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Camões dos Santos J, Appleton C, Cazaux Mateus F, Covas R, Bekman EP, da Rocha ST. Stem cell models of Angelman syndrome. Front Cell Dev Biol 2023; 11:1274040. [PMID: 37928900 PMCID: PMC10620611 DOI: 10.3389/fcell.2023.1274040] [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: 08/07/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Angelman syndrome (AS) is an imprinted neurodevelopmental disorder that lacks a cure, characterized by developmental delay, intellectual impairment, seizures, ataxia, and paroxysmal laughter. The condition arises due to the loss of the maternally inherited copy of the UBE3A gene in neurons. The paternally inherited UBE3A allele is unable to compensate because it is silenced by the expression of an antisense transcript (UBE3A-ATS) on the paternal chromosome. UBE3A, encoding enigmatic E3 ubiquitin ligase variants, regulates target proteins by either modifying their properties/functions or leading them to degradation through the proteasome. Over time, animal models, particularly the Ube3a mat-/pat+ Knock-Out (KO) mice, have significantly contributed to our understanding of the molecular mechanisms underlying AS. However, a shift toward human pluripotent stem cell models (PSCs), such as human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), has gained momentum. These stem cell models accurately capture human genetic and cellular characteristics, offering an alternative or a complement to animal experimentation. Human stem cells possess the remarkable ability to recapitulate neurogenesis and generate "brain-in-a-dish" models, making them valuable tools for studying neurodevelopmental disorders like AS. In this review, we provide an overview of the current state-of-the-art human stem cell models of AS and explore their potential to become the preclinical models of choice for drug screening and development, thus propelling AS therapeutic advancements and improving the lives of affected individuals.
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Affiliation(s)
- João Camões dos Santos
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Carolina Appleton
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Animal Biology, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Francisca Cazaux Mateus
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Rita Covas
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Evguenia Pavlovna Bekman
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- The Egas Moniz Center for Interdisciplinary Research (CiiEM), Caparica, Portugal
| | - Simão Teixeira da Rocha
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Winsauer AG, Thornberg DC, Rodriguez SM, Poppino KF, Ramo BA. Angelman and Prader-Willi Syndromes: Sister Imprinting Disorders With High Complication Rates Following Spinal Deformity Surgery. Orthopedics 2023; 46:e223-e229. [PMID: 36779733 DOI: 10.3928/01477447-20230207-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
We sought to examine the modern surgical treatment of spinal deformity associated with sister imprinting disorders, Prader-Willi syndrome (PWS) and Angelman syndrome (AS), with emphasis on the specific complications encountered in these patient populations. Fifteen patients with PWS and 5 patients with AS who underwent surgical intervention for spinal deformity between 2000 and 2018 were identified. Postoperative complications were classified using the modified Clavien-Dindo-Sink (CDS) system and further categorized into specific subtypes including excessive drainage, dehiscence, implant failure, infection, and delayed wound healing. Perioperative and final follow-up radiographic data were analyzed. Mean age at surgery was 12.9 years (range, 4-21 years) with mean follow-up of 46.1 months (range, 1-145 months). There were postoperative complications in 17 patients (85%). Ten major complications (CDS ≥ 3) occurred in 9 patients (45%). These included 5 infections requiring reoperation, 1 seroma requiring drainage, 2 severe cervical-thoracic deformities requiring reoperation, 1 implant failure requiring reoperation, and 1 death secondary to fungal sepsis and thromboembolic disease. Eight additional patients (40%) had minor complications (CDS 1 or 2). Eight intraoperative complications occurred in 5 patients (25%), including loss of neuromonitoring signals and cerebrospinal fluid leaks. Surgical intervention for scoliosis in PWS and AS continues to have high complication rates secondary to medical and behavioral comorbidities found in these patient populations. The exact etiology of the high complication rates encountered cannot be definitively stated, but both syndromes frequently present with a number of unique features that may predispose patients to develop surgical complications. [Orthopedics. 2023;46(4):e223-e229.].
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Akter H, Rahman MM, Sarker S, Basiruzzaman M, Islam MM, Rahaman MA, Rahaman MA, Eshaque TB, Dity NJ, Sarker S, Amin MR, Hossain MM, Lopa M, Jahan N, Hossain S, Islam A, Mondol A, Faruk MO, Saha N, Kundu GK, Kanta SI, Kazal RK, Fatema K, Rahman MA, Hasan M, Hossain Mollah MA, Hosen MI, Karuvantevida N, Begum G, Zehra B, Nassir N, Nabi AHMN, Uddin KMF, Uddin M. Construction of copy number variation landscape and characterization of associated genes in a Bangladeshi cohort of neurodevelopmental disorders. Front Genet 2023; 14:955631. [PMID: 36959829 PMCID: PMC10028086 DOI: 10.3389/fgene.2023.955631] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction: Copy number variations (CNVs) play a critical role in the pathogenesis of neurodevelopmental disorders (NDD) among children. In this study, we aim to identify clinically relevant CNVs, genes and their phenotypic characteristics in an ethnically underrepresented homogenous population of Bangladesh. Methods: We have conducted chromosomal microarray analysis (CMA) for 212 NDD patients with male to female ratio of 2.2:1.0 to identify rare CNVs. To identify candidate genes within the rare CNVs, gene constraint metrics [i.e., "Critical-Exon Genes (CEGs)"] were applied to the population data. Autism Diagnostic Observation Schedule-Second Edition (ADOS-2) was followed in a subset of 95 NDD patients to assess the severity of autism and all statistical tests were performed using the R package. Results: Of all the samples assayed, 12.26% (26/212) and 57.08% (121/212) patients carried pathogenic and variant of uncertain significance (VOUS) CNVs, respectively. While 2.83% (6/212) patients' pathogenic CNVs were found to be located in the subtelomeric regions. Further burden test identified females are significant carriers of pathogenic CNVs compared to males (OR = 4.2; p = 0.0007). We have observed an increased number of Loss of heterozygosity (LOH) within cases with 23.85% (26/109) consanguineous parents. Our analyses on imprinting genes show, 36 LOH variants disrupting 69 unique imprinted genes and classified these variants as VOUS. ADOS-2 subset shows severe social communication deficit (p = 0.014) and overall ASD symptoms severity (p = 0.026) among the patients carrying duplication CNV compared to the CNV negative group. Candidate gene analysis identified 153 unique CEGs in pathogenic CNVs and 31 in VOUS. Of the unique genes, 18 genes were found to be in smaller (<1 MB) focal CNVs in our NDD cohort and we identified PSMC3 gene as a strong candidate gene for Autism Spectrum Disorder (ASD). Moreover, we hypothesized that KMT2B gene duplication might be associated with intellectual disability. Conclusion: Our results show the utility of CMA for precise genetic diagnosis and its integration into the diagnosis, therapy and management of NDD patients.
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Affiliation(s)
- Hosneara Akter
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Muhammad Mizanur Rahman
- Department of Paediatric Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shaoli Sarker
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Paediatric Neuroscience, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Mohammed Basiruzzaman
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Neurology, National Institute of Neurosciences and Hospital, Dhaka, Bangladesh
| | - Md. Mazharul Islam
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Neurology, National Institute of Neurosciences and Hospital, Dhaka, Bangladesh
| | - Md. Atikur Rahaman
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | | | | | - Nushrat Jahan Dity
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Shouvik Sarker
- Institute of Plant Genetics, Department of Plant Biotechnology, Leibniz University Hannover, Hanover, Germany
| | - Md. Robed Amin
- Department of Medicine, Dhaka Medical College, Dhaka, Bangladesh
| | - Mohammad Monir Hossain
- Department of Paediatric Neurology, National Institute of Neuroscience and Hospital, Dhaka, Bangladesh
| | - Maksuda Lopa
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Nargis Jahan
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Shafaat Hossain
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Amirul Islam
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Cellular Intelligence Lab, GenomeArc Inc, Toronto, ON, Canada
| | | | - Md Omar Faruk
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Narayan Saha
- Department of Paediatric Neurology, National Institute of Neuroscience and Hospital, Dhaka, Bangladesh
| | - Gopen kumar Kundu
- Department of Child Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shayla Imam Kanta
- Department of Paediatric Neuroscience, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Rezaul Karim Kazal
- Department of Obstetrics and Gynaecology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Kanij Fatema
- Department of Paediatric Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md. Ashrafur Rahman
- Department of Pharmaceutical Sciences, Wilkes University, Pennsylvania, PA, United States
| | - Maruf Hasan
- Department of Biomedical Engineering, Military Institute of Science and Technology, Dhaka, Bangladesh
| | | | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ghausia Begum
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Binte Zehra
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Nasna Nassir
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - A. H. M. Nurun Nabi
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - K. M. Furkan Uddin
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Biochemistry, Holy Family Red Crescent Medical College, Dhaka, Bangladesh
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Cellular Intelligence (Ci) Lab, GenomeArc Inc, Toronto, ON, Canada
- *Correspondence: Mohammed Uddin,
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Oztan O, Zyga O, Stafford DEJ, Parker KJ. Linking oxytocin and arginine vasopressin signaling abnormalities to social behavior impairments in Prader-Willi syndrome. Neurosci Biobehav Rev 2022; 142:104870. [PMID: 36113782 PMCID: PMC11024898 DOI: 10.1016/j.neubiorev.2022.104870] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 11/19/2022]
Abstract
Prader-Willi syndrome (PWS) is a genetic neurodevelopmental disorder. Global hypothalamic dysfunction is a core feature of PWS and has been implicated as a driver of many of PWS's phenotypic characteristics (e.g., hyperphagia-induced obesity, hypogonadism, short stature). Although the two neuropeptides (i.e., oxytocin [OXT] and arginine vasopressin [AVP]) most implicated in mammalian prosocial functioning are of hypothalamic origin, and social functioning is markedly impaired in PWS, there has been little consideration of how dysregulation of these neuropeptide signaling pathways may contribute to PWS's social behavior impairments. The present article addresses this gap in knowledge by providing a comprehensive review of the preclinical and clinical PWS literature-spanning endogenous neuropeptide measurement to exogenous neuropeptide administration studies-to better understand the roles of OXT and AVP signaling in this population. The preponderance of evidence indicates that OXT and AVP signaling are indeed dysregulated in PWS, and that these neuropeptide pathways may provide promising targets for therapeutic intervention in a patient population that currently lacks a pharmacological strategy for its debilitating social behavior symptoms.
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Affiliation(s)
- Ozge Oztan
- 1201 Welch Road, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Olena Zyga
- 1201 Welch Road, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Diane E J Stafford
- Center for Academic Medicine, 453 Quarry Road, Department of Pediatrics, Division of Pediatric Endocrinology, Stanford University, Palo Alto, CA 94304, USA
| | - Karen J Parker
- 1201 Welch Road, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; 300 Pasteur Drive, Department of Comparative Medicine, Stanford University, Stanford, CA 94305, USA.
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Atypical 15q11.2-q13 Deletions and the Prader-Willi Phenotype. J Clin Med 2022; 11:jcm11154636. [PMID: 35956251 PMCID: PMC9369699 DOI: 10.3390/jcm11154636] [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: 07/20/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Prader-Willi syndrome (PWS) is a rare genetic disorder resulting from the lack of expression of the PWS region (locus q11-q13) on the paternally derived chromosome 15, as a result of a type I or II paternal deletion (50%), maternal uniparental disomy (43%), imprinting defect (4%) or translocation (<1%). In very rare cases, atypical deletions, smaller or larger than the typical deletion, are identified. These patients may have distinct phenotypical features and provide further information regarding the genotype−phenotype correlation in PWS. Methods: A prospective study in eight patients (six males and two females) with an atypical deletion in the PWS region accompanies an overview of reported cases. Results: All patients had hypotonia (100%) and many had typical PWS facial characteristics (75%), social and emotional developmental delays (75%), intellectual disabilities (50%), neonatal feeding problems and tube feeding (63%), history of obesity (50%), hyperphagia (50%) and scoliosis (50%). All males had cryptorchidism. Two patients had two separate deletions in the PWS critical region. Conclusions: Our findings provide further insight into PWS genotype−phenotype correlations; our results imply that inclusion of both SNURF-SNPRN and SNORD-116 genes in the deletion leads to a more complete PWS phenotype. A larger deletion, extending further upstream and downstream from these genes, does not cause a more severe phenotype. Conventional PWS methylation testing may miss small deletions, which can be identified using targeted next generation sequencing. PWS’s phenotypic diversity might be caused by differentially methylated regions outside the 15q11.2 locus.
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Watson CM, Jackson L, Crinnion LA, Bonthron DT, Sheridan E. Long-read sequencing to resolve the parent of origin of a de novo pathogenic UBE3A variant. J Med Genet 2022; 59:1082-1086. [PMID: 35414530 DOI: 10.1136/jmedgenet-2021-108314] [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: 01/19/2022] [Accepted: 03/24/2022] [Indexed: 11/04/2022]
Abstract
BackgroundThe ever-increasing capacity of short-read sequencing instruments is driving the adoption of whole genome sequencing (WGS) as a universal approach to the diagnosis of rare genetic disorders. However, many challenging genomic regions remain, for which alternative technologies must be deployed in order to address the clinical question satisfactorily.MethodsHere we report the use of long-read sequencing to resolve ambiguity over a suspected diagnosis of Angelman syndrome.ResultsDespite a normal chromosomal microarray result and methylation studies at the imprinted 15q11q13 locus, the continued clinical suspicion of Angelman Syndrome prompted trio WGS of the proband and his parents. A de novo heterozygous frameshift variant, c.2370_2373del (NM_130838.2) p.(Asp790Glufs*7), in UBE3A was identified. To determine the parental allele on which this variant arose, long-read sequencing of the flanking genomic region was performed. Comparison of the resulting haplotypes allowed us to determine that the pathogenic frameshift variant arose on the maternal allele, confirming a diagnosis of Angelman syndrome in this case.ConclusionLong-read nanopore sequencing provides significant clinical utility when assessing the parental origin of de novo variants.
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Affiliation(s)
- Christopher Mark Watson
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK .,Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Lucy Jackson
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Laura A Crinnion
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK.,Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
| | - David T Bonthron
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK.,Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Eamonn Sheridan
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK.,Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
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Fanis P, Morrou M, Tomazou M, Michailidou K, Spyrou GM, Toumba M, Skordis N, Neocleous V, Phylactou LA. Methylation status of hypothalamic Mkrn3 promoter across puberty. Front Endocrinol (Lausanne) 2022; 13:1075341. [PMID: 36714607 PMCID: PMC9880154 DOI: 10.3389/fendo.2022.1075341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023] Open
Abstract
Makorin RING finger protein 3 (MKRN3) is an important factor located on chromosome 15 in the imprinting region associated with Prader-Willi syndrome. Imprinted MKRN3 is expressed in hypothalamic regions essential for the onset of puberty and mutations in the gene have been found in patients with central precocious puberty. The pubertal process is largely controlled by epigenetic mechanisms that include, among other things, DNA methylation at CpG dinucleotides of puberty-related genes. In the present study, we investigated the methylation status of the Mkrn3 promoter in the hypothalamus of the female mouse before, during and after puberty. Initially, we mapped the 32 CpG dinucleotides in the promoter, the 5'UTR and the first 50 nucleotides of the coding region of the Mkrn3 gene. Moreover, we identified a short CpG island region (CpG islet) located within the promoter. Methylation analysis using bisulfite sequencing revealed that CpG dinucleotides were methylated regardless of developmental stage, with the lowest levels of methylation being found within the CpG islet region. In addition, the CpG islet region showed significantly lower methylation levels at the pre-pubertal stage when compared with the pubertal or post-pubertal stage. Finally, in silico analysis of transcription factor binding sites on the Mkrn3 CpG islet identified the recruitment of 29 transcriptional regulators of which 14 were transcriptional repressors. Our findings demonstrate the characterization and differential methylation of the CpG dinucleotides located in the Mkrn3 promoter that could influence the transcriptional activity in pre-pubertal compared to pubertal or post-pubertal period. Further studies are needed to clarify the possible mechanisms and effects of differential methylation of the Mkrn3 promoter.
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Affiliation(s)
- Pavlos Fanis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Maria Morrou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios Tomazou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M. Spyrou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Meropi Toumba
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Child Endocrine Care, Department of Pediatrics, Aretaeio Hospital, Nicosia, Cyprus
| | - Nicos Skordis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Division of Pediatric Endocrinology, Paedi Center for Specialized Pediatrics, Nicosia, Cyprus
- Medical School, University of Nicosia, Nicosia, Cyprus
| | - Vassos Neocleous
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Leonidas A. Phylactou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- *Correspondence: Leonidas A. Phylactou,
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Wang T, Li J, Yang L, Wu M, Ma Q. The Role of Long Non-coding RNAs in Human Imprinting Disorders: Prospective Therapeutic Targets. Front Cell Dev Biol 2021; 9:730014. [PMID: 34760887 PMCID: PMC8573313 DOI: 10.3389/fcell.2021.730014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022] Open
Abstract
Genomic imprinting is a term used for an intergenerational epigenetic inheritance and involves a subset of genes expressed in a parent-of-origin-dependent way. Imprinted genes are expressed preferentially from either the paternally or maternally inherited allele. Long non-coding RNAs play essential roles in regulating this allele-specific expression. In several well-studied imprinting clusters, long non-coding RNAs have been found to be essential in regulating temporal- and spatial-specific establishment and maintenance of imprinting patterns. Furthermore, recent insights into the epigenetic pathological mechanisms underlying human genomic imprinting disorders suggest that allele-specific expressed imprinted long non-coding RNAs serve as an upstream regulator of the expression of other protein-coding or non-coding imprinted genes in the same cluster. Aberrantly expressed long non-coding RNAs result in bi-allelic expression or silencing of neighboring imprinted genes. Here, we review the emerging roles of long non-coding RNAs in regulating the expression of imprinted genes, especially in human imprinting disorders, and discuss three strategies targeting the central long non-coding RNA UBE3A-ATS for the purpose of developing therapies for the imprinting disorders Prader-Willi syndrome and Angelman syndrome. In summary, a better understanding of long non-coding RNA-related mechanisms is key to the development of potential therapeutic targets for human imprinting disorders.
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Affiliation(s)
- Tingxuan Wang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jianjian Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liuyi Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Manyin Wu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qing Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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9
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Santiago-Rodriguez TM, Hollister EB. Multi 'omic data integration: A review of concepts, considerations, and approaches. Semin Perinatol 2021; 45:151456. [PMID: 34256961 DOI: 10.1016/j.semperi.2021.151456] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The application of 'omic techniques including, but not limited to genomics/metagenomics, transcriptomics/meta-transcriptomics, proteomics/meta-proteomics, and metabolomics to generate multiple datasets from a single sample have facilitated hypothesis generation leading to the identification of biological, molecular and ecological functions and mechanisms, as well as associations and correlations. Despite their power and promise, a variety of challenges must be considered in the successful design and execution of a multi-omics study. In this review, various 'omic technologies applicable to single- and meta-organisms (i.e., host + microbiome) are described, and considerations for sample collection, storage and processing prior to data generation and analysis, as well as approaches to data storage, dissemination and analysis are discussed. Finally, case studies are included as examples of multi-omic applications providing novel insights and a more holistic understanding of biological processes.
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Affiliation(s)
| | - Emily B Hollister
- Diversigen, Inc, 3 Greenway Plaza, Suite 1575, Houston, TX 77046, USA.
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Ruiz de la Cruz M, de la Cruz Montoya AH, Rojas Jiménez EA, Martínez Gregorio H, Díaz Velásquez CE, Paredes de la Vega J, de la Cruz Hernández-Hernández F, Vaca Paniagua F. Cis-Acting Factors Causing Secondary Epimutations: Impact on the Risk for Cancer and Other Diseases. Cancers (Basel) 2021; 13:cancers13194807. [PMID: 34638292 PMCID: PMC8508567 DOI: 10.3390/cancers13194807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 12/25/2022] Open
Abstract
Epigenetics affects gene expression and contributes to disease development by alterations known as epimutations. Hypermethylation that results in transcriptional silencing of tumor suppressor genes has been described in patients with hereditary cancers and without pathogenic variants in the coding region of cancer susceptibility genes. Although somatic promoter hypermethylation of these genes can occur in later stages of the carcinogenic process, constitutional methylation can be a crucial event during the first steps of tumorigenesis, accelerating tumor development. Primary epimutations originate independently of changes in the DNA sequence, while secondary epimutations are a consequence of a mutation in a cis or trans-acting factor. Secondary epimutations have a genetic basis in cis of the promoter regions of genes involved in familial cancers. This highlights epimutations as a novel carcinogenic mechanism whose contribution to human diseases is underestimated by the scarcity of the variants described. In this review, we provide an overview of secondary epimutations and present evidence of their impact on cancer. We propose the necessity for genetic screening of loci associated with secondary epimutations in familial cancer as part of prevention programs to improve molecular diagnosis, secondary prevention, and reduce the mortality of these diseases.
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Affiliation(s)
- Miguel Ruiz de la Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | | | - Ernesto Arturo Rojas Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Héctor Martínez Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Clara Estela Díaz Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
| | - Jimena Paredes de la Vega
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Fidel de la Cruz Hernández-Hernández
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | - Felipe Vaca Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 14080, Mexico
- Correspondence: ; Tel.: +52-55-5623-1333 (ext. 39788)
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11
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Langouët M, Gorka D, Orniacki C, Dupont-Thibert CM, Chung MS, Glatt-Deeley HR, Germain N, Crandall LJ, Cotney JL, Stoddard CE, Lalande M, Chamberlain SJ. Specific ZNF274 binding interference at SNORD116 activates the maternal transcripts in Prader-Willi syndrome neurons. Hum Mol Genet 2021; 29:3285-3295. [PMID: 32977341 DOI: 10.1093/hmg/ddaa210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/15/2020] [Accepted: 08/26/2020] [Indexed: 12/27/2022] Open
Abstract
Prader-Willi syndrome (PWS) is characterized by neonatal hypotonia, developmental delay and hyperphagia/obesity. This disorder is caused by the absence of paternally expressed gene products from chromosome 15q11-q13. We previously demonstrated that knocking out ZNF274, a Kruppel-associated box-A-domain zinc finger protein capable of recruiting epigenetic machinery to deposit the H3K9me3 repressive histone modification, can activate expression from the normally silent maternal allele of SNORD116 in neurons derived from PWS induced pluripotent stem cells (iPSCs). However, ZNF274 has many other targets in the genome in addition to SNORD116. Depleting ZNF274 will surely affect the expression of other important genes and disrupt other pathways. Here, we used CRISPR/Cas9 to delete ZNF274 binding sites at the SNORD116 locus to determine whether activation of the maternal copy of SNORD116 could be achieved without altering ZNF274 protein levels. We obtained similar activation of gene expression from the normally silenced maternal allele in neurons derived from PWS iPSCs, compared with ZNF274 knockout, demonstrating that ZNF274 is directly involved in the repression of SNORD116. These results suggest that interfering with ZNF274 binding at the maternal SNORD116 locus is a potential therapeutic strategy for PWS.
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Affiliation(s)
- Maéva Langouët
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Dea Gorka
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Clarisse Orniacki
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Clémence M Dupont-Thibert
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Michael S Chung
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Heather R Glatt-Deeley
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Noelle Germain
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Leann J Crandall
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030, USA
| | - Christopher E Stoddard
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Marc Lalande
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030, USA
| | - Stormy J Chamberlain
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030, USA
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12
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Zhang K, Liu S, Gu W, Lv Y, Yu H, Gao M, Wang D, Zhao J, Li X, Gai Z, Zhao S, Liu Y, Yuan Y. Transmission of a Novel Imprinting Center Deletion Associated With Prader-Willi Syndrome Through Three Generations of a Chinese Family: Case Presentation, Differential Diagnosis, and a Lesson Worth Thinking About. Front Genet 2021; 12:630650. [PMID: 34504512 PMCID: PMC8421676 DOI: 10.3389/fgene.2021.630650] [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: 12/03/2020] [Accepted: 07/19/2021] [Indexed: 12/02/2022] Open
Abstract
Prader-Willi syndrome (PWS) is a complex genetic syndrome caused by the loss of function of genes in 15q11-q13 that are subject to regulation by genomic imprinting and expressed from the paternal allele only. The main clinical features of PWS patients are hypotonia during the neonatal and infantile stages, accompanied by delayed neuropsychomotor development, hyperphagia, obesity, hypogonadism, short stature, small hands and feet, mental disabilities, and behavioral problems. However, PWS has a clinical overlap with other disorders, especially those with other gene variations or chromosomal imbalances but sharing part of the similar clinical manifestations with PWS, which are sometimes referred to as Prader-Willi syndrome-like (PWS-like) disorders. Furthermore, it is worth mentioning that significant obesity as a consequence of hyperphagia in PWS usually develops between the ages of 1 and 6 years, which makes early diagnosis difficult. Thus, PWS is often not clinically recognized in infants and, on the other hand, may be wrongly suspected in obese and intellectually disabled patients. Therefore, an accurate investigation is necessary to differentiate classical PWS from PWS-like phenotypes, which is imperative for further treatment. For PWS, it is usually sporadic, and very rare family history and affected siblings have been described. Here, we report the clinical and molecular findings in a three-generation family with a novel 550-kb microdeletion affecting the chromosome 15 imprinting center (IC). Overall, the present study finds that the symptoms of our patient are somewhat different from those of typical PWS cases diagnosed and given treatment in our hospital. The familial occurrence and clinical features were challenging to our diagnostic strategy. The microdeletion included a region within the complex small nuclear ribonucleoprotein polypeptide protein N (SNRPN) gene locus encompassing the PWS IC and was identified by using a variety of techniques. Haplotype studies suggest that the IC microdeletion was vertically transmitted from an unaffected paternal grandmother to an unaffected father and then caused PWS in two sibling grandchildren when the IC microdeletion was inherited paternally. Based on the results of our study, preimplantation genetic diagnosis (PGD) was applied successfully to exclude imprinting deficiency in preimplantation embryos before transfer into the mother's uterus. Our study may be especially instructive regarding accurate diagnosis, differential diagnosis, genetic counseling, and PGD for familial PWS patients.
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Affiliation(s)
- Kaihui Zhang
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, China
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Jinan, China
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai, China
| | - Shu Liu
- Children Inherited Metabolism and Endocrine Department, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wenjun Gu
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai, China
| | - Yuqiang Lv
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Jinan, China
| | - Haihua Yu
- Neonatal Intensive Care Unit, Qilu Children’s Hospital of Shandong University, Jinan, China
| | - Min Gao
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Jinan, China
| | - Dong Wang
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Jinan, China
| | - Jianyuan Zhao
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoying Li
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Jinan, China
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Jinan, China
| | - Shimin Zhao
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics and Development, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yi Liu
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Jinan, China
| | - Yiyuan Yuan
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai, China
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13
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Markouli M, Strepkos D, Piperi C. Structure, Activity and Function of the SETDB1 Protein Methyltransferase. Life (Basel) 2021; 11:life11080817. [PMID: 34440561 PMCID: PMC8397983 DOI: 10.3390/life11080817] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
The SET Domain Bifurcated Histone Lysine Methyltransferase 1 (SETDB1) is a prominent member of the Suppressor of Variegation 3–9 (SUV39)-related protein lysine methyltransferases (PKMTs), comprising three isoforms that differ in length and domain composition. SETDB1 is widely expressed in human tissues, methylating Histone 3 lysine 9 (H3K9) residues, promoting chromatin compaction and exerting negative regulation on gene expression. SETDB1 has a central role in normal physiology and nervous system development, having been implicated in the regulation of cell cycle progression, inactivation of the X chromosome, immune cells function, expression of retroelements and formation of promyelocytic leukemia (PML) nuclear bodies (NB). SETDB1 has been frequently deregulated in carcinogenesis, being implicated in the pathogenesis of gliomas, melanomas, as well as in lung, breast, gastrointestinal and ovarian tumors, where it mainly exerts an oncogenic role. Aberrant activity of SETDB1 has also been implicated in several neuropsychiatric, cardiovascular and gastrointestinal diseases, including schizophrenia, Huntington’s disease, congenital heart defects and inflammatory bowel disease. Herein, we provide an update on the unique structural and biochemical features of SETDB1 that contribute to its regulation, as well as its molecular and cellular impact in normal physiology and disease with potential therapeutic options.
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14
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Yang L, Shu X, Mao S, Wang Y, Du X, Zou C. Genotype-Phenotype Correlations in Angelman Syndrome. Genes (Basel) 2021; 12:987. [PMID: 34203304 PMCID: PMC8304328 DOI: 10.3390/genes12070987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022] Open
Abstract
Angelman syndrome (AS) is a rare neurodevelopmental disease that is caused by the loss of function of the maternal copy of ubiquitin-protein ligase E3A (UBE3A) on the chromosome 15q11-13 region. AS is characterized by global developmental delay, severe intellectual disability, lack of speech, happy disposition, ataxia, epilepsy, and distinct behavioral profile. There are four molecular mechanisms of etiology: maternal deletion of chromosome 15q11-q13, paternal uniparental disomy of chromosome 15q11-q13, imprinting defects, and maternally inherited UBE3A mutations. Different genetic types may show different phenotypes in performance, seizure, behavior, sleep, and other aspects. AS caused by maternal deletion of 15q11-13 appears to have worse development, cognitive skills, albinism, ataxia, and more autistic features than those of other genotypes. Children with a UBE3A mutation have less severe phenotypes and a nearly normal development quotient. In this review, we proposed to review genotype-phenotype correlations based on different genotypes. Understanding the pathophysiology of the different genotypes and the genotype-phenotype correlations will offer an opportunity for individualized treatment and genetic counseling. Genotype-phenotype correlations based on larger data should be carried out for identifying new treatment modalities.
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Affiliation(s)
- Lili Yang
- Department of Genetics and Metabolism, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China;
| | - Xiaoli Shu
- Department of Laboratory Center, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China;
| | - Shujiong Mao
- Division of Neonatology, Department of Pediatrics, Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China;
| | - Yi Wang
- Department of Neurology, Children’s Hospital of Fudan University, Shanghai 201102, China; (Y.W.); (X.D.)
| | - Xiaonan Du
- Department of Neurology, Children’s Hospital of Fudan University, Shanghai 201102, China; (Y.W.); (X.D.)
| | - Chaochun Zou
- Department of Endocrinology, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
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15
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Pellikaan K, van Woerden GM, Kleinendorst L, Rosenberg AGW, Horsthemke B, Grosser C, van Zutven LJCM, van Rossum EFC, van der Lely AJ, Resnick JL, Brüggenwirth HT, van Haelst MM, de Graaff LCG. The Diagnostic Journey of a Patient with Prader-Willi-Like Syndrome and a Unique Homozygous SNURF-SNRPN Variant; Bio-Molecular Analysis and Review of the Literature. Genes (Basel) 2021; 12:genes12060875. [PMID: 34200226 PMCID: PMC8227738 DOI: 10.3390/genes12060875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Prader–Willi syndrome (PWS) is a rare genetic condition characterized by hypotonia, intellectual disability, and hypothalamic dysfunction, causing pituitary hormone deficiencies and hyperphagia, ultimately leading to obesity. PWS is most often caused by the loss of expression of a cluster of genes on chromosome 15q11.2-13. Patients with Prader–Willi-like syndrome (PWLS) display features of the PWS phenotype without a classical PWS genetic defect. We describe a 46-year-old patient with PWLS, including hypotonia, intellectual disability, hyperphagia, and pituitary hormone deficiencies. Routine genetic tests for PWS were normal, but a homozygous missense variant NM_003097.3(SNRPN):c.193C>T, p.(Arg65Trp) was identified. Single nucleotide polymorphism array showed several large regions of homozygosity, caused by high-grade consanguinity between the parents. Our functional analysis, the ‘Pipeline for Rapid in silico, in vivo, in vitro Screening of Mutations’ (PRiSM) screen, showed that overexpression of SNRPN-p.Arg65Trp had a dominant negative effect, strongly suggesting pathogenicity. However, it could not be confirmed that the variant was responsible for the phenotype of the patient. In conclusion, we present a unique homozygous missense variant in SNURF-SNRPN in a patient with PWLS. We describe the diagnostic trajectory of this patient and the possible contributors to her phenotype in light of the current literature on the genotype–phenotype relationship in PWS.
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Affiliation(s)
- Karlijn Pellikaan
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (K.P.); (A.G.W.R.); (E.F.C.v.R.); (A.J.v.d.L.)
- Dutch Centre of Reference for Prader-Willi Syndrome, 3015 GD Rotterdam, The Netherlands
| | - Geeske M. van Woerden
- Department of Neuroscience, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands;
- The ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands; (L.J.C.M.v.Z.); (H.T.B.)
| | - Lotte Kleinendorst
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1081 HV Amsterdam, The Netherlands; (L.K.); (M.M.v.H.)
| | - Anna G. W. Rosenberg
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (K.P.); (A.G.W.R.); (E.F.C.v.R.); (A.J.v.d.L.)
- Dutch Centre of Reference for Prader-Willi Syndrome, 3015 GD Rotterdam, The Netherlands
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (B.H.); (C.G.)
| | - Christian Grosser
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (B.H.); (C.G.)
- Praxis für Humangenetik Tübingen, 72076 Tuebingen, Germany
| | - Laura J. C. M. van Zutven
- Department of Clinical Genetics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands; (L.J.C.M.v.Z.); (H.T.B.)
| | - Elisabeth F. C. van Rossum
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (K.P.); (A.G.W.R.); (E.F.C.v.R.); (A.J.v.d.L.)
- Obesity Center CGG, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands
| | - Aart J. van der Lely
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (K.P.); (A.G.W.R.); (E.F.C.v.R.); (A.J.v.d.L.)
| | - James L. Resnick
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Hennie T. Brüggenwirth
- Department of Clinical Genetics, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands; (L.J.C.M.v.Z.); (H.T.B.)
| | - Mieke M. van Haelst
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1081 HV Amsterdam, The Netherlands; (L.K.); (M.M.v.H.)
| | - Laura C. G. de Graaff
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands; (K.P.); (A.G.W.R.); (E.F.C.v.R.); (A.J.v.d.L.)
- Dutch Centre of Reference for Prader-Willi Syndrome, 3015 GD Rotterdam, The Netherlands
- The ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
- Academic Centre for Growth Disorders, Erasmus MC Rotterdam, 3015 GD Rotterdam, The Netherlands
- Correspondence: ; Tel.: +31-618843010
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16
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Eggermann T, Davies JH, Tauber M, van den Akker E, Hokken-Koelega A, Johansson G, Netchine I. Growth Restriction and Genomic Imprinting-Overlapping Phenotypes Support the Concept of an Imprinting Network. Genes (Basel) 2021; 12:genes12040585. [PMID: 33920525 PMCID: PMC8073901 DOI: 10.3390/genes12040585] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
Intrauterine and postnatal growth disturbances are major clinical features of imprinting disorders, a molecularly defined group of congenital syndromes caused by molecular alterations affecting parentally imprinted genes. These genes are expressed monoallelically and in a parent-of-origin manner, and they have an impact on human growth and development. In fact, several genes with an exclusive expression from the paternal allele have been shown to promote foetal growth, whereas maternally expressed genes suppress it. The evolution of this correlation might be explained by the different interests of the maternal and paternal genomes, aiming for the conservation of maternal resources for multiple offspring versus extracting maximal maternal resources. Since not all imprinted genes in higher mammals show the same imprinting pattern in different species, the findings from animal models are not always transferable to human. Therefore, human imprinting disorders might serve as models to understand the complex regulation and interaction of imprinted loci. This knowledge is a prerequisite for the development of precise diagnostic tools and therapeutic strategies for patients affected by imprinting disorders. In this review we will specifically overview the current knowledge on imprinting disorders associated with growth retardation, and its increasing relevance in a personalised medicine direction and the need for a multidisciplinary therapeutic approach.
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Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, 52062 Aachen, Germany
- Correspondence: ; Tel.: +49-241-8088008; Fax: +49-241-8082394
| | - Justin H. Davies
- Department of Paediatric Endocrinology, University Hospital Southampton, Southampton SO16 6YD, UK;
| | - Maithé Tauber
- Research centre of rare diseases PRADORT, Childrens Hospital, CHU Toulouse, Toulouse Institute of Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291-CNRS UMR5051-Tolouse III University, 31062 Toulouse, France;
| | - Erica van den Akker
- Erasmus University Medical Center, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Anita Hokken-Koelega
- Erasmus University Medical Center, Pediatrics, Subdivision of Endocrinology, 3015 GD Rotterdam, The Netherlands;
| | - Gudmundur Johansson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg and Department of Endocrinology, Sahlgrenska University Hospital, 413 45 Gothenburg, Sweden;
| | - Irène Netchine
- Medical Faculty, AP-HP, Armand Trousseau Hospital-Functional Endocrine Research Unit, INSERM, Research Centre Saint-Antoine, Sorbonne University, 75012 Paris, France;
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17
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Kummerfeld DM, Raabe CA, Brosius J, Mo D, Skryabin BV, Rozhdestvensky TS. A Comprehensive Review of Genetically Engineered Mouse Models for Prader-Willi Syndrome Research. Int J Mol Sci 2021; 22:3613. [PMID: 33807162 PMCID: PMC8037846 DOI: 10.3390/ijms22073613] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 02/05/2023] Open
Abstract
Prader-Willi syndrome (PWS) is a neurogenetic multifactorial disorder caused by the deletion or inactivation of paternally imprinted genes on human chromosome 15q11-q13. The affected homologous locus is on mouse chromosome 7C. The positional conservation and organization of genes including the imprinting pattern between mice and men implies similar physiological functions of this locus. Therefore, considerable efforts to recreate the pathogenesis of PWS have been accomplished in mouse models. We provide a summary of different mouse models that were generated for the analysis of PWS and discuss their impact on our current understanding of corresponding genes, their putative functions and the pathogenesis of PWS. Murine models of PWS unveiled the contribution of each affected gene to this multi-facetted disease, and also enabled the establishment of the minimal critical genomic region (PWScr) responsible for core symptoms, highlighting the importance of non-protein coding genes in the PWS locus. Although the underlying disease-causing mechanisms of PWS remain widely unresolved and existing mouse models do not fully capture the entire spectrum of the human PWS disorder, continuous improvements of genetically engineered mouse models have proven to be very powerful and valuable tools in PWS research.
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Affiliation(s)
- Delf-Magnus Kummerfeld
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
| | - Carsten A. Raabe
- Research Group Regulatory Mechanisms of Inflammation, Institute of Medical Biochemistry (ZMBE), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
| | - Juergen Brosius
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Dingding Mo
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;
| | - Boris V. Skryabin
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
| | - Timofey S. Rozhdestvensky
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
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18
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Chen CP, Lin MH, Chen YY, Chern SR, Wu PS, Chen SW, Wu FT, Town DD, Lee MS, Pan CW, Wang W. Prenatal diagnosis of a 15q11.2-q14 deletion of paternal origin associated with increased nuchal translucency, mosaicism for de novo multiple unbalanced translocations involving 15q11-q14, 5qter, 15qter, 17pter and 3qter and Prader-Willi syndrome. Taiwan J Obstet Gynecol 2021; 60:335-340. [PMID: 33678338 DOI: 10.1016/j.tjog.2021.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2020] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis of a 15q11.2-q14 deletion of paternal origin associated with increased nuchal translucency (NT), mosaicism for de novo multiple unbalanced translocations involving 15q11-q14, 5qter, 15qter, 17pter and 3qter, and Prader-Willi syndrome (PWS). CASE REPORT A 32-year-old, primigravid woman underwent amniocentesis at 18 weeks of gestation because of an increased NT thickness of 5.6 mm and abnormal maternal serum screening results in the first trimester. The pregnancy was conceived by in vitro fertilization and embryo transfer. Amniocentesis revealed a karyotype of 45,XX,der(5)t(5;15)(q35;q14),-15 [16]/45,XX,-15,der(17)t(15;17)(q14;p13)[3]/45,XX,der(15)t(15;15)(q35;q14),-15[2]. The parental karyotypes were normal. Prenatal ultrasound findings were unremarkable. Array comparative genomic hybridization (aCGH) analysis on the DNA extracted from cultured amniocytes revealed the result of arr 15q11.2q14 (22,765,628-38,651,755) × 1.0 [GRCh37 (hg19)] with a 15.886-Mb 15q11.2-q14 deletion encompassing TUBGCP5, CYFIP1, NIPA2, NIPA1, SNRPN, SNURF, SNORD116-1, IPW, UBE3A, ACTC1 and MEIS2. The pregnancy was subsequently terminated, and a malformed fetus with facial dysmorphism was delivered. The cord blood had a karyotype of 45,XX,der(5)t(5;15)(q35;q14),-15[46]/45,XX,der(3)t(3;15) (q29;q14),-15[2]/45,XX,-15,der(17)t(15;17)(q14;p13)[2]. The placenta had a karyotype of 45,XX,der(5) t(5;15)(q35;q14),-15. Polymorphic DNA marker analysis confirmed a paternal origin of the proximal 15q deletion. CONCLUSION Increased NT and abnormal maternal serum screening results may prenatally be associated with PWS. Chromosome 15 rearrangements in PWS include mosaicism for de novo multiple unbalanced translocations.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan.
| | - Ming-Huei Lin
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yi-Yung Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Fang-Tzu Wu
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Dai-Dyi Town
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Meng-Shan Lee
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chen-Wen Pan
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
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19
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Mendiola AJP, LaSalle JM. Epigenetics in Prader-Willi Syndrome. Front Genet 2021; 12:624581. [PMID: 33659026 PMCID: PMC7917289 DOI: 10.3389/fgene.2021.624581] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/18/2021] [Indexed: 11/16/2022] Open
Abstract
Prader-Willi Syndrome (PWS) is a rare neurodevelopmental disorder that affects approximately 1 in 20,000 individuals worldwide. Symptom progression in PWS is classically characterized by two nutritional stages. Stage 1 is hypotonia characterized by poor muscle tone that leads to poor feeding behavior causing failure to thrive in early neonatal life. Stage 2 is followed by the development of extreme hyperphagia, also known as insatiable eating and fixation on food that often leads to obesity in early childhood. Other major features of PWS include obsessive-compulsive and hoarding behaviors, intellectual disability, and sleep abnormalities. PWS is genetic disorder mapping to imprinted 15q11.2-q13.3 locus, specifically at the paternally expressed SNORD116 locus of small nucleolar RNAs and noncoding host gene transcripts. SNORD116 is processed into several noncoding components and is hypothesized to orchestrate diurnal changes in metabolism through epigenetics, according to functional studies. Here, we review the current status of epigenetic mechanisms in PWS, with an emphasis on an emerging role for SNORD116 in circadian and sleep phenotypes. We also summarize current ongoing therapeutic strategies, as well as potential implications for more common human metabolic and psychiatric disorders.
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Affiliation(s)
| | - Janine M. LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, MIND Institute, University of California, Davis, Davis, CA, United States
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20
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Markouli M, Strepkos D, Chlamydas S, Piperi C. Histone lysine methyltransferase SETDB1 as a novel target for central nervous system diseases. Prog Neurobiol 2020; 200:101968. [PMID: 33279625 DOI: 10.1016/j.pneurobio.2020.101968] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/31/2020] [Accepted: 11/29/2020] [Indexed: 12/14/2022]
Abstract
Epigenetic changes that regulate chromatin structure have a major impact in genome stabilization and maintenance of cellular homeostasis, been recently implicated in the pathophysiology of central nervous system (CNS). Aberrant expression and dysregulation of histone modification enzymes has been associated with the development of several CNS disorders, revealing these enzymes as putative targets for drug development and novel therapeutic approaches. SETDB1 is a histone lysine methyltransferase responsible for the di- and tri-methylation of histone 3 (H3) at lysine (K) 9 in euchromatic regions further promoting gene silencing through heterochromatin formation. By this way, SETDB1 has been shown to regulate gene expression and influence normal cellular homeostasis required for nervous system function while it is also implicated in the pathogenesis of CNS disorders. Among them, brain tumors, schizophrenia, Huntington's disease, autism spectrum disorders along with alcohol-induced fetal neurobehavioral deficits and Prader-Willi syndrome are representative examples, indicating the aberrant expression and function of SETDB1 as a common pathogenic factor. In this review, we focus on SETDB1-associated molecular mechanisms implicated in CNS physiology and disease while we further discuss current pharmacological approaches targeting SETDB1 enzymatic activity with beneficial effects.
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Affiliation(s)
- Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Strepkos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Sarantis Chlamydas
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece.
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21
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Abstract
Abstract
Imprinting disorders are a group of rare diseases with a broad phenotypic spectrum caused by a wide variety of genetic and epigenetic disturbances of imprinted genes or gene clusters. The molecular genetic causes and their respective frequencies vary between the different imprinting disorders so that each has its unique requirements for the diagnostic workflow, making it challenging. To add even more complexity to this field, new molecular genetic causes have been identified over time and new technologies have enhanced the detectability e. g. of mosaic disturbances.
The precise identification of the underlying molecular genetic cause is of utmost importance in regard to recurrence risk in the families, tumour risk, clinical management and conventional and in the future therapeutic managements.
Here we give an overview of the imprinting disorders, their specific requirements for the diagnostic workup and the most common techniques used and point out possible pitfalls.
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Affiliation(s)
- Jasmin Beygo
- Institute of Human Genetics, University Hospital Essen , University of Duisburg-Essen , Essen , Germany
| | - Deniz Kanber
- Institute of Human Genetics, University Hospital Essen , University of Duisburg-Essen , Essen , Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty , RWTH Aachen University , Aachen , Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty , RWTH Aachen University , Aachen , Germany
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22
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Shubina J, Barkov IY, Stupko OK, Kuznetsova MV, Goltsov AY, Kochetkova TO, Trofimov DY, Sukhikh GT. Prenatal diagnosis of Prader-Willi syndrome due to uniparental disomy with NIPS: Case report and literature review. Mol Genet Genomic Med 2020; 8:e1448. [PMID: 32857485 PMCID: PMC7549559 DOI: 10.1002/mgg3.1448] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
Background PWS is challenging to diagnose prenatally due to a lack of precise and well‐characterized fetal phenotypes and noninvasive markers. Here we present the case of prenatal diagnosis of Prader‐Willi syndrome, which was suspected with whole‐genome NIPS. Methods Whole‐genome noninvasive prenatal screening showed a high risk for trisomy 15. Amniocentesis followed by FISH analysis and SNP‐based chromosomal microarray was performed. Results Simultaneous analysis of maternal and fetal samples with SNP microarrays demonstrated maternal uniparental disomy (UPD). Conclusion The presented case is the first case of PWS described in detail, which was suspected by NIPS results. It demonstrates that the choice of confirmation methods concerning the time needed is crucial for the right diagnosis. We suppose that prenatal testing of UPD is essential for chromosome regions, which play a key role in the appearance of various gene‐imprinting failure syndromes like PWS or AS.
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Affiliation(s)
- Jekaterina Shubina
- Federal State Budget Institution "National Medical Research Center for Obstetrics Gynecology and Perinatology named after Academician V I Kulakov", Moscow, Russia
| | - Ilya Y Barkov
- Federal State Budget Institution "National Medical Research Center for Obstetrics Gynecology and Perinatology named after Academician V I Kulakov", Moscow, Russia
| | - Olga K Stupko
- Federal State Budget Institution "National Medical Research Center for Obstetrics Gynecology and Perinatology named after Academician V I Kulakov", Moscow, Russia
| | - Maria V Kuznetsova
- Federal State Budget Institution "National Medical Research Center for Obstetrics Gynecology and Perinatology named after Academician V I Kulakov", Moscow, Russia
| | - Andrey Y Goltsov
- Federal State Budget Institution "National Medical Research Center for Obstetrics Gynecology and Perinatology named after Academician V I Kulakov", Moscow, Russia
| | - Taisya O Kochetkova
- Federal State Budget Institution "National Medical Research Center for Obstetrics Gynecology and Perinatology named after Academician V I Kulakov", Moscow, Russia
| | - Dmitry Y Trofimov
- Federal State Budget Institution "National Medical Research Center for Obstetrics Gynecology and Perinatology named after Academician V I Kulakov", Moscow, Russia
| | - Gennady T Sukhikh
- Federal State Budget Institution "National Medical Research Center for Obstetrics Gynecology and Perinatology named after Academician V I Kulakov", Moscow, Russia
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23
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Javed S, Selliah T, Lee YJ, Huang WH. Dosage-sensitive genes in autism spectrum disorders: From neurobiology to therapy. Neurosci Biobehav Rev 2020; 118:538-567. [PMID: 32858083 DOI: 10.1016/j.neubiorev.2020.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/26/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of heterogenous neurodevelopmental disorders affecting 1 in 59 children. Syndromic ASDs are commonly associated with chromosomal rearrangements or dosage imbalance involving a single gene. Many of these genes are dosage-sensitive and regulate transcription, protein homeostasis, and synaptic function in the brain. Despite vastly different molecular perturbations, syndromic ASDs share core symptoms including social dysfunction and repetitive behavior. However, each ASD subtype has a unique pathogenic mechanism and combination of comorbidities that require individual attention. We have learned a great deal about how these dosage-sensitive genes control brain development and behaviors from genetically-engineered mice. Here we describe the clinical features of eight monogenic neurodevelopmental disorders caused by dosage imbalance of four genes, as well as recent advances in using genetic mouse models to understand their pathogenic mechanisms and develop intervention strategies. We propose that applying newly developed quantitative molecular and neuroscience technologies will advance our understanding of the unique neurobiology of each disorder and enable the development of personalized therapy.
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Affiliation(s)
- Sehrish Javed
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Tharushan Selliah
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yu-Ju Lee
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Wei-Hsiang Huang
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada.
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24
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A newborn screening pilot study using methylation-sensitive high resolution melting on dried blood spots to detect Prader-Willi and Angelman syndromes. Sci Rep 2020; 10:13026. [PMID: 32747801 PMCID: PMC7400512 DOI: 10.1038/s41598-020-69750-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/14/2020] [Indexed: 12/24/2022] Open
Abstract
Prader-Willi (PWS) and Angelman (AS) syndromes are two clinically distinct imprinted disorders characterized by genetic abnormalities at 15q11-q13. Early diagnosis of both syndromes provides improved treatment and accurate genetic counseling. Whole blood (WB) is the most common DNA source of many methodologies to detect PWS and AS, however, the need of WB makes a massive screening difficult in newborns due to economic and technical limitations. The aim of this study was to adapt a Methylation-sensitive High-Resolution Melting (MS-HRM) approach from dried blood spot (DBS) samples, assessing the different DNA isolation techniques and diagnostic performance. Over a 1-year period, we collected 125 DBS cards, of which 45 had already been diagnosed by MS-HRM (20 PWS, 1 AS, and 24 healthy individuals). We tested three different DBS-DNA extraction techniques assessing the DNA concentration and quality, followed by MS-HRM and statistical comparison. Each DBS-DNA extraction method was capable of accuracy in detecting all PWS and AS individuals. However, the efficiency to detect healthy individuals varied according to methodology. In our experience, DNA extracted from DBS analyzed by the MS-HRM methodology provides an accurate approach for genetic screening of imprinting related disorders in newborns, offering several benefits compared to traditional whole blood methods.
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25
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Khosravizadeh Z, Hassanzadeh G, Tavakkoly Bazzaz J, Alizadeh F, Totonchi M, Salehi E, Khodamoradi K, Khanehzad M, Hosseini SR, Abolhassani F. The effect of cryopreservation on DNA methylation patterns of the chromosome 15q11-q13 region in human spermatozoa. Cell Tissue Bank 2020; 21:433-445. [PMID: 32253620 DOI: 10.1007/s10561-020-09828-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 03/11/2020] [Indexed: 01/23/2023]
Abstract
Human sperm cryopreservation is a common technique which is used in assisted reproductive technologies. Despite the existence of evidence supporting the production of ROS and DNA fragmentation during sperm cryopreservation, there is little and equivocal information about the cryopreservation effects on methylation of imprinted genes and imprinting control regions. In this study, we have investigated the effects of cryopreservation on DNA methylation in promoter regions of SNURF-SNRPN and UBE3A imprinted genes, PWS-ICR and AS-ICR in the chromosome 15q11-q13 region. Semen samples from 10 healthy normozoospermic men were collected and each sample was divided into four equal aliquots: fresh, cryoprotectant, cryopreservation, and H2O2. We measured the ROS levels and DNA fragmentation using DCFH-DA and TUNEL assay respectively by flow cytometry. DNA methylation in promoter regions of SNURF-SNRPN and UBE3A imprinted genes, PWS-ICR and AS-ICR in the chromosome 15q11-q13 region were evaluated by quantitative methylation-specific PCR technique. Intracellular levels of ROS and percentage of TUNEL-positive spermatozoa significantly increased in cryopreservation group compared to fresh group. Exposure to cryoprotectant had no significant effect on ROS levels and DNA fragmentation. Neither cryopreservation nor exposure to cryoprotectant significantly affected DNA methylation of the selected gene regions. However, DNA fragmentation had positive correlation with DNA methylation of AS-ICR. In conclusion, based on our study, clinical use of sperm cryopreservation for fertility treatments appear to be safe in regard to DNA methylation in the chromosome 15q11-q13 region.
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Affiliation(s)
- Zahra Khosravizadeh
- Faculty of Anatomy, School of Medicine, Tehran University of Medical Science, 16 Azar Avenue, Poor Sina Street, Tehran, Iran
| | - Gholamreza Hassanzadeh
- Faculty of Anatomy, School of Medicine, Tehran University of Medical Science, 16 Azar Avenue, Poor Sina Street, Tehran, Iran
| | - Javad Tavakkoly Bazzaz
- Faculty of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, 16 Azar Avenue, Poor Sina Street, Tehran, Iran
| | - Fatemeh Alizadeh
- Faculty of Genomic Psychiatry and Behavioral Genomics (DGPBG), Roozbeh Hospital, School of Medicine, Tehran University of Medical Science, South Kargar Avenue, Tehran, Iran
| | - Mehdi Totonchi
- Faculty of Stem Cells and Developmental Biology, Royan Institute, Tehran, Iran
| | - Ensieh Salehi
- Faculty of Gynecology, School of Medicine, Fertility and Infertility Research Center, Bandar Abbas, Iran.,Dr. Ali Shariati Hospital, Shahid Mohammadi Hospital, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Kajal Khodamoradi
- Faculty of Anatomy, School of Medicine, Tehran University of Medical Science, 16 Azar Avenue, Poor Sina Street, Tehran, Iran
| | - Maryam Khanehzad
- Faculty of Anatomy, School of Medicine, Tehran University of Medical Science, 16 Azar Avenue, Poor Sina Street, Tehran, Iran
| | - Seyed Reza Hosseini
- Faculty of Urology, Sina Hospital, Tehran University of Medical Science, Imam Khomeini Street, Tehran, Iran.
| | - Farid Abolhassani
- Faculty of Anatomy, School of Medicine, Tehran University of Medical Science, 16 Azar Avenue, Poor Sina Street, Tehran, Iran.
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26
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Common genetic variation in the Angelman syndrome imprinting centre affects the imprinting of chromosome 15. Eur J Hum Genet 2020; 28:835-839. [PMID: 32152487 PMCID: PMC7253442 DOI: 10.1038/s41431-020-0595-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/21/2020] [Accepted: 02/04/2020] [Indexed: 11/17/2022] Open
Abstract
Angelman syndrome (AS) is a rare neurogenetic imprinting disorder caused by the loss of function of UBE3A. In ~3–5% of AS patients, the disease is due to an imprinting defect (ID). These patients lack DNA methylation of the maternal SNRPN promotor so that a large SNRPN sense/UBE3A antisense transcript (SNHG14) is expressed, which silences UBE3A. In very rare cases, the ID is caused by a deletion of the AS imprinting centre (AS-IC). To search for sequence alterations, we sequenced this region in 168 patients without an AS-IC deletion, but did not detect any sequence alteration. However, the AS-IC harbours six common variants (five single nucleotide variants and one TATG insertion/deletion variant), which constitute five common haplotypes. To determine if any of these haplotypes is associated with an increased risk for an ID, we investigated 119 informative AS-ID trios with the transmission disequilibrium test, which is a family-based association test that measures the over-transmission of an allele or haplotype from heterozygous parents to affected offspring. By this we observed maternal over-transmission of haplotype H-AS3 (p = 0.0073). Interestingly, H-AS3 is the only haplotype that includes the TATG deletion allele. We conclude that this haplotype and possibly the TATG deletion, which removes a SOX2 binding site, increases the risk for a maternal ID and AS. Our data strengthen the notion that the AS-IC is important for establishing and/or maintaining DNA methylation at the SNRPN promotor and show that common genetic variation can affect genomic imprinting.
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27
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Abstract
Imprinting disorders are a group of congenital diseases caused by dysregulation of genomic imprinting, affecting prenatal and postnatal growth, neurocognitive development, metabolism and cancer predisposition. Aberrant expression of imprinted genes can be achieved through different mechanisms, classified into epigenetic - if not involving DNA sequence change - or genetic in the case of altered genomic sequence. Despite the underlying mechanism, the phenotype depends on the parental allele affected and opposite phenotypes may result depending on the involvement of the maternal or the paternal chromosome. Imprinting disorders are largely underdiagnosed because of the broad range of clinical signs, the overlap of presentation among different disorders, the presence of mild phenotypes, the mitigation of the phenotype with age and the limited availability of molecular techniques employed for diagnosis. This review briefly illustrates the currently known human imprinting disorders, highlighting endocrinological aspects of pediatric interest.
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Affiliation(s)
- Diana Carli
- University of Torino, Department of Pediatric and Public Health Sciences, Torino, Italy
| | - Evelise Riberi
- University of Torino, Department of Pediatric and Public Health Sciences, Torino, Italy
| | | | - Alessandro Mussa
- University of Torino, Department of Pediatric and Public Health Sciences, Torino, Italy,* Address for Correspondence: University of Torino, Department of Pediatric and Public Health Sciences, Torino, Italy Phone: +39-011-313-1985 E-mail:
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28
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Oldzej J, Manazir J, Gold JA, Mahmoud R, Osann K, Flodman P, Cassidy SB, Kimonis VE. Molecular subtype and growth hormone effects on dysmorphology in Prader-Willi syndrome. Am J Med Genet A 2019; 182:169-175. [PMID: 31782896 DOI: 10.1002/ajmg.a.61408] [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: 05/11/2019] [Revised: 09/28/2019] [Accepted: 10/18/2019] [Indexed: 12/27/2022]
Abstract
Prader-Willi syndrome (PWS) affects 1/15,000-1/30,000 live births and is characterized by lack of expression of paternally inherited genes on 15q11.2-15q13 caused by paternal deletions, maternal uniparental disomy (UPD), or imprinting defects. Affected individuals have distinct physical features, and growth hormone (GH) deficiency occurs in some individuals with PWS. The aim of this study is to test the hypotheses that (a) individuals with deletions and UPD have different physical and dysmorphic features, (b) individuals treated with GH have different physical and dysmorphic features than those not treated, and (c) GH treatment effects are different for individuals with UPD in comparison to those with deletions. Study participants included 30 individuals with deletions or UPD, who did or did not have GH treatment. Participants' molecular abnormalities were determined by molecular and cytogenetic analysis. Clinical data were obtained by a single dysmorphologist. Individuals with deletions were found to be heavier (p = .001), taller (p = .031), with smaller head circumferences (p = .042) and were more likely to have fair skin and hair than their family members (p = .031, .049, respectively) compared to UPD patients. Females with deletions more commonly had hypoplastic labia minora (p = .009) and clitoris (.030) in comparison to those with UPD. Individuals who received GH in both deletion and UPD groups were taller (p = .004), had larger hands (p = .011) and feet (p = .006) and a trend for a larger head circumference (p = .103). Interestingly, the GH-treated group also had a lower rate of strabismus (esotropia [p = .017] and exotropia [p = .039]). This study showed statistically significant correlations between phenotype and molecular subtypes and also between phenotype and GH treatment.
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Affiliation(s)
- Jeannine Oldzej
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, California
| | - Javeria Manazir
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, California
| | - June-Anne Gold
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, California.,Division of Biochemical and Clinical Genetics, Children's Hospital of Orange County, Orange, California.,Division of Genetics and Metabolism, Department of Pediatrics, Loma Linda University Medical School, Loma Linda, California
| | - Ranim Mahmoud
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, California.,Genetics Unit, Department of Pediatrics, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Kathryn Osann
- Department of Medicine, University of California, Irvine, California
| | - Pamela Flodman
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, California
| | - Suzanne B Cassidy
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, California.,Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, California
| | - Virginia E Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, California.,Division of Biochemical and Clinical Genetics, Children's Hospital of Orange County, Orange, California
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29
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Beygo J, Buiting K, Ramsden SC, Ellis R, Clayton-Smith J, Kanber D. Update of the EMQN/ACGS best practice guidelines for molecular analysis of Prader-Willi and Angelman syndromes. Eur J Hum Genet 2019; 27:1326-1340. [PMID: 31235867 PMCID: PMC6777528 DOI: 10.1038/s41431-019-0435-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/20/2019] [Accepted: 05/07/2019] [Indexed: 11/23/2022] Open
Abstract
This article is an update of the best practice guidelines for the molecular analysis of Prader-Willi and Angelman syndromes published in 2010 in BMC Medical Genetics [1]. The update takes into account developments in terms of techniques, differential diagnoses and (especially) reporting standards. It highlights the advantages and disadvantages of each method and moreover, is meant to facilitate the interpretation of the obtained results - leading to improved standardised reports.
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Affiliation(s)
- Jasmin Beygo
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.
| | - Karin Buiting
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Rachael Ellis
- Department of Medical Genetics, Yorkhill NHS Trust, Yorkhill Hospital, Glasgow, G3 8SJ, UK
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
- Division of Evolution and Genomic Sciences School of Biological Sciences University of Manchester, Manchester, UK
| | - Deniz Kanber
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.
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30
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Carson RP, Bird L, Childers AK, Wheeler F, Duis J. Preserved expressive language as a phenotypic determinant of Mosaic Angelman Syndrome. Mol Genet Genomic Med 2019; 7:e837. [PMID: 31400086 PMCID: PMC6732290 DOI: 10.1002/mgg3.837] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/19/2022] Open
Abstract
Background Angelman Syndrome (AS) is a neurodevelopmental disorder with core features of intellectual disability, speech impairment, movement disorders, and a unique behavioral profile. Typically, AS results from absent maternal expression of UBE3A, but some individuals have imprinting defects in a portion of their cells. These individuals are mosaic for normal and defective UBE3A expression, resulting in mosaic AS (mAS) with a partial loss of gene expression. Methods This study aims to contrast the mAS phenotype to that of AS. Clinical characteristics of mAS were obtained from a parental survey of 22 mAS patients and from the Angelman Natural History study. These were contrasted with those of AS using historical data. Results Developmental delay was present in nearly all mAS patients, whereas the core features of AS were reported in less than 40%. While language and ability to manage activities of daily living were markedly improved over that expected in AS, mAS patients demonstrated a high incidence of behavioral challenges. Conclusion Clinical work‐up of an individual with developmental delay, hyperactivity, anxiety, and an uncharacteristically happy demeanor should prompt methylation studies to rule out mAS. We expand the phenotypic spectrum of AS to include features that overlap with Prader‐Willi such as hyperphagia.
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Affiliation(s)
- Robert P Carson
- Divisions of Child Neurology and Epilepsy, Department of Pediatrics, Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Pharmacology, Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lynne Bird
- Division of Genetics/Dysmorphology, Department of Pediatrics, Rady Children's Hospital, University of California San Diego, San Diego, California
| | - Anna K Childers
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ferrin Wheeler
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jessica Duis
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
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31
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Kim Y, Wang SE, Jiang YH. Epigenetic therapy of Prader-Willi syndrome. Transl Res 2019; 208:105-118. [PMID: 30904443 PMCID: PMC6527448 DOI: 10.1016/j.trsl.2019.02.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 01/05/2023]
Abstract
Prader-Willi syndrome (PWS) is a complex and multisystem neurobehavioral disorder. The molecular mechanism of PWS is deficiency of paternally expressed gene gene or genes from the chromosome 15q11-q13. Due to imprinted gene regulation, the same genes in the maternal chromosome 15q11-q13 are structurally intact but transcriptionally repressed by an epigenetic mechanism. The unique molecular defect underlying PWS renders an exciting opportunity to explore epigenetic-based therapy to reactivate the expression of repressed PWS genes from the maternal chromosome. Inactivation of H3K9m3 methyltransferase SETDB1 and zinc finger protein ZNF274 results in reactivation of SNRPN and SNORD116 cluster from the maternal chromosomes in PWS patient iPSCs and iPSC-derived neurons, respectively. High content screening of small molecule libraries using cells derived from transgenic mice carrying the SNRPN-EGFP fusion protein has discovered that inhibitors of EHMT2/G9a, a histone 3 lysine 9 methyltransferase, are capable of reactivating expression of paternally expressed SNRPN and SNORD116 from the maternal chromosome, both in cultured PWS patient-derived fibroblasts and in a PWS mouse model. Treatment with an EMHT2/G9a inhibitor also rescues perinatal lethality and failure to thrive phenotypes in a PWS mouse model. These findings present the first evidence to support a proof-of-principle for epigenetic-based therapy for the PWS in humans.
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Affiliation(s)
- Yuna Kim
- Department of Pediatrics, Duke University of School of Medicine, Durham, North Carolina
| | - Sung Eun Wang
- Department of Pediatrics, Duke University of School of Medicine, Durham, North Carolina
| | - Yong-Hui Jiang
- Department of Pediatrics, Duke University of School of Medicine, Durham, North Carolina; Department of Neurobiology, Duke University of School of Medicine, Durham, North Carolina; Department of Program in Genetics and Genomics, Duke University of School of Medicine, Durham, North Carolina; Department of Program in Cellular and Molecular Biology, Duke University of School of Medicine, Durham, North Carolina.
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32
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Coulson RL, Powell WT, Yasui DH, Dileep G, Resnick J, LaSalle JM. Prader-Willi locus Snord116 RNA processing requires an active endogenous allele and neuron-specific splicing by Rbfox3/NeuN. Hum Mol Genet 2018; 27:4051-4060. [PMID: 30124848 PMCID: PMC6240740 DOI: 10.1093/hmg/ddy296] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/10/2018] [Accepted: 07/03/2018] [Indexed: 12/18/2022] Open
Abstract
Prader-Willi syndrome (PWS), an imprinted neurodevelopmental disorder characterized by metabolic, sleep and neuropsychiatric features, is caused by the loss of paternal SNORD116, containing only non-coding RNAs (ncRNAs). The primary SNORD116 transcript is processed into small nucleolar RNAs (snoRNAs), which localize to nucleoli, and their spliced host gene 116HG, which is retained at its site of transcription. While functional complementation of the SNORD116 ncRNAs is a desirable goal for treating PWS, the mechanistic requirements of SNORD116 RNA processing are poorly understood. Here we developed and tested a novel transgenic mouse which ubiquitously expresses Snord116 on both a wild-type and a Snord116 paternal deletion (Snord116+/-) background. Interestingly, while the Snord116 transgene was ubiquitously expressed in multiple tissues, splicing of the transgene and production of snoRNAs was limited to brain tissues. Knockdown of Rbfox3, encoding neuron-specific splicing factor neuronal nuclei (NeuN) in Snord116+/--derived neurons, reduced splicing of the transgene in neurons. RNA fluorescence in situ hybridization for 116HG revealed a single significantly larger signal in transgenic mice, demonstrating colocalization of transgenic and endogenous 116HG RNAs. Similarly, significantly increased snoRNA levels were detected in transgenic neuronal nucleoli, indicating that transgenic Snord116 snoRNAs were effectively processed and localized. In contrast, neither transgenic 116HG nor snoRNAs were detectable in either non-neuronal tissues or Snord116+/- neurons. Together, these results demonstrate that exogenous expression and neuron-specific splicing of the Snord116 locus are insufficient to rescue the genetic deficiency of Snord116 paternal deletion. Elucidating the mechanisms regulating Snord116 processing and localization is essential to develop effective gene replacement therapies for PWS.
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Affiliation(s)
- Rochelle L Coulson
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - Weston T Powell
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - Dag H Yasui
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - Gayathri Dileep
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - James Resnick
- Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Janine M LaSalle
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
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33
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Roth M, Florez-Rueda AM, Paris M, Städler T. Wild tomato endosperm transcriptomes reveal common roles of genomic imprinting in both nuclear and cellular endosperm. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1084-1101. [PMID: 29953688 DOI: 10.1111/tpj.14012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 06/01/2018] [Accepted: 06/20/2018] [Indexed: 05/06/2023]
Abstract
Genomic imprinting is a conspicuous feature of the endosperm, a triploid tissue nurturing the embryo and synchronizing angiosperm seed development. An unknown subset of imprinted genes (IGs) is critical for successful seed development and should have highly conserved functions. Recent genome-wide studies have found limited conservation of IGs among distantly related species, but there is a paucity of data from closely related lineages. Moreover, most studies focused on model plants with nuclear endosperm development, and comparisons with properties of IGs in cellular-type endosperm development are lacking. Using laser-assisted microdissection, we characterized parent-specific expression in the cellular endosperm of three wild tomato lineages (Solanum section Lycopersicon). We identified 1025 candidate IGs and 167 with putative homologs previously identified as imprinted in distantly related taxa with nuclear-type endosperm. Forty-two maternally expressed genes (MEGs) and 17 paternally expressed genes (PEGs) exhibited conserved imprinting status across all three lineages, but differences in power to assess imprinted expression imply that the actual degree of conservation might be higher than that directly estimated (20.7% for PEGs and 10.4% for MEGs). Regardless, the level of shared imprinting status was higher for PEGs than for MEGs, indicating dissimilar evolutionary trajectories. Expression-level data suggest distinct epigenetic modulation of MEGs and PEGs, and gene ontology analyses revealed MEGs and PEGs to be enriched for different functions. Importantly, our data provide evidence that MEGs and PEGs interact in modulating both gene expression and the endosperm cell cycle, and uncovered conserved cellular functions of IGs uniting taxa with cellular- and nuclear-type endosperm.
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Affiliation(s)
- Morgane Roth
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
| | - Ana M Florez-Rueda
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
| | - Margot Paris
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
| | - Thomas Städler
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, 8092, Zurich, Switzerland
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Hartin SN, Hossain WA, Weisensel N, Butler MG. Three siblings with Prader-Willi syndrome caused by imprinting center microdeletions and review. Am J Med Genet A 2018; 176:886-895. [PMID: 29437285 PMCID: PMC6688622 DOI: 10.1002/ajmg.a.38627] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/21/2017] [Accepted: 01/16/2018] [Indexed: 12/14/2022]
Abstract
Prader-Willi syndrome (PWS) is a complex genetic imprinting disorder characterized by childhood obesity, short stature, hypogonadism/hypogenitalism, hypotonia, cognitive impairment, and behavioral problems. Usually PWS occurs sporadically due to the loss of paternally expressed genes on chromosome 15 with the majority of individuals having the 15q11-q13 region deleted. Examples of familial PWS have been reported but rarely. To date 13 families have been reported with more than one child with PWS and without a 15q11-q13 deletion secondary to a chromosome 15 translocation, inversion, or uniparental maternal disomy 15. Ten of those 13 families were shown to carry microdeletions in the PWS imprinting center. The microdeletions were found to be of paternal origin in nine of the ten cases in which family studies were carried out. Using a variety of techniques, the microdeletions were identified in regions within the complex SNRPN gene locus encompassing the PWS imprinting center. Here, we report the clinical and genetic findings in three adult siblings with PWS caused by a microdeletion in the chromosome 15 imprinting center inherited from an unaffected father that controls the activity of genes in the 15q11-q13 region and summarize the 13 reported cases in the literature.
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Affiliation(s)
- Samantha N. Hartin
- Departments of Psychiatry and Behavioral Sciences and
Pediatrics, University of Kansas Medical Center, Kansas City, Kansas
| | - Waheeda A. Hossain
- Departments of Psychiatry and Behavioral Sciences and
Pediatrics, University of Kansas Medical Center, Kansas City, Kansas
| | | | - Merlin G. Butler
- Departments of Psychiatry and Behavioral Sciences and
Pediatrics, University of Kansas Medical Center, Kansas City, Kansas
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35
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Ogata H, Ihara H, Gito M, Sayama M, Murakami N, Ayabe T, Oto Y, Nagai T, Shimoda K. Aberrant, autistic, and food-related behaviors in adults with Prader-Willi syndrome. The comparison between young adults and adults. RESEARCH IN DEVELOPMENTAL DISABILITIES 2018; 73:126-134. [PMID: 29324255 DOI: 10.1016/j.ridd.2017.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 12/15/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
This study aims to explore the differences of age as well as genotype in regards to the severity of behavioral symptoms in Prader-Willi syndrome (PWS), with emphasis on the comparison between youngadults and adults.The Food Related Problem Questionnaire (FRPQ), the Aberrant Behavior Checklist Japanese Version (ABC-J), and the Pervasive Developmental Disorders Autism Society Japan Rating Scale (PARS) were administered to 46 PWS patients, including 33 young adults (ages 18-28) and 13 adults(ages 30-45). To examine the differences between young adults and adults, Mann-Whitney U tests were conducted. Statistically significant differences were found in ABC-J (p = .027) and PARS (p = .046), with higher scores in young adults than adults. Such differences between the two age groups were still true for the subgroups having a paternal chromosome 15q deletion (DEL) for ABC-J (p = .050) and part of PARS ("Problematic behavior"; p = .007). By contrast, there was no significant differences between young adults and adults regarding FRPQ (p = .65).These results suggest that aberrant behaviors decline from around the ages of thirty, in PWS patients in general and in DEL subgroups in particular, while food-related behaviors give no indication of diminishing in spite of developmental growth.
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Affiliation(s)
- Hiroyuki Ogata
- Department of Psychiatry, Dokkyo Medical University Saitama Medical Center, Saitama, Japan; Department of Psychiatry, Dokkyo Medical University School of Medicine, Tochigi, Japan
| | - Hiroshi Ihara
- Department of Psychiatry, Dokkyo Medical University Saitama Medical Center, Saitama, Japan.
| | - Masao Gito
- Department of Psychiatry, Dokkyo Medical University Saitama Medical Center, Saitama, Japan; Department of Psychiatry, Dokkyo Medical University School of Medicine, Tochigi, Japan; Department of Psychiatry, Ikezawa Hospital, Hanyu, Japan
| | - Masayuki Sayama
- Department of Psychiatry, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Nobuyuki Murakami
- Department of Pediatrics, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Tadayuki Ayabe
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuji Oto
- Department of Pediatrics, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | | | - Kazutaka Shimoda
- Department of Psychiatry, Dokkyo Medical University School of Medicine, Tochigi, Japan
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36
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Gui B, Slone J, Huang T. Perspective: Is Random Monoallelic Expression a Contributor to Phenotypic Variability of Autosomal Dominant Disorders? Front Genet 2017; 8:191. [PMID: 29250101 PMCID: PMC5718016 DOI: 10.3389/fgene.2017.00191] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/14/2017] [Indexed: 11/13/2022] Open
Abstract
Several factors have been proposed as contributors to interfamilial and intrafamilial phenotypic variability in autosomal dominant disorders, including allelic variation, modifier genes, environmental factors and complex genetic and environmental interactions. However, regardless of the similarity of genetic background and environmental factors, asymmetric limb or trunk anomalies in a single individual and variable manifestation between monozygotic twins have been observed, indicating other mechanisms possibly involved in expressivity of autosomal dominant diseases. One such example is Holt-Oram syndrome (HOS), which is characterized by congenital cardiac defects and forelimb anomalies, mainly attributed to mutations in the TBX5 gene. We hypothesize that monoallelic expression of the TBX5 gene occurs during embryo development, and, in the context of a mutation, random monoallelic expression (RME) can create discrepant functions in a proportion of cells and thus contribute to variable phenotypes. A hybrid mouse model was used to investigate the occurrence of RME with the Tbx5 gene, and single-cell reverse transcription PCR and restriction digestion were performed for limb bud cells from developing embryos (E11.5) of the hybrid mice. RME of Tbx5 was observed in approximately two-thirds of limb bud cells. These results indicate that RME of the Tbx5 gene occurs frequently during embryo development, resulting in a mosaic expression signature (monoallelic, biallelic, or null) that may provide a potential explanation for the widespread phenotypic variability in HOS. This model will further provide novel insights into the variability of autosomal dominant traits and a better understanding of the complex expressivity of disease conditions.
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Affiliation(s)
- Baoheng Gui
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jesse Slone
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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37
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Lukoshe A, van den Bosch GE, van der Lugt A, Kushner SA, Hokken-Koelega AC, White T. Aberrant White Matter Microstructure in Children and Adolescents With the Subtype of Prader-Willi Syndrome at High Risk for Psychosis. Schizophr Bull 2017; 43:1090-1099. [PMID: 28510708 PMCID: PMC5581891 DOI: 10.1093/schbul/sbx052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Prader-Willi Syndrome (PWS) is a complex neurogenetic disorder caused by loss of the paternal 15q11.2-q13 locus, due to deletion (DEL), maternal uniparental disomy (mUPD), or imprinting center defects. Individuals with mUPD have up to 60% risk of developing psychosis in early adulthood. Given the increasing evidence for white matter abnormalities in psychotic disorders, we investigated white matter microstructure in children and adolescents with PWS, with a particular emphasis on the DEL and mUPD subtypes. Magnetic resonance diffusion weighted images were acquired in 35 directions at 3T and analyzed using fractional anisotropy (FA), mean, axial, and radial diffusivity (MD, AD, RD) values obtained by tract-based spatial statistics (TBSS) in 28 children and adolescents with PWS and 61 controls. In addition, we employed a recently developed white matter pothole approach, which does not require local FA differences to be spatially co-localized across subjects. After accounting for age and gender, individuals with PWS had significantly lower global FA and higher MD, compared with controls. Individuals with mUPD had lower FA in multiple regions including the corpus callosum, cingulate, and superior longitudinal fasciculus and larger potholes, compared with DEL and controls. The observed differences in individuals with mUPD are similar to the white matter abnormalities in individuals with psychotic disorders. Conversely, the subtle white matter abnormalities in individuals with DEL are consistent with their substantially lower risk of psychosis. Future studies to investigate the specific neurobiological mechanism underlying the differential psychosis risk between the DEL and mUPD subtypes of PWS are highly warranted.
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Affiliation(s)
- Akvile Lukoshe
- Dutch Growth Research Foundation, Rotterdam, The Netherlands;,Department of Pediatrics, Erasmus Medical Centre Rotterdam/Sophia Children’s Hospital Rotterdam, Rotterdam, The Netherlands
| | - Gerbrich E van den Bosch
- Intensive Care and Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Aad van der Lugt
- Department of Radiology, Erasmus Medical Centre Rotterdam, Postbus 2040, 3000 CA Rotterdam, The Netherlands
| | - Steven A Kushner
- Department of Psychiatry, Erasmus Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Anita C Hokken-Koelega
- Dutch Growth Research Foundation, Rotterdam, The Netherlands;,Department of Pediatrics, Erasmus Medical Centre Rotterdam/Sophia Children’s Hospital Rotterdam, Rotterdam, The Netherlands;,These authors contributed equally to the article
| | - Tonya White
- Department of Radiology, Erasmus Medical Centre Rotterdam, Postbus 2040, 3000 CA Rotterdam, The Netherlands;,Department of Child and Adolescent Psychiatry, Erasmus Medical Centre Rotterdam—Sophia Children’s Hospital, Rotterdam, The Netherlands,These authors contributed equally to the article.,To whom correspondence should be addressed; tel: +31-0-10-703-70-72, e-mail:
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38
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Elhamamsy AR. Role of DNA methylation in imprinting disorders: an updated review. J Assist Reprod Genet 2017; 34:549-562. [PMID: 28281142 PMCID: PMC5427654 DOI: 10.1007/s10815-017-0895-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/23/2017] [Indexed: 12/20/2022] Open
Abstract
Genomic imprinting is a complex epigenetic process that contributes substantially to embryogenesis, reproduction, and gametogenesis. Only small fraction of genes within the whole genome undergoes imprinting. Imprinted genes are expressed in a monoallelic parent-of-origin-specific manner, which means that only one of the two inherited alleles is expressed either from the paternal or maternal side. Imprinted genes are typically arranged in clusters controlled by differentially methylated regions or imprinting control regions. Any defect or relaxation in imprinting process can cause loss of imprinting in the key imprinted loci. Loss of imprinting in most cases has a harmful effect on fetal development and can result in neurological, developmental, and metabolic disorders. Since DNA methylation and histone modifications play a key role in the process of imprinting. This review focuses on the role of DNA methylation in imprinting process and describes DNA methylation aberrations in different imprinting disorders.
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Affiliation(s)
- Amr Rafat Elhamamsy
- Department of Clinical Pharmacy, School of Pharmacy, Tanta University, Tanta, 31512, Gharbia, Egypt.
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39
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Lyall K, Croen L, Daniels J, Fallin MD, Ladd-Acosta C, Lee BK, Park BY, Snyder NW, Schendel D, Volk H, Windham GC, Newschaffer C. The Changing Epidemiology of Autism Spectrum Disorders. Annu Rev Public Health 2017; 38:81-102. [PMID: 28068486 PMCID: PMC6566093 DOI: 10.1146/annurev-publhealth-031816-044318] [Citation(s) in RCA: 550] [Impact Index Per Article: 78.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with lifelong impacts. Genetic and environmental factors contribute to ASD etiology, which remains incompletely understood. Research on ASD epidemiology has made significant advances in the past decade. Current prevalence is estimated to be at least 1.5% in developed countries, with recent increases primarily among those without comorbid intellectual disability. Genetic studies have identified a number of rare de novo mutations and gained footing in the areas of polygenic risk, epigenetics, and gene-by-environment interaction. Epidemiologic investigations focused on nongenetic factors have established advanced parental age and preterm birth as ASD risk factors, indicated that prenatal exposure to air pollution and short interpregnancy interval are potential risk factors, and suggested the need for further exploration of certain prenatal nutrients, metabolic conditions, and exposure to endocrine-disrupting chemicals. We discuss future challenges and goals for ASD epidemiology as well as public health implications.
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Affiliation(s)
- Kristen Lyall
- A.J. Drexel Autism Institute, Philadelphia, Pennsylvania 19104;
| | - Lisa Croen
- Kaiser Permanente Division of Research, Oakland, California 94612
| | - Julie Daniels
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, North Carolina 27599
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Brian K Lee
- Department of Epidemiology and Biostatistics, Drexel University School of Public Health, Philadelphia, Pennsylvania 19104
- Department of Medical Epidemiology and Biostatistics and Department of Public Health Sciences, Karolinska Institute, SE 171-77 Stockholm, Sweden
| | - Bo Y Park
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | | | - Diana Schendel
- Department of Economics and Business, National Centre for Register-Based Research, Aarhus University, DK-8210 Aarhus, Denmark
- Department of Public Health, Section for Epidemiology, Aarhus University, DK-8000 Aarhus, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Heather Volk
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Gayle C Windham
- California Department of Public Health, Division of Environmental and Occupational Disease Control, Richmond, California 94805
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Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain. Proc Natl Acad Sci U S A 2017; 114:E2882-E2890. [PMID: 28320934 DOI: 10.1073/pnas.1611905114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA methylation at gene promoters in a CG context is associated with transcriptional repression, including at genes silenced on the inactive X chromosome in females. Non-CG methylation (mCH) is a distinct feature of the neuronal epigenome that is differentially distributed between males and females on the X chromosome. However, little is known about differences in mCH on the active (Xa) and inactive (Xi) X chromosomes because stochastic X-chromosome inactivation (XCI) confounds allele-specific epigenomic profiling. We used whole-genome bisulfite sequencing in a mouse model with nonrandom XCI to examine allele-specific DNA methylation in frontal cortex. Xi was largely devoid of mCH, whereas Xa contained abundant mCH similar to the male X chromosome and the autosomes. In contrast to the repressive association of DNA methylation at CG dinucleotides (mCG), mCH accumulates on Xi in domains with transcriptional activity, including the bodies of most genes that escape XCI and at the X-inactivation center, validating this epigenetic mark as a signature of transcriptional activity. Escape genes showing CH hypermethylation were the only genes with CG-hypomethylated promoters on Xi, a well-known mark of active transcription. Finally, we found extensive allele-specific mCH and mCG at autosomal imprinted regions, some with a negative correlation between methylation in the two contexts, further supporting their distinct functions. Our findings show that neuronal mCH functions independently of mCG and is a highly dynamic epigenomic correlate of allele-specific gene regulation.
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41
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Mastrototaro G, Zaghi M, Sessa A. Epigenetic Mistakes in Neurodevelopmental Disorders. J Mol Neurosci 2017; 61:590-602. [DOI: 10.1007/s12031-017-0900-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/15/2017] [Indexed: 12/28/2022]
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42
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The inheritance of epigenetic defects. MED GENET-BERLIN 2017. [DOI: 10.1007/s11825-017-0120-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Lukoshe A, van Dijk SE, van den Bosch GE, van der Lugt A, White T, Hokken-Koelega AC. Altered functional resting-state hypothalamic connectivity and abnormal pituitary morphology in children with Prader-Willi syndrome. J Neurodev Disord 2017; 9:12. [PMID: 28331554 PMCID: PMC5356363 DOI: 10.1186/s11689-017-9188-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 01/26/2017] [Indexed: 11/17/2022] Open
Abstract
Background Prader-Willi syndrome (PWS) is a complex neurodevelopmental disorder, characterized by endocrine problems and hyperphagia, indicating hypothalamic-pituitary dysfunction. However, few studies have explored the underlying neurobiology of the hypothalamus and its functional connectivity with other brain regions. Thus, the aim of this study was to examine the anatomical differences of the hypothalamus, mammillary bodies, and pituitary gland as well as resting state functional connectivity of the hypothalamus in children with PWS. Methods Twenty-seven children with PWS (13 DEL, 14 mUPD) and 28 typically developing children were included. Manual segmentations by a blinded investigator were performed to determine the volumes of the hypothalamus, mammillary bodies, and pituitary gland. In addition, brain-wide functional connectivity analysis was performed using the obtained masks of the hypothalamus. Results Children with PWS showed altered resting state functional connectivity between hypothalamus and right and left lateral occipital complex, compared to healthy controls. In addition, children with PWS had on average a 50% smaller pituitary volume, an irregular shape of the pituitary, and a longer pituitary stalk. Pituitary volume did not increase in volume during puberty in PWS. No volumetric differences in the hypothalamus and mammillary bodies were found. In all subjects, the posterior pituitary bright spot was observed. Conclusions We report altered functional hypothalamic connectivity with lateral occipital complexes in both hemispheres, which are implicated in response to food and reward system, and absence of connectivity might therefore at least partially contribute to the preoccupation with food in PWS.
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Affiliation(s)
- Akvile Lukoshe
- Dutch Growth Research Foundation, Postbus 23068, 3001 KB Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, Postbus 2060, 3000 CB Rotterdam, The Netherlands
| | - Suzanne E van Dijk
- Department of Child and Adolescent Psychiatry, Erasmus MC-Sophia Children's Hospital, Postbus 2060, 3000 CB Rotterdam, The Netherlands
| | - Gerbrich E van den Bosch
- Intensive Care and department of pediatric surgery, Erasmus MC-Sophia Children's Hospital, Postbus 2060, 3000 CB Rotterdam, The Netherlands
| | - Aad van der Lugt
- Department of Radiology, Erasmus Medical Centre-Sophia Children's Hospital, Postbus 2040, 3000 CA Rotterdam, The Netherlands
| | - Tonya White
- Department of Child and Adolescent Psychiatry, Erasmus MC-Sophia Children's Hospital, Postbus 2060, 3000 CB Rotterdam, The Netherlands.,Department of Radiology, Erasmus Medical Centre-Sophia Children's Hospital, Postbus 2040, 3000 CA Rotterdam, The Netherlands
| | - Anita C Hokken-Koelega
- Dutch Growth Research Foundation, Postbus 23068, 3001 KB Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, Postbus 2060, 3000 CB Rotterdam, The Netherlands
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Abstract
Although Prader-Willi syndrome (PWS) is a well-described clinical dysmorphic syndrome, DNA testing is required for a definitive diagnosis. A definitive diagnosis can be made in approximately 99% of cases using DNA testing; there are a number of DNA tests that can be used for this purpose, although there is no set standard algorithm of testing. The dilemma arises because of the complex genetic mechanisms at the basis of PWS, which need to be elucidated. To establish the molecular mechanism with a complete work up, involves at least 2 tests. Here we discuss the commonly used tests currently available and suggest a cost-effective approach to diagnostic testing.
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Affiliation(s)
- Arabella Smith
- University of Sydney Clinical School, Children's Hospital at Westmead, Westmead, Australia
| | - Dorothy Hung
- Children's Hospital at Westmead, Sydney Genome Diagnostics (Cytogenetics), Children's Hospital Network, PO Box 4001, Westmead, Australia
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NDN is an imprinted tumor suppressor gene that is downregulated in ovarian cancers through genetic and epigenetic mechanisms. Oncotarget 2016; 7:3018-32. [PMID: 26689988 PMCID: PMC4823087 DOI: 10.18632/oncotarget.6576] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 11/21/2015] [Indexed: 12/18/2022] Open
Abstract
NDN is a maternally imprinted gene consistently expressed in normal ovarian epithelium, is dramatically downregulated in the majority of ovarian cancers. Little or no NDN expression could be detected in 73% of 351 epithelial ovarian cancers. NDN was also downregulated in 10 ovarian cancer cell lines with total loss in 6 of 10. Re-expression of NDN decreased Bcl-2 levels and induced apoptosis, which significantly inhibited ovarian cancer cell growth in cell culture and in xenografts. In addition, re-expression of NDN inhibited cell migration by decreasing actin stress fiber and focal adhesion complex formation through deactivation of Src, FAK and RhoA. Loss of NDN expression in ovarian cancers could be attributed to LOH in 28% of 18 informative cases and to hypermethylation of CpG sites 1 and 2 of NDN promoter in 23% and 30% of 43 ovarian cancers, respectively. Promoter hypermethylation was also found in 5 of 10 ovarian cancer cell lines. Treatment with the demethylating agent 5-aza-2′-deoxycytidine restored NDN expression in 4 of 7 cell lines with enhanced promoter methylation levels. These observations support the conclusion that NDN is an imprinted tumor suppressor gene which affects cancer cell motility, invasion and growth and that its loss of function in ovarian cancer can be caused by both genetic and epigenetic mechanisms.
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Thakur A, Mackin SJ, Irwin RE, O’Neill KM, Pollin G, Walsh C. Widespread recovery of methylation at gametic imprints in hypomethylated mouse stem cells following rescue with DNMT3A2. Epigenetics Chromatin 2016; 9:53. [PMID: 27895716 PMCID: PMC5118886 DOI: 10.1186/s13072-016-0104-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/08/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Imprinted loci are paradigms of epigenetic regulation and are associated with a number of genetic disorders in human. A key characteristic of imprints is the presence of a gametic differentially methylated region (gDMR). Previous studies have indicated that DNA methylation lost from gDMRs could not be restored by DNMT1, or the de novo enzymes DNMT3A or 3B in stem cells, indicating that imprinted regions must instead undergo passage through the germline for reprogramming. However, previous studies were non-quantitative, were unclear on the requirement for DNMT3A/B and showed some inconsistencies. In addition, new putative gDMR has recently been described, along with an improved delineation of the existing gDMR locations. We therefore aimed to re-examine the dependence of methylation at gDMRs on the activities of the methyltransferases in mouse embryonic stem cells (ESCs). RESULTS We examined the most complete current set of imprinted gDMRs that could be assessed using quantitative pyrosequencing assays in two types of ESCs: those lacking DNMT1 (1KO) and cells lacking a combination of DNMT3A and DNMT3B (3abKO). We further verified results using clonal analysis and combined bisulfite and restriction analysis. Our results showed that loss of methylation was approximately equivalent in both cell types. 1KO cells rescued with a cDNA-expressing DNMT1 could not restore methylation at the imprinted gDMRs, confirming some previous observations. However, nearly all gDMRs were remethylated in 3abKO cells rescued with a DNMT3A2 expression construct (3abKO + 3a2). Transcriptional activity at the H19/Igf2 locus also tracked with the methylation pattern, confirming functional reprogramming in the latter. CONCLUSIONS These results suggested (1) a vital role for DNMT3A/B in methylation maintenance at imprints, (2) that loss of DNMT1 and DNMT3A/B had equivalent effects, (3) that rescue with DNMT3A2 can restore imprints in these cells. This may provide a useful system in which to explore factors influencing imprint reprogramming.
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Affiliation(s)
- Avinash Thakur
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
- Terry Fox Laboratory, BC Cancer Agency, 675 W 10th Ave, Vancouver, BC V5Z 1G1 Canada
| | - Sarah-Jayne Mackin
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
| | - Rachelle E. Irwin
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
| | - Karla M. O’Neill
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
- Centre for Experimental Medicine, The Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7AE UK
| | - Gareth Pollin
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
| | - Colum Walsh
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA UK
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Butler MG. Benefits and limitations of prenatal screening for Prader-Willi syndrome. Prenat Diagn 2016; 37:81-94. [PMID: 27537837 DOI: 10.1002/pd.4914] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 12/15/2022]
Abstract
This review summarizes the status of genetic laboratory testing in Prader-Willi syndrome (PWS) with different genetic subtypes, most often a paternally derived 15q11-q13 deletion and discusses benefits and limitations related to prenatal screening. Medical literature was searched for prenatal screening and genetic laboratory testing methods in use or under development and discussed in relationship to PWS. Genetic testing includes six established laboratory diagnostic approaches for PWS with direct application to prenatal screening. Ultrasonographic, obstetric and cytogenetic reports were summarized in relationship to the cause of PWS and identification of specific genetic subtypes including maternal disomy 15. Advances in genetic technology were described for diagnosing PWS specifically DNA methylation and high-resolution chromosomal SNP microarrays as current tools for genetic screening and incorporating next generation DNA sequencing for noninvasive prenatal testing (NIPT) using cell-free fetal DNA. Positive experiences are reported with NIPT for detection of numerical chromosomal problems (aneuploidies) but not for structural problems (microdeletions). These reports will be discussed along with future directions for genetic screening of PWS. In summary, this review describes and discusses the status of established and ongoing genetic testing options for PWS applicable in prenatal screening including NIPT and future directions for early diagnosis in PWS. © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Merlin G Butler
- Departments of Psychiatry and Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS, USA
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Buiting K, Williams C, Horsthemke B. Angelman syndrome — insights into a rare neurogenetic disorder. Nat Rev Neurol 2016; 12:584-93. [DOI: 10.1038/nrneurol.2016.133] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Cai Z, Li S, Li S, Song F, Zhang Z, Qi G, Li T, Qiu J, Wan J, Sui H, Guo H. Antagonist Targeting microRNA-155 Protects against Lithium-Pilocarpine-Induced Status Epilepticus in C57BL/6 Mice by Activating Brain-Derived Neurotrophic Factor. Front Pharmacol 2016; 7:129. [PMID: 27303295 PMCID: PMC4885878 DOI: 10.3389/fphar.2016.00129] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/05/2016] [Indexed: 11/13/2022] Open
Abstract
Epilepsy is a severe brain disorder affecting numerous patients. Recently, it is inferred that modulation of microRNA-155 (miR-155) could serve as a promising treatment of mesial temporal lobe epilepsy. In the current study, the therapeutic potential of miR-155 antagonist against temporal lobe epilepsy (TLE) was evaluated and the underlying mechanism involved in this regulation was explored. TLE model was induced by lithium-pilocarpine method. The effect of miR-155 antagonist on epilepticus symptoms of TLE mice was assessed using Racine classification and electroencephalogram (EEG) recordings. The expression of brain-derived neurotrophic factor (BDNF) and its association with miR-155 were also assessed with a series of experiments. Our results showed that level of miR-155 was significantly up-regulated after induction of TLE model. Based on the results of EEG and behavior analyses, seizures in mice were alleviated by miR-155 antagonist. Moreover, administration of miR-155 antagonist also significantly increased the level of BDNF. The results of dual luciferase assay and Western blotting showed that miR-155 antagonist exerted its action on status epilepticus by directly regulating the activity of BDNF. Taken all the information together, our results demonstrated that miR-155 antagonist might firstly induce the expression of BDNF, which then contributed to the alleviation of epilepsy in the current study.
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Affiliation(s)
- Zhengxu Cai
- Department of Neurology, The First Affiliated Hospital of Dalian Medical University Dalian, China
| | - Song Li
- Center for Translational Research on Neurological Diseases, The First Affiliated Hospital of Dalian Medical University Dalian, China
| | - Sheng Li
- Department of Neurology, The First Affiliated Hospital of Dalian Medical University Dalian, China
| | - Fan Song
- Department of Neurology, The First Affiliated Hospital of Dalian Medical University Dalian, China
| | - Zhen Zhang
- Department of Neurology, The First Affiliated Hospital of Dalian Medical University Dalian, China
| | - Guanhua Qi
- Department of Neurology, The First Affiliated Hospital of Dalian Medical University Dalian, China
| | - Tianbai Li
- Center for Translational Research on Neurological Diseases, The First Affiliated Hospital of Dalian Medical University Dalian, China
| | - Juanjuan Qiu
- Central Laboratory, The First Affiliated Hospital of Dalian Medical University Dalian, China
| | - Jiajia Wan
- Central Laboratory, The First Affiliated Hospital of Dalian Medical University Dalian, China
| | - Hua Sui
- Central Laboratory, The First Affiliated Hospital of Dalian Medical UniversityDalian, China; Institute of Basic Research of Integrative Medicine, Dalian Medical UniversityDalian, China
| | - Huishu Guo
- Department of Neurology, The First Affiliated Hospital of Dalian Medical UniversityDalian, China; Central Laboratory, The First Affiliated Hospital of Dalian Medical UniversityDalian, China
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Wianny F, Blachère T, Godet M, Guillermas R, Cortay V, Bourillot PY, Lefèvre A, Savatier P, Dehay C. Epigenetic status of H19/IGF2 and SNRPN imprinted genes in aborted and successfully derived embryonic stem cell lines in non-human primates. Stem Cell Res 2016; 16:557-67. [DOI: 10.1016/j.scr.2016.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 03/04/2016] [Accepted: 03/07/2016] [Indexed: 12/20/2022] Open
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