lu
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Jiang Yang
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Li-Kun Gao
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Jie Min
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Jian-Ming Tang
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Ming Hu
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Yang Li
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Su-Ting Li
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Jing Chen
- Department of Pathology, Molecular Diagnostics Laboratory, University of Michigan, Ann Arbor, MI 48109, USA
| | - Li Hong
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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157
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A comparative analysis of KMT2D missense variants in Kabuki syndrome, cancers and the general population. J Hum Genet 2018; 64:161-170. [PMID: 30459467 DOI: 10.1038/s10038-018-0536-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/10/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022]
Abstract
Determining the clinical significance of germline and somatic KMT2D missense variants (MVs) in Kabuki syndrome (KS) and cancers can be challenging. We analysed 1920 distinct KMT2D MVs that included 1535 germline MVs in controls (Control-MVs), 584 somatic MVs in cancers (Cancer-MVs) and 201 MV in individuals with KS (KS-MVs). The proportion of MVs likely to affect splicing was significantly higher for Cancer-MVs and KS-MVs than in Control-MVs (p = 0.000018). Our analysis identified significant clustering of Cancer-MVs and KS-MVs in the PHD#3 and #4, RING#4 and SET domains. Areas of enrichment restricted to just Cancer-MVs (FYR-C and between amino acids 3043-3248) or KS-MVs (coiled-coil#5, FYR-N and between amino acids 4995-5090) were also found. Cancer-MVs and KS-MVs tended to affect more conserved residues (lower BLOSUM scores, p < 0.001 and p = 0.007). KS-MVs are more likely to increase the energy for protein folding (higher ELASPIC ∆∆G scores, p = 0.03). Cancer-MVs are more likely to disrupt protein interactions (higher StructMAn scores, p = 0.019). We reclassify several presumed pathogenic MVs as benign or as variants of uncertain significance. We raise the possibility of as yet unrecognised 'non-KS' phenotype(s) associated with some germline pathogenic KMT2D MVs. Overall, this work provides insights into the disease mechanism of KMT2D variants and can be extended to other genes, mutations in which also cause developmental syndromes and cancer.
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158
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Martin HC, Jones WD, McIntyre R, Sanchez-Andrade G, Sanderson M, Stephenson JD, Jones CP, Handsaker J, Gallone G, Bruntraeger M, McRae JF, Prigmore E, Short P, Niemi M, Kaplanis J, Radford EJ, Akawi N, Balasubramanian M, Dean J, Horton R, Hulbert A, Johnson DS, Johnson K, Kumar D, Lynch SA, Mehta SG, Morton J, Parker MJ, Splitt M, Turnpenny PD, Vasudevan PC, Wright M, Bassett A, Gerety SS, Wright CF, FitzPatrick DR, Firth HV, Hurles ME, Barrett JC. Quantifying the contribution of recessive coding variation to developmental disorders. Science 2018; 362:1161-1164. [PMID: 30409806 DOI: 10.1126/science.aar6731] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 08/10/2018] [Accepted: 10/29/2018] [Indexed: 12/13/2022]
Abstract
We estimated the genome-wide contribution of recessive coding variation in 6040 families from the Deciphering Developmental Disorders study. The proportion of cases attributable to recessive coding variants was 3.6% in patients of European ancestry, compared with 50% explained by de novo coding mutations. It was higher (31%) in patients with Pakistani ancestry, owing to elevated autozygosity. Half of this recessive burden is attributable to known genes. We identified two genes not previously associated with recessive developmental disorders, KDM5B and EIF3F, and functionally validated them with mouse and cellular models. Our results suggest that recessive coding variants account for a small fraction of currently undiagnosed nonconsanguineous individuals, and that the role of noncoding variants, incomplete penetrance, and polygenic mechanisms need further exploration.
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Affiliation(s)
- Hilary C Martin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
| | - Wendy D Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Great Ormond Street Hospital for Children, National Health Service (NHS) Foundation Trust, Great Ormond Street Hospital, Great Ormond Street, London WC1N 3JH, UK
| | - Rebecca McIntyre
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Mark Sanderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - James D Stephenson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Carla P Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Juliet Handsaker
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Giuseppe Gallone
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Jeremy F McRae
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Elena Prigmore
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Patrick Short
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mari Niemi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Joanna Kaplanis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Elizabeth J Radford
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Paediatrics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nadia Akawi
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, OPD2, Northern General Hospital, Herries Rd., Sheffield, S5 7AU, UK
| | - John Dean
- Department of Genetics, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Rachel Horton
- Wessex Clinical Genetics Service, G Level, Princess Anne Hospital, Coxford Road, Southampton SO16 5YA, UK
| | - Alice Hulbert
- Cheshire and Merseyside Clinical Genetic Service, Liverpool Women's NHS Foundation Trust, Crown Street, Liverpool L8 7SS, UK
| | - Diana S Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, OPD2, Northern General Hospital, Herries Rd., Sheffield, S5 7AU, UK
| | - Katie Johnson
- Department of Clinical Genetics, City Hospital Campus, Hucknall Road, Nottingham NG5 1PB, UK
| | - Dhavendra Kumar
- Institute of Cancer and Genetics, University Hospital of Wales, Cardiff, UK
| | | | - Sarju G Mehta
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jenny Morton
- Clinical Genetics Unit, Birmingham Women's Hospital, Edgbaston, Birmingham B15 2TG, UK
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter D Turnpenny
- Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Pradeep C Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester LE1 5WW, UK
| | - Michael Wright
- Northern Genetics Service, Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Andrew Bassett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sebastian S Gerety
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Caroline F Wright
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Research, Innovation, Learning and Development (RILD), Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - David R FitzPatrick
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
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159
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Helbig KL, Lauerer RJ, Bahr JC, Souza IA, Myers CT, Uysal B, Schwarz N, Gandini MA, Huang S, Keren B, Mignot C, Afenjar A, Billette de Villemeur T, Héron D, Nava C, Valence S, Buratti J, Fagerberg CR, Soerensen KP, Kibaek M, Kamsteeg EJ, Koolen DA, Gunning B, Schelhaas HJ, Kruer MC, Fox J, Bakhtiari S, Jarrar R, Padilla-Lopez S, Lindstrom K, Jin SC, Zeng X, Bilguvar K, Papavasileiou A, Xing Q, Zhu C, Boysen K, Vairo F, Lanpher BC, Klee EW, Tillema JM, Payne ET, Cousin MA, Kruisselbrink TM, Wick MJ, Baker J, Haan E, Smith N, Sadeghpour A, Davis EE, Katsanis N, Corbett MA, MacLennan AH, Gecz J, Biskup S, Goldmann E, Rodan LH, Kichula E, Segal E, Jackson KE, Asamoah A, Dimmock D, McCarrier J, Botto LD, Filloux F, Tvrdik T, Cascino GD, Klingerman S, Neumann C, Wang R, Jacobsen JC, Nolan MA, Snell RG, Lehnert K, Sadleir LG, Anderlid BM, Kvarnung M, Guerrini R, Friez MJ, Lyons MJ, Leonhard J, Kringlen G, Casas K, El Achkar CM, Smith LA, Rotenberg A, Poduri A, Sanchis-Juan A, Carss KJ, Rankin J, Zeman A, Raymond FL, Blyth M, Kerr B, Ruiz K, Urquhart J, Hughes I, Banka S, Hedrich UB, Scheffer IE, Helbig I, Zamponi GW, Lerche H, Mefford HC, Allori A, Angrist M, Ashley P, Bidegain M, Boyd B, Chambers E, Cope H, Cotten CM, Curington T, Davis EE, Ellestad S, Fisher K, French A, Gallentine W, Goldberg R, Hill K, Kansagra S, Katsanis N, Katsanis S, Kurtzberg J, Marcus J, McDonald M, Mikati M, Miller S, Murtha A, Perilla Y, Pizoli C, Purves T, Ross S, Sadeghpour A, Smith E, Wiener J. De Novo Pathogenic Variants in CACNA1E Cause Developmental and Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesias. Am J Hum Genet 2018; 103:666-678. [PMID: 30343943 DOI: 10.1016/j.ajhg.2018.09.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/17/2018] [Indexed: 12/27/2022] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) are severe neurodevelopmental disorders often beginning in infancy or early childhood that are characterized by intractable seizures, abundant epileptiform activity on EEG, and developmental impairment or regression. CACNA1E is highly expressed in the central nervous system and encodes the α1-subunit of the voltage-gated CaV2.3 channel, which conducts high voltage-activated R-type calcium currents that initiate synaptic transmission. Using next-generation sequencing techniques, we identified de novo CACNA1E variants in 30 individuals with DEE, characterized by refractory infantile-onset seizures, severe hypotonia, and profound developmental impairment, often with congenital contractures, macrocephaly, hyperkinetic movement disorders, and early death. Most of the 14, partially recurring, variants cluster within the cytoplasmic ends of all four S6 segments, which form the presumed CaV2.3 channel activation gate. Functional analysis of several S6 variants revealed consistent gain-of-function effects comprising facilitated voltage-dependent activation and slowed inactivation. Another variant located in the domain II S4-S5 linker results in facilitated activation and increased current density. Five participants achieved seizure freedom on the anti-epileptic drug topiramate, which blocks R-type calcium channels. We establish pathogenic variants in CACNA1E as a cause of DEEs and suggest facilitated R-type calcium currents as a disease mechanism for human epilepsy and developmental disorders.
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160
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Lebrun N, Mehler-Jacob C, Poirier K, Zordan C, Lacombe D, Carion N, Billuart P, Bienvenu T. Novel KDM5B splice variants identified in patients with developmental disorders: Functional consequences. Gene 2018; 679:305-313. [PMID: 30217758 DOI: 10.1016/j.gene.2018.09.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/28/2018] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
Histone lysine methylation influences processes such as gene expression and DNA repair. Thirty Jumonji C (JmjC) domain-containing proteins have been identified and phylogenetically clustered into seven subfamilies. Most JmjC domain-containing proteins have been shown to possess histone demethylase activity toward specific histone methylation marks. One of these subfamilies, the KDM5 family, is characterized by five conserved domains and includes four members. Interestingly, de novo loss-of-function and missense variants in KDM5B were identified in patients with intellectual disability (ID) and autism spectrum disorder (ASD) but also in unaffected individuals. Here, we report two novel de novo splice variants in the KDM5B gene in three patients with ID and ASD. The c.808 + 1G > A variant was identified in a boy with mild ID and autism traits and is associated with a significant reduced KDM5B mRNA expression without alteration of its H3K4me3 pattern. In contrast, the c.576 + 2T > C variant was found in twins with global delay in developmental milestones, poor language and ASD. This variant causes the production of an abnormal transcript which may produce an altered protein with the loss of the ARID1B domain with an increase in global gene H3K4me3. Our data reinforces the recent observation that the KDM5B haploinsufficiency is not a mechanism involved in intellectual disability and that KDM5B disorder associated with LOF variants is a recessive disorder. However, some variants may also cause gain of function, and need to be interpreted with caution, and functional studies should be performed to identify the molecular consequences of these different rare variants.
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Affiliation(s)
- Nicolas Lebrun
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France; Institut de Psychiatrie et de Neurosciences de Paris, 102 rue de la santé, 75014 Paris, France
| | - Claire Mehler-Jacob
- Service de Neuropédiatrie, HU-Paris Sud site Bicêtre AP-HP, 78 rue du Général Leclerc, 94270 Le Kremlin-Bicêtre, France
| | - Karine Poirier
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France
| | - Cecile Zordan
- Service de Génétique Médicale, Hôpital Pellegrin, Place Amélie Raba-Léon, CHU de Bordeaux, 33076 Bordeaux Cedex, France
| | - Didier Lacombe
- Service de Génétique Médicale, Hôpital Pellegrin, Place Amélie Raba-Léon, CHU de Bordeaux, 33076 Bordeaux Cedex, France
| | - Nathalie Carion
- Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, AP-HP, Paris, France
| | - Pierre Billuart
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France; Institut de Psychiatrie et de Neurosciences de Paris, 102 rue de la santé, 75014 Paris, France
| | - Thierry Bienvenu
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France; Institut de Psychiatrie et de Neurosciences de Paris, 102 rue de la santé, 75014 Paris, France; Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, AP-HP, Paris, France.
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161
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Dai L, Ding C, Fang F. An inherited KMT2B duplication variant in a Chinese family with dystonia and/or development delay. Parkinsonism Relat Disord 2018; 63:227-228. [PMID: 30196991 DOI: 10.1016/j.parkreldis.2018.08.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/29/2018] [Accepted: 08/28/2018] [Indexed: 02/08/2023]
Affiliation(s)
- Lifang Dai
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center For Children's Health, China, Nanlishi Road No 56, Xi Strict, Beijing, 100045, China
| | - Changhong Ding
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center For Children's Health, China, Nanlishi Road No 56, Xi Strict, Beijing, 100045, China.
| | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center For Children's Health, China, Nanlishi Road No 56, Xi Strict, Beijing, 100045, China.
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162
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Stoyle G, Banka S, Langley C, Jones EA, Banerjee I. Growth hormone deficiency as a cause for short stature in Wiedemann-Steiner Syndrome. Endocrinol Diabetes Metab Case Rep 2018; 2018:EDM180085. [PMID: 30159147 PMCID: PMC6109209 DOI: 10.1530/edm-18-0085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 08/06/2018] [Indexed: 01/02/2023] Open
Abstract
Wiedemann-Steiner Syndrome (WSS) is a rare condition characterised by short stature, hypertrichosis of the elbow, intellectual disability and characteristic facial dysmorphism due to heterozygous loss of function mutations in KMT2A, a gene encoding a histone 3 lysine 4 methyltransferase. Children with WSS are often short and until recently, it had been assumed that short stature is an intrinsic part of the syndrome. GHD has recently been reported as part of the phenotypic spectrum of WSS. We describe the case of an 8-year-old boy with a novel heterozygous variant in KMT2A and features consistent with a diagnosis of WSS who also had growth hormone deficiency (GHD). GHD was diagnosed on dynamic function testing for growth hormone (GH) secretion, low insulin-like growth factor I (IGF-I) levels and pituitary-specific MRI demonstrating anterior pituitary hypoplasia and an ectopic posterior pituitary. Treatment with GH improved height performance with growth trajectory being normalised to the parental height range. Our case highlights the need for GH testing in children with WSS and short stature as treatment with GH improves growth trajectory. Learning points Growth hormone deficiency might be part of the phenotypic spectrum of Wiedemann-Steiner Syndrome (WSS).Investigation of pituitary function should be undertaken in children with WSS and short stature. A pituitary MR scan should be considered if there is biochemical evidence of growth hormone deficiency (GHD).Recombinant human growth hormone treatment should be considered for treatment of GHD.
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Affiliation(s)
- George Stoyle
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK.,Manchester Medical School, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University, NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Claire Langley
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University, NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Elizabeth A Jones
- Manchester Centre for Genomic Medicine, Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University, NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Indraneel Banerjee
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
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163
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Bhushan B, Erdmann A, Zhang Y, Belle R, Johannson C, Oppermann U, Hopkinson RJ, Schofield CJ, Kawamura A. Investigations on small molecule inhibitors targeting the histone H3K4 tri-methyllysine binding PHD-finger of JmjC histone demethylases. Bioorg Med Chem 2018; 26:2984-2991. [PMID: 29764755 PMCID: PMC6380468 DOI: 10.1016/j.bmc.2018.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/10/2018] [Accepted: 03/18/2018] [Indexed: 12/12/2022]
Abstract
Plant homeodomain (PHD) containing proteins are important epigenetic regulators and are of interest as potential drug targets. Inspired by the amiodarone derivatives reported to inhibit the PHD finger 3 of KDM5A (KDM5A(PHD3)), a set of compounds were synthesised. Amiodarone and its derivatives were observed to weakly disrupt the interactions of a histone H3K4me3 peptide with KDM5A(PHD3). Selected amiodarone derivatives inhibited catalysis of KDM5A, but in a PHD-finger independent manner. Amiodarone derivatives also bind to H3K4me3-binding PHD-fingers from the KDM7 subfamily. Further work is required to develop potent and selective PHD finger inhibitors.
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Affiliation(s)
- Bhaskar Bhushan
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Alexandre Erdmann
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Yijia Zhang
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Roman Belle
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Catrine Johannson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, United Kingdom
| | - Udo Oppermann
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, United Kingdom
| | - Richard J Hopkinson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Akane Kawamura
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.
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164
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Shen W, Krautscheid P, Rutz AM, Bayrak-Toydemir P, Dugan SL. De novo loss-of-function variants of ASH1L are associated with an emergent neurodevelopmental disorder. Eur J Med Genet 2018; 62:55-60. [PMID: 29753921 DOI: 10.1016/j.ejmg.2018.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/23/2018] [Accepted: 05/08/2018] [Indexed: 01/09/2023]
Abstract
De novo variants of ASH1L, which encodes a histone methyltransferase, have been reported in a few patients with intellectual disability and autistic features. Here, we identified a novel de novo frame-shift variant, c.2422_2423delAAinsT which predicts p.(Lys808TyrfsTer40), in ASH1L in a patient with multiple congenital anomalies (MCA), fine motor developmental delay, learning difficulties, attention deficit hyperactivity disorder, sleep apnea, and scoliosis. This frame-shift variant is expected to result in loss-of-function. Our report provides further evidence to support loss-of-function alterations of ASH1L as causative for an emergent neurodevelopmental syndrome characterized by MCA, intellectual disability, and behavioral problems, and further delineates this genetic disorder.
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Affiliation(s)
- Wei Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA; ARUP Laboratories, Salt Lake City, UT, USA.
| | - Patti Krautscheid
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Audrey M Rutz
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Pinar Bayrak-Toydemir
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA; ARUP Laboratories, Salt Lake City, UT, USA
| | - Sarah L Dugan
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
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165
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Genetic and Epigenetic Control of CDKN1C Expression: Importance in Cell Commitment and Differentiation, Tissue Homeostasis and Human Diseases. Int J Mol Sci 2018; 19:ijms19041055. [PMID: 29614816 PMCID: PMC5979523 DOI: 10.3390/ijms19041055] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 03/31/2018] [Accepted: 03/31/2018] [Indexed: 12/28/2022] Open
Abstract
The CDKN1C gene encodes the p57Kip2 protein which has been identified as the third member of the CIP/Kip family, also including p27Kip1 and p21Cip1. In analogy with these proteins, p57Kip2 is able to bind tightly and inhibit cyclin/cyclin-dependent kinase complexes and, in turn, modulate cell division cycle progression. For a long time, the main function of p57Kip2 has been associated only to correct embryogenesis, since CDKN1C-ablated mice are not vital. Accordingly, it has been demonstrated that CDKN1C alterations cause three human hereditary syndromes, characterized by altered growth rate. Subsequently, the p57Kip2 role in several cell phenotypes has been clearly assessed as well as its down-regulation in human cancers. CDKN1C lies in a genetic locus, 11p15.5, characterized by a remarkable regional imprinting that results in the transcription of only the maternal allele. The control of CDKN1C transcription is also linked to additional mechanisms, including DNA methylation and specific histone methylation/acetylation. Finally, long non-coding RNAs and miRNAs appear to play important roles in controlling p57Kip2 levels. This review mostly represents an appraisal of the available data regarding the control of CDKN1C gene expression. In addition, the structure and function of p57Kip2 protein are briefly described and correlated to human physiology and diseases.
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