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Liu AC, Shen Y, Serbinski CR, He H, Roman D, Endale M, Aschbacher-Smith L, King KA, Granadillo JL, López I, Krueger DA, Dye TJ, Smith DF, Hogenesch JB, Prada CE. Clinical and functional studies of MTOR variants in Smith-Kingsmore syndrome reveal deficits of circadian rhythm and sleep-wake behavior. HGG ADVANCES 2024; 5:100333. [PMID: 39030910 PMCID: PMC11342114 DOI: 10.1016/j.xhgg.2024.100333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024] Open
Abstract
Heterozygous de novo or inherited gain-of-function mutations in the MTOR gene cause Smith-Kingsmore syndrome (SKS). SKS is a rare autosomal dominant condition, and individuals with SKS display macrocephaly/megalencephaly, developmental delay, intellectual disability, and seizures. A few dozen individuals are reported in the literature. Here, we report a cohort of 28 individuals with SKS that represent nine MTOR pathogenic variants. We conducted a detailed natural history study and found pathophysiological deficits among individuals with SKS in addition to the common neurodevelopmental symptoms. These symptoms include sleep-wake disturbance, hyperphagia, and hyperactivity, indicative of homeostatic imbalance. To characterize these variants, we developed cell models and characterized their functional consequences. We showed that these SKS variants display a range of mechanistic target of rapamycin (mTOR) activities and respond to the mTOR inhibitor, rapamycin, differently. For example, the R1480_C1483del variant we identified here and the previously known C1483F are more active than wild-type controls and less responsive to rapamycin. Further, we showed that SKS mutations dampened circadian rhythms and low-dose rapamycin improved the rhythm amplitude, suggesting that optimal mTOR activity is required for normal circadian function. As SKS is caused by gain-of-function mutations in MTOR, rapamycin was used to treat several patients. While higher doses of rapamycin caused delayed sleep-wake phase disorder in a subset of patients, optimized lower doses improved sleep. Our study expands the clinical and molecular spectrum of SKS and supports further studies for mechanism-guided treatment options to improve sleep-wake behavior and overall health.
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Affiliation(s)
- Andrew C Liu
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, FL 32610, USA.
| | - Yang Shen
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Carolyn R Serbinski
- Divisions of Human Genetics, Neurology, Immunobiology, Pediatric Otolaryngology, and Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Genetics, Genomics & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Hongzhi He
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Destino Roman
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Mehari Endale
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Lindsey Aschbacher-Smith
- Divisions of Human Genetics, Neurology, Immunobiology, Pediatric Otolaryngology, and Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Katherine A King
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Isabel López
- Pediatric Neurology Unit, Department of Neurology, Clínica Las Condes, Santiago, Chile
| | - Darcy A Krueger
- Divisions of Human Genetics, Neurology, Immunobiology, Pediatric Otolaryngology, and Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Thomas J Dye
- Divisions of Human Genetics, Neurology, Immunobiology, Pediatric Otolaryngology, and Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - David F Smith
- Divisions of Pediatric Otolaryngology and Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; The Sleep Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; The Center for Circadian Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Otolaryngology Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - John B Hogenesch
- Divisions of Human Genetics, Neurology, Immunobiology, Pediatric Otolaryngology, and Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Carlos E Prada
- Divisions of Human Genetics, Neurology, Immunobiology, Pediatric Otolaryngology, and Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Genetics, Genomics & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine of Northwestern University, Chicago, IL 60611, USA.
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Heimdörfer D, Vorleuter A, Eschlböck A, Spathopoulou A, Suarez-Cubero M, Farhan H, Reiterer V, Spanjaard M, Schaaf CP, Huber LA, Kremser L, Sarg B, Edenhofer F, Geley S, de Araujo MEG, Huettenhofer A. Truncated variants of MAGEL2 are involved in the etiologies of the Schaaf-Yang and Prader-Willi syndromes. Am J Hum Genet 2024; 111:1383-1404. [PMID: 38908375 PMCID: PMC11267527 DOI: 10.1016/j.ajhg.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/24/2024] Open
Abstract
The neurodevelopmental disorders Prader-Willi syndrome (PWS) and Schaaf-Yang syndrome (SYS) both arise from genomic alterations within human chromosome 15q11-q13. A deletion of the SNORD116 cluster, encoding small nucleolar RNAs, or frameshift mutations within MAGEL2 result in closely related phenotypes in individuals with PWS or SYS, respectively. By investigation of their subcellular localization, we observed that in contrast to a predominant cytoplasmic localization of wild-type (WT) MAGEL2, a truncated MAGEL2 mutant was evenly distributed between the cytoplasm and the nucleus. To elucidate regulatory pathways that may underlie both diseases, we identified protein interaction partners for WT or mutant MAGEL2, in particular the survival motor neuron protein (SMN), involved in spinal muscular atrophy, and the fragile-X-messenger ribonucleoprotein (FMRP), involved in autism spectrum disorders. The interactome of the non-coding RNA SNORD116 was also investigated by RNA-CoIP. We show that WT and truncated MAGEL2 were both involved in RNA metabolism, while regulation of transcription was mainly observed for WT MAGEL2. Hence, we investigated the influence of MAGEL2 mutations on the expression of genes from the PWS locus, including the SNORD116 cluster. Thereby, we provide evidence for MAGEL2 mutants decreasing the expression of SNORD116, SNORD115, and SNORD109A, as well as protein-coding genes MKRN3 and SNRPN, thus bridging the gap between PWS and SYS.
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Affiliation(s)
- David Heimdörfer
- Institute of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
| | - Alexander Vorleuter
- Institute of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Alexander Eschlböck
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Angeliki Spathopoulou
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Marta Suarez-Cubero
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Hesso Farhan
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Veronika Reiterer
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Melanie Spanjaard
- Institute of Human Genetics, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Lukas A Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Leopold Kremser
- Institute of Medical Biochemistry, Protein Core Facility, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Bettina Sarg
- Institute of Medical Biochemistry, Protein Core Facility, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Frank Edenhofer
- Institute for Molecular Biology, Genomics, Stem Cell Biology & Regenerative Medicine Group, University of Innsbruck and CMBI, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Stephan Geley
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Mariana E G de Araujo
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Alexander Huettenhofer
- Institute of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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3
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Richter E, Patel P, Babu JR, Wang X, Geetha T. The Importance of Sleep in Overcoming Childhood Obesity and Reshaping Epigenetics. Biomedicines 2024; 12:1334. [PMID: 38927541 PMCID: PMC11201669 DOI: 10.3390/biomedicines12061334] [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: 05/14/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The development of childhood obesity is a complex process influenced by a combination of genetic predisposition and environmental factors, such as sleep, diet, physical activity, and socioeconomic status. Long-term solutions for decreasing the risk of childhood obesity remain elusive, despite significant advancements in promoting health and well-being in school and at home. Challenges persist in areas such as adherence to interventions, addressing underlying social determinants, and individual differences in response to treatment. Over the last decade, there has been significant progress in epigenetics, along with increased curiosity in gaining insights into how sleep and lifestyle decisions impact an individual's health. Epigenetic modifications affect the expression of genes without causing changes to the fundamental DNA sequence. In recent years, numerous research studies have explored the correlation between sleep and the epigenome, giving a better understanding of DNA methylation, histone modification, and non-coding RNAs. Although significant findings have been made about the influence of sleep on epigenetics, a notable gap exists in the literature concerning sleep-related genes specifically associated with childhood obesity. Consequently, it is crucial to delve deeper into this area to enhance our understanding. Therefore, this review primarily focuses on the connection between sleep patterns and epigenetic modifications in genes related to childhood obesity. Exploring the interplay between sleep, epigenetics, and childhood obesity can potentially contribute to improved overall health outcomes. This comprehensive review encompasses studies focusing on sleep-related genes linked to obesity.
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Affiliation(s)
- Erika Richter
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
| | - Priyadarshni Patel
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jeganathan Ramesh Babu
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA
- Alabama Agricultural Experiment Station, Auburn University, Auburn, AL 36849, USA
| | - Xu Wang
- Alabama Agricultural Experiment Station, Auburn University, Auburn, AL 36849, USA
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Thangiah Geetha
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA
- Alabama Agricultural Experiment Station, Auburn University, Auburn, AL 36849, USA
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4
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Ryabykh GK, Kuznetsov SV, Korostelev YD, Sigorskikh AI, Zharikova AA, Mironov AA. RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome. Database (Oxford) 2023; 2023:baad025. [PMID: 37221043 PMCID: PMC10205464 DOI: 10.1093/database/baad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/12/2023] [Accepted: 04/01/2023] [Indexed: 05/25/2023]
Abstract
Every year there is more and more evidence that non-coding RNAs play an important role in biological processes affecting various levels of organization of living systems: from the cellular (regulation of gene expression, remodeling and maintenance of chromatin structure, co-transcriptional suppression of transposons, splicing, post-transcriptional RNA modifications, etc.) to cell populations and even organismal ones (development, aging, cancer, cardiovascular and many other diseases). The development and creation of mutually complementary databases that will aggregate, unify and structure different types of data can help to reach the system level of studying non-coding RNAs. Here we present the RNA-Chrom manually curated analytical database, which contains the coordinates of billions of contacts of thousands of human and mouse RNAs with chromatin. Through the user-friendly web interface (https://rnachrom2.bioinf.fbb.msu.ru/), two approaches to the analysis of the RNA-chromatin interactome were implemented. Firstly, to find out whether the RNA of interest to a user contacts with chromatin, and if so, with which genes or DNA loci? Secondly, to find out which RNAs are in contact with the DNA locus of interest to a user (and probably participate in its regulation), and if there are such, what is the nature of their interaction? For a more detailed study of contact maps and their comparison with other data, the web interface allows a user to view them in the UCSC Genome Browser. Database URL https://genome.ucsc.edu/.
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Affiliation(s)
- G K Ryabykh
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
| | - S V Kuznetsov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
| | - Y D Korostelev
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
| | - A I Sigorskikh
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
| | - A A Zharikova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigsky per., Moscow, 101000, Russia
| | - A A Mironov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
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5
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Becker J, Sun B, Alammari F, Haerty W, Vance KW, Szele FG. What has single-cell transcriptomics taught us about long non-coding RNAs in the ventricular-subventricular zone? Stem Cell Reports 2022; 18:354-376. [PMID: 36525965 PMCID: PMC9860170 DOI: 10.1016/j.stemcr.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) function is mediated by the process of transcription or through transcript-dependent associations with proteins or nucleic acids to control gene regulatory networks. Many lncRNAs are transcribed in the ventricular-subventricular zone (V-SVZ), a postnatal neural stem cell niche. lncRNAs in the V-SVZ are implicated in neurodevelopmental disorders, cancer, and brain disease, but their functions are poorly understood. V-SVZ neurogenesis capacity declines with age due to stem cell depletion and resistance to neural stem cell activation. Here we analyzed V-SVZ transcriptomics by pooling current single-cell RNA-seq data. They showed consistent lncRNA expression during stem cell activation, lineage progression, and aging. In conjunction with epigenetic and genetic data, we predicted V-SVZ lncRNAs that regulate stem cell activation and differentiation. Some of the lncRNAs validate known epigenetic mechanisms, but most remain uninvestigated. Our analysis points to several lncRNAs that likely participate in key aspects of V-SVZ stem cell activation and neurogenesis in health and disease.
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Affiliation(s)
- Jemima Becker
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Bin Sun
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia,Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | - Keith W. Vance
- Department of Life Sciences, University of Bath, Bath, UK
| | - Francis George Szele
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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6
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Duis J, Pullen LC, Picone M, Friedman N, Hawkins S, Sannar E, Pfalzer AC, Shelton AR, Singh D, Zee PC, Glaze DG, Revana A. Diagnosis and management of sleep disorders in Prader-Willi syndrome. J Clin Sleep Med 2022; 18:1687-1696. [PMID: 35172921 PMCID: PMC9163612 DOI: 10.5664/jcsm.9938] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Clinical experience and a growing body of evidence suggest that sleep disturbances are common in people with Prader-Willi syndrome (PWS). PWS is a rare neuroendocrine disorder characterized by early hypotonia and feeding difficulties; developmental delays; endocrinopathies; and behavioral concerns, especially rigidity, anxiety, and behavioral outbursts. PWS is also characterized by decreased resting energy expenditure and transition to hyperphagia and obesity. We propose that, for many people with PWS, clinical diagnosis and management of sleep disorders is an unmet need. We present current information to suggest disordered sleep is a significant burden for individuals with PWS and often overlooked. While central and obstructive sleep apnea are more widely recognized in PWS, other sleep disorders have increasingly gained recognition, including hypersomnia, narcolepsy-like phenotypes, and insomnia. Sleep disorders can impact behavior, cognition, and quality of life and health for individuals with PWS. Our goal is to bring sleep disorders to the forefront of therapeutic intervention for patients with PWS. This paper presents a review of the literature and recommendations for clinical practice based on published research and our clinical experience as sleep specialists, geneticists, psychiatrists, pediatricians, otolaryngologists, and pulmonologists with extensive experience with this patient population. We recommend that management of sleep be considered an integral part of successful medical management of PWS. Further research concerning sleep problems in PWS is urgently needed to develop best practices and work toward a consensus statement for medical management to meet the needs of people with PWS. CITATION Duis J, Pullen LC, Picone M, et al. Diagnosis and management of sleep disorders in Prader-Willi syndrome. J Clin Sleep Med. 2022;18(6):1687-1696.
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Affiliation(s)
- Jessica Duis
- Section of Genetics and Inherited Metabolic Diseases, Section of Pediatrics Special Care Clinic, Prader-Willi Syndrome Multidisciplinary Clinic, Children’s Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado,Address correspondence to: Jessica Duis, MD, MS, Assistant Professor of Pediatrics and Genetics, Section of Genetics and Inherited Metabolic Diseases, Section of Pediatrics Special Care Clinic, Director, Prader-Willi Syndrome Multidisciplinary Clinic, Children’s Hospital Colorado, University of Colorado Anschutz Medical Campus, 13123 E 16th Ave, Aurora, CO 80045; Tel: (303) 724-2370;
| | | | | | - Norman Friedman
- Children’s Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Stephen Hawkins
- Breathing Institute, Children’s Hospital Colorado, Aurora, Colorado
| | - Elise Sannar
- Children’s Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | | | - Deepan Singh
- Department of Psychiatry, Maimonides Medical Center, Brooklyn, New York
| | - Phyllis C. Zee
- Department of Neurology, Center for Circadian and Sleep Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Daniel G. Glaze
- The Children’s Sleep Center, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas
| | - Amee Revana
- Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas
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7
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Hsu NW, Chou KC, Wang YTT, Hung CL, Kuo CF, Tsai SY. Building a model for predicting metabolic syndrome using artificial intelligence based on an investigation of whole-genome sequencing. J Transl Med 2022; 20:190. [PMID: 35484552 PMCID: PMC9052619 DOI: 10.1186/s12967-022-03379-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 12/02/2022] Open
Abstract
Background The circadian system is responsible for regulating various physiological activities and behaviors and has been gaining recognition. The circadian rhythm is adjusted in a 24-h cycle and has transcriptional–translational feedback loops. When the circadian rhythm is interrupted, affecting the expression of circadian genes, the phenotypes of diseases could amplify. For example, the importance of maintaining the internal temporal homeostasis conferred by the circadian system is revealed as mutations in genes coding for core components of the clock result in diseases. This study will investigate the association between circadian genes and metabolic syndromes in a Taiwanese population. Methods We performed analysis using whole-genome sequencing, read vcf files and set target circadian genes to determine if there were variants on target genes. In this study, we have investigated genetic contribution of circadian-related diseases using population-based next generation whole genome sequencing. We also used significant SNPs to create a metabolic syndrome prediction model. Logistic regression, random forest, adaboost, and neural network were used to predict metabolic syndrome. In addition, we used random forest model variables importance matrix to select 40 more significant SNPs, which were subsequently incorporated to create new prediction models and to compare with previous models. The data was then utilized for training set and testing set using five-fold cross validation. Each model was evaluated with the following criteria: area under the receiver operating characteristics curve (AUC), precision, F1 score, and average precision (the area under the precision recall curve). Results After searching significant variants, we used Chi-Square tests to find some variants. We found 186 significant SNPs, and four predicting models which used 186 SNPs (logistic regression, random forest, adaboost and neural network), AUC were 0.68, 0.8, 0.82, 0.81 respectively. The F1 scores were 0.412, 0.078, 0.295, 0.552, respectively. The other three models which used the 40 SNPs (logistic regression, adaboost and neural network), AUC were 0.82, 0.81, 0.81 respectively. The F1 scores were 0.584, 0.395, 0.574, respectively. Conclusions Circadian gene defect may also contribute to metabolic syndrome. Our study found several related genes and building a simple model to predict metabolic syndrome. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03379-7.
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Affiliation(s)
- Nai-Wei Hsu
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Kai-Chen Chou
- Department of Laboratory Medicine, MacKay Memorial Hospital, Taipei City, Taiwan
| | - Yu-Ting Tina Wang
- Department of Laboratory Medicine, MacKay Memorial Hospital, Taipei City, Taiwan
| | - Chung-Lieh Hung
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan.,Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Chien-Feng Kuo
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan.,Department of Nursing, MacKay Junior College of Medicine, Nursing and Management, New Taipei City, Taiwan.,Division of Infectious Diseases, Department of Internal Medicine, Mackay Memorial Hospital, Taipei, Taiwan
| | - Shin-Yi Tsai
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan. .,Department of Laboratory Medicine, MacKay Memorial Hospital, Taipei City, Taiwan. .,Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 21205, USA. .,Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan. .,Institute of Long-Term Care, Mackay Medical College, New Taipei City, Taiwan.
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8
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Ryabykh GK, Mylarshchikov DE, Kuznetsov SV, Sigorskikh AI, Ponomareva TY, Zharikova AA, Mironov AA. RNA–Chromatin Interactome: What? Where? When? Mol Biol 2022. [DOI: 10.1134/s0026893322020121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Zaletaev DV, Nemtsova MV, Strelnikov VV. Epigenetic Regulation Disturbances on Gene Expression in Imprinting Diseases. Mol Biol 2022. [DOI: 10.1134/s0026893321050149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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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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11
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Saad L, Zwiller J, Kalsbeek A, Anglard P. Epigenetic Regulation of Circadian Clocks and Its Involvement in Drug Addiction. Genes (Basel) 2021; 12:1263. [PMID: 34440437 PMCID: PMC8394526 DOI: 10.3390/genes12081263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 12/19/2022] Open
Abstract
Based on studies describing an increased prevalence of addictive behaviours in several rare sleep disorders and shift workers, a relationship between circadian rhythms and addiction has been hinted for more than a decade. Although circadian rhythm alterations and molecular mechanisms associated with neuropsychiatric conditions are an area of active investigation, success is limited so far, and further investigations are required. Thus, even though compelling evidence connects the circadian clock to addictive behaviour and vice-versa, yet the functional mechanism behind this interaction remains largely unknown. At the molecular level, multiple mechanisms have been proposed to link the circadian timing system to addiction. The molecular mechanism of the circadian clock consists of a transcriptional/translational feedback system, with several regulatory loops, that are also intricately regulated at the epigenetic level. Interestingly, the epigenetic landscape shows profound changes in the addictive brain, with significant alterations in histone modification, DNA methylation, and small regulatory RNAs. The combination of these two observations raises the possibility that epigenetic regulation is a common plot linking the circadian clocks with addiction, though very little evidence has been reported to date. This review provides an elaborate overview of the circadian system and its involvement in addiction, and we hypothesise a possible connection at the epigenetic level that could further link them. Therefore, we think this review may further improve our understanding of the etiology or/and pathology of psychiatric disorders related to drug addiction.
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Affiliation(s)
- Lamis Saad
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364 CNRS, Université de Strasbourg, Neuropôle de Strasbourg, 67000 Strasbourg, France; (L.S.); (J.Z.)
- The Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), 1105 BA Amsterdam, The Netherlands;
- Department of Endocrinology and Metabolism, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Jean Zwiller
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364 CNRS, Université de Strasbourg, Neuropôle de Strasbourg, 67000 Strasbourg, France; (L.S.); (J.Z.)
- Centre National de la Recherche Scientifique (CNRS), 75016 Paris, France
| | - Andries Kalsbeek
- The Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), 1105 BA Amsterdam, The Netherlands;
- Department of Endocrinology and Metabolism, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Patrick Anglard
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364 CNRS, Université de Strasbourg, Neuropôle de Strasbourg, 67000 Strasbourg, France; (L.S.); (J.Z.)
- Institut National de la Santé et de la Recherche Médicale (INSERM), 75013 Paris, France
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12
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Tauber M, Diene G. Prader-Willi syndrome: Hormone therapies. HANDBOOK OF CLINICAL NEUROLOGY 2021; 181:351-367. [PMID: 34238470 DOI: 10.1016/b978-0-12-820683-6.00026-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Prader-Willi syndrome (PWS) is a rare genetic neurodevelopmental disorder linked to the lack of expression of specific maternally imprinted genes located in the chromosomal region 15q11-q13. Impaired hypothalamic development and function explain most of the phenotype that is characterized by a specific trajectory from anorexia at birth to excessive weight gain at later ages, which is accompanied by hyperphagia and early severe obesity, as well as by other hormonal deficiencies, behavioral deficits, and dysautonomia. In almost all patients, their endocrine dysfunction involves growth hormone deficiency and hypogonadism, which originate from a combination of both peripheral and hypothalamic origin, central hypothyroidism in 40%, precocious adrenarche in 30% of the cases, and in rare cases, also adrenocorticotropin deficiency and precocious puberty. In addition, the oxytocin (OXT) and ghrelin systems are impaired in most patients and involved in a poor suckling response at birth, and hyperphagia with food addiction, poor social skills, and emotional dysregulation. Current hormonal replacement treatments are the same as used in classical hormonal deficiencies, and recombinant human GH treatment is registered since 2000 and has dramatically changed the phenotype of these children. OXT and OXT analogue treatments are currently investigated as well as new molecules targeting the ghrelin system. The severe condition of PWS can be seen as a model to improve the fine description and treatments of hypothalamic dysfunction.
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Affiliation(s)
- Maithé Tauber
- Centre de Référence du Syndrome de Prader-Willi, Hôpital des Enfants, CHU Toulouse, Toulouse, France.
| | - Gwenaelle Diene
- Centre de Référence du Syndrome de Prader-Willi, Hôpital des Enfants, CHU Toulouse, Toulouse, France
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13
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Kocher MA, Huang FW, Le E, Good DJ. Snord116 Post-transcriptionally Increases Nhlh2 mRNA Stability: Implications for Human Prader-Willi Syndrome. Hum Mol Genet 2021; 30:1101-1110. [PMID: 33856031 DOI: 10.1093/hmg/ddab103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/25/2022] Open
Abstract
The smallest genomic region causing Prader-Willi Syndrome (PWS) deletes the non-coding RNA SNORD116 cluster; however, the function of SNORD116 remains a mystery. Previous work in the field revealed the tantalizing possibility that expression of NHLH2, a gene previously implicated in both obesity and hypogonadism, was downregulated in PWS patients and differentiated stem cells. In silico RNA: RNA modeling identified several potential interaction domains between SNORD116 and NHLH2 mRNA. One of these interaction domains was highly conserved in most vertebrate NHLH2 mRNAs examined. A construct containing the Nhlh2 mRNA, including its 3'-UTR, linked to a c-myc tag was transfected into a hypothalamic neuron cell line in the presence and absence of exogenously-expressed Snord116. Nhlh2 mRNA expression was upregulated in the presence of Snord116 dependent on the length and type of 3'UTR used on the construct. Furthermore, use of actinomycin D to stop new transcription in N29/2 cells demonstrated that the upregulation occurred through increased stability of the Nhlh2 mRNA in the 45 minutes immediately following transcription. In silico modeling also revealed that a single nucleotide variant (SNV) in the NHLH2 mRNA could reduce the predicted interaction strength of the NHLH2:SNORD116 diad. Indeed, use of an Nhlh2 mRNA construct containing this SNV significantly reduces the ability of Snord116 to increase Nhlh2 mRNA levels. For the first time, these data identify a motif and mechanism for SNORD116-mediated regulation of NHLH2, clarifying the mechanism by which deletion of the SNORD116 snoRNAs locus leads to PWS phenotypes.
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Affiliation(s)
- Matthew A Kocher
- Translational Biology, Medicine and Health Graduate Program, 1 Riverside Circle, Virginia Tech, Roanoke, VA 24016
| | - Fenix W Huang
- Biocomplexity Institute & Initiative, University of Virginia, 995 Research Park Blvd, Town Center III, 4th Floor, Charlottesville, VA 22911
| | - Erin Le
- Department of Human Nutrition, Foods, and Exercise, 1981 Kraft Drive (0913), Integrated Life Sciences Building, Virginia Tech, Blacksburg, VA 24060
| | - Deborah J Good
- Translational Biology, Medicine and Health Graduate Program, 1 Riverside Circle, Virginia Tech, Roanoke, VA 24016.,Department of Human Nutrition, Foods, and Exercise, 1981 Kraft Drive (0913), Integrated Life Sciences Building, Virginia Tech, Blacksburg, VA 24060
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14
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Dysregulated CRMP Mediates Circadian Deficits in a Drosophila Model of Fragile X Syndrome. Neurosci Bull 2021; 37:973-984. [PMID: 33856646 DOI: 10.1007/s12264-021-00682-z] [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: 12/23/2019] [Accepted: 11/09/2020] [Indexed: 10/21/2022] Open
Abstract
Fragile X syndrome (FXS) is the leading inherited cause of intellectual disability, resulting from the lack of functional fragile X mental retardation protein (FMRP), an mRNA binding protein mainly serving as a translational regulator. Loss of FMRP leads to dysregulation of target mRNAs. The Drosophila model of FXS show an abnormal circadian rhythm with disruption of the output pathway downstream of the clock network. Yet the FMRP targets involved in circadian regulation have not been identified. Here, we identified collapsing response mediator protein (CRMP) mRNA as a target of FMRP. Knockdown of pan-neuronal CRMP expression ameliorated the circadian defects and abnormal axonal structures of clock neurons (ventral lateral neurons) in dfmr1 mutant flies. Furthermore, specific reduction of CRMP in the downstream output insulin-producing cells attenuated the aberrant circadian behaviors. Molecular analyses revealed that FMRP binds with CRMP mRNA and negatively regulates its translation. Our results indicate that CRMP is an FMRP target and establish an essential role for CRMP in the circadian output in FXS Drosophila.
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15
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Tauber M, Hoybye C. Endocrine disorders in Prader-Willi syndrome: a model to understand and treat hypothalamic dysfunction. Lancet Diabetes Endocrinol 2021; 9:235-246. [PMID: 33647242 DOI: 10.1016/s2213-8587(21)00002-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022]
Abstract
Prader-Willi syndrome is a rare genetic neurodevelopmental disorder resulting from the loss of expression of maternally imprinted genes located in the paternal chromosomal region, 15q11-13. Impaired hypothalamic development and function is the cause of most of the phenotypes comprising the developmental trajectory of Prader-Willi syndrome: from anorexia at birth to excessive weight gain preceding hyperphagia, and early severe obesity with hormonal deficiencies, behavioural problems, and dysautonomia. Growth hormone deficiency, hypogonadism, hypothyroidism, premature adrenarche, corticotropin deficiency, precocious puberty, and glucose metabolism disorders are the main endocrine dysfunctions observed. Additionally, as a result of hypothalamic dysfunction, oxytocin and ghrelin systems are impaired in most patients. Standard pituitary and gonadal hormone replacement therapies are required. In this Review, we discuss Prader-Willi syndrome as a model of hypothalamic dysfunction, and provide a comprehensive description of the accumulated knowledge on genetics, pathophysiology, and treatment approaches of this rare disorder.
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Affiliation(s)
- Maithé Tauber
- Centre de Référence du Syndrome de Prader-Willi, Hôpital des Enfants, Toulouse, France; Axe Pédiatrique du CIC 9302/INSERM, Hôpital des Enfants, Toulouse, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires, INSERM UMR1291, CNRS UMR5051, Université Toulouse III, Toulouse, France, France; International Prader-Willi Syndrome Organisation, Cambridge, UK.
| | - Charlotte Hoybye
- International Prader-Willi Syndrome Organisation, Cambridge, UK; Department of Endocrinology, Karolinska University Hospital and Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
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16
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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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17
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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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18
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Cataldi M, Arnaldi D, Tucci V, De Carli F, Patti G, Napoli F, Pace M, Maghnie M, Nobili L. Sleep disorders in Prader-Willi syndrome, evidence from animal models and humans. Sleep Med Rev 2021; 57:101432. [PMID: 33567377 DOI: 10.1016/j.smrv.2021.101432] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023]
Abstract
Prader-Willi Syndrome (PWS) is a complex genetic disorder with multiple cognitive, behavioral and endocrine dysfunctions. Sleep alterations and sleep disorders such as Sleep-disordered breathing and Central disorders of hypersomnolence are frequently recognized (either isolated or in comorbidity). The aim of the review is to highlight the pathophysiology and the clinical features of sleep disorders in PWS, providing the basis for early diagnosis and management. We reviewed the genetic features of the syndrome and the possible relationship with sleep alterations in animal models, and we described sleep phenotypes, diagnostic tools and therapeutic approaches in humans. Moreover, we performed a meta-analysis of cerebrospinal fluid orexin levels in patients with PWS; significantly lower levels of orexin were detected in PWS with respect to control subjects (although significantly higher than the ones of narcoleptic patients). Sleep disorders in humans with PWS are multifaceted and are often the result of different mechanisms. Since hypothalamic dysfunction seems to partially influence metabolic, respiratory and sleep/wake characteristics of this syndrome, additional studies are required in this framework.
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Affiliation(s)
- Matteo Cataldi
- Unit of Child Neuropsychiatry, Department of Medical and Surgical Neuroscience and Rehabilitation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Dario Arnaldi
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Valter Tucci
- Genetics and Epigenetics of Behaviour Laboratory, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Fabrizio De Carli
- Institute of Bioimaging and Molecular Physiology, National Research Council, Genoa, Italy
| | - Giuseppa Patti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy; Department of Pediatrics, Istituto Giannina Gaslini, University of Genoa, Genoa, Italy
| | - Flavia Napoli
- Department of Pediatrics, Istituto Giannina Gaslini, University of Genoa, Genoa, Italy
| | - Marta Pace
- Genetics and Epigenetics of Behaviour Laboratory, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Mohamad Maghnie
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy; Department of Pediatrics, Istituto Giannina Gaslini, University of Genoa, Genoa, Italy
| | - Lino Nobili
- Unit of Child Neuropsychiatry, Department of Medical and Surgical Neuroscience and Rehabilitation, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy.
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19
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Abstract
Prader-Willi syndrome (PWS) is a neurodevelopmental disorder characterized by hyperphagia, hypotonia, learning disability, as well as a range of psychiatric conditions. The conservation of the PWS genetic interval on chromosome 15q11-q13 in human, and a cluster of genes on mouse chromosome 7, has facilitated the use of mice as animal models for PWS. Some models faithfully mimic the loss of all gene expression from the paternally inherited PWS genetic interval, whereas others target smaller regions or individual genes. Collectively, these models have provided insight into the mechanisms, many of which lead to alterations in hypothalamic function, underlying the core symptoms of PWS, including growth retardation, hyperphagia and metabolism, reproductive maturation and endophenotypes of relevance to behavioral and psychiatric problems. Here we review and summarize these studies.
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Affiliation(s)
- Simona Zahova
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Anthony R Isles
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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20
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Salles J, Lacassagne E, Eddiry S, Franchitto N, Salles JP, Tauber M. What can we learn from PWS and SNORD116 genes about the pathophysiology of addictive disorders? Mol Psychiatry 2021; 26:51-59. [PMID: 33082508 DOI: 10.1038/s41380-020-00917-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/16/2020] [Accepted: 10/05/2020] [Indexed: 02/07/2023]
Abstract
Addictive disorders have been much investigated and many studies have underlined the role of environmental factors such as social interaction in the vulnerability to and maintenance of addictive behaviors. Research on addiction pathophysiology now suggests that certain behavioral disorders are addictive, one example being food addiction. Yet, despite the growing body of knowledge on addiction, it is still unknown why only some of the individuals exposed to a drug become addicted to it. This observation has prompted the consideration of genetic heritage, neurodevelopmental trajectories, and gene-environment interactions in addiction vulnerability. Prader-Willi syndrome (PWS) is a rare neurodevelopmental disorder in which children become addicted to food and show early social impairment. PWS is caused by the deficiency of imprinted genes located on the 15q11-q13 chromosome. Among them, the SNORD116 gene was identified as the minimal gene responsible for the PWS phenotype. Several studies have also indicated the role of the Snord116 gene in animal and cellular models to explain PWS pathophysiology and phenotype (including social impairment and food addiction). We thus present here the evidence suggesting the potential involvement of the SNORD116 gene in addictive disorders.
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Affiliation(s)
- Juliette Salles
- Université de Toulouse III, F-31000, Toulouse, France.,CHU de Toulouse, Service de psychiatrie et psychologie, psychiatrie Toulouse, F-31000, Toulouse, France.,Inserm Unité 1043, CNRS 5828, Université Paul Sabatier, Toulouse III, F-31000, Toulouse, France.,CHU de Toulouse, Institut des Handicaps Neurologiques, Psychiatriques et Sensoriels, F-31000, Toulouse, France
| | - Emmanuelle Lacassagne
- Inserm Unité 1043, CNRS 5828, Université Paul Sabatier, Toulouse III, F-31000, Toulouse, France
| | - Sanaa Eddiry
- Inserm Unité 1043, CNRS 5828, Université Paul Sabatier, Toulouse III, F-31000, Toulouse, France
| | - Nicolas Franchitto
- Université de Toulouse III, F-31000, Toulouse, France.,CHU de Toulouse, Service d'addictologie clinique, urgences réanimation médecine, F-31000, Toulouse, France
| | - Jean-Pierre Salles
- Inserm Unité 1043, CNRS 5828, Université Paul Sabatier, Toulouse III, F-31000, Toulouse, France
| | - Maithé Tauber
- Université de Toulouse III, F-31000, Toulouse, France. .,Inserm Unité 1043, CNRS 5828, Université Paul Sabatier, Toulouse III, F-31000, Toulouse, France. .,CHU de Toulouse, Institut des Handicaps Neurologiques, Psychiatriques et Sensoriels, F-31000, Toulouse, France. .,CHU de Toulouse, Centre de référence du Syndrome de Prader-Willi et autres syndromes avec troubles du comportement alimentaire, Unité d'endocrinologie, obésités, maladies osseuses, génétique et gynécologie médicale, F-31000, Toulouse, France.
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21
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Abstract
K-mer based comparisons have emerged as powerful complements to BLAST-like alignment algorithms, particularly when the sequences being compared lack direct evolutionary relationships. In this chapter, we describe methods to compare k-mer content between groups of long noncoding RNAs (lncRNAs), to identify communities of lncRNAs with related k-mer contents, to identify the enrichment of protein-binding motifs in lncRNAs, and to scan for domains of related k-mer contents in lncRNAs. Our step-by-step instructions are complemented by Python code deposited in Github. Though our chapter focuses on lncRNAs, the methods we describe could be applied to any set of nucleic acid sequences.
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Affiliation(s)
- Jessime M Kirk
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Invitae Corporation, San Francisco, CA, USA
| | - Daniel Sprague
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Flagship Pioneering, Boston, MA, USA
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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22
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Aznaourova M, Schmerer N, Schmeck B, Schulte LN. Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci. Front Genet 2020; 11:527484. [PMID: 33329688 PMCID: PMC7735109 DOI: 10.3389/fgene.2020.527484] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
The classic understanding of molecular disease-mechanisms is largely based on protein-centric models. During the past decade however, genetic studies have identified numerous disease-loci in the human genome that do not encode proteins. Such non-coding DNA variants increasingly gain attention in diagnostics and personalized medicine. Of particular interest are long non-coding RNA (lncRNA) genes, which generate transcripts longer than 200 nucleotides that are not translated into proteins. While most of the estimated ~20,000 lncRNAs currently remain of unknown function, a growing number of genetic studies link lncRNA gene aberrations with the development of human diseases, including diabetes, AIDS, inflammatory bowel disease, or cancer. This suggests that the protein-centric view of human diseases does not capture the full complexity of molecular patho-mechanisms, with important consequences for molecular diagnostics and therapy. This review illustrates well-documented lncRNA gene aberrations causatively linked to human diseases and discusses potential lessons for molecular disease models, diagnostics, and therapy.
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Affiliation(s)
- Marina Aznaourova
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Nils Schmerer
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Leon N Schulte
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany
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23
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Chowdhury D, Wang C, Lu A, Zhu H. Identifying Transcription Factor Combinations to Modulate Circadian Rhythms by Leveraging Virtual Knockouts on Transcription Networks. iScience 2020; 23:101490. [PMID: 32920484 PMCID: PMC7492989 DOI: 10.1016/j.isci.2020.101490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/24/2020] [Accepted: 08/19/2020] [Indexed: 02/02/2023] Open
Abstract
The mammalian circadian systems consist of indigenous, self-sustained 24-h rhythm generators. They comprise many genes, molecules, and regulators. To decode their systematic controls, a robust computational approach was employed. It integrates transcription-factor-occupancy and time-series gene-expression data as input. The model equations were constructed and solved to determine the transcriptional regulatory logics in the mouse transcriptome network. This hypothesizes to explore the underlying mechanisms of combinatorial transcriptional regulations for circadian rhythms in mouse. We reconstructed the quantitative transcriptional-regulatory networks for circadian gene regulation at a dynamic scale. Transcriptional-simulations with virtually knocked-out mutants were performed to estimate their influence on networks. The potential transcriptional-regulators-combinations modulating the circadian rhythms were identified. Of them, CLOCK/CRY1 double knockout preserves the highest modulating capacity. Our quantitative framework offers a quick, robust, and physiologically relevant way to characterize the druggable targets to modulate the circadian rhythms at a dynamic scale effectively.
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Affiliation(s)
- Debajyoti Chowdhury
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
| | - Chao Wang
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
| | - Aiping Lu
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
| | - Hailong Zhu
- HKBU Institute for Research and Continuing Education, Shenzhen 518057, China
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
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24
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The RDoC approach for translational psychiatry: Could a genetic disorder with psychiatric symptoms help fill the matrix? the example of Prader-Willi syndrome. Transl Psychiatry 2020; 10:274. [PMID: 32772048 PMCID: PMC7415132 DOI: 10.1038/s41398-020-00964-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
The Research Domain Criteria project (RDoc) proposes a new classification system based on information from several fields in order to encourage translational perspectives. Nevertheless, integrating genetic markers into this classification has remained difficult because of the lack of powerful associations between targeted genes and RDoC domains. We hypothesized that genetic diseases with psychiatric manifestations would be good models for RDoC gene investigations and would thereby extend the translational approach to involve targeted gene pathways. To explore this possibility, we reviewed the current knowledge on Prader-Willi syndrome, a genetic disorder caused by the absence of expression of some of the genes of the chromosome 15q11-13 region inherited from the father. Indeed, we found that the associations between genes of the PW locus and the modification identified in the relevant behavioral, physiological, and brain imaging studies followed the structure of the RDoC matrix and its six domains (positive valence, negative valence, social processing, cognitive systems, arousal/regulatory systems, and sensorimotor systems).
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25
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Lopez SJ, Laufer BI, Beitnere U, Berg EL, Silverman JL, O'Geen H, Segal DJ, LaSalle JM. Imprinting effects of UBE3A loss on synaptic gene networks and Wnt signaling pathways. Hum Mol Genet 2020; 28:3842-3852. [PMID: 31625566 DOI: 10.1093/hmg/ddz221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/21/2019] [Accepted: 09/04/2019] [Indexed: 12/13/2022] Open
Abstract
Ubiquitin E3 ligase 3A (UBE3A) encodes an E3 ubiquitin ligase whose loss from the maternal allele causes the neurodevelopmental disorder Angelman syndrome (AS). Previous studies of UBE3A function have not examined full Ube3a deletion in mouse, the complexity of imprinted gene networks in brain nor the molecular basis of systems-level cognitive dysfunctions in AS. We therefore utilized a systems biology approach to elucidate how UBE3A loss impacts the early postnatal brain in a novel CRISPR/Cas9-engineered rat Angelman model of a complete Ube3a deletion. Strand-specific transcriptome analysis of offspring from maternally or paternally inherited Ube3a deletions revealed the expected parental expression patterns of Ube3a sense and antisense transcripts by postnatal day 2 (P2) in hypothalamus and day 9 (P9) in cortex, compared to wild-type littermates. The dependency of genome-wide effects on parent-of-origin, Ube3a genotype and time (P2 and P9) was investigated through transcriptome (RNA sequencing of cortex and hypothalamus) and methylome (whole-genome bisulfite sequencing of hypothalamus). Weighted gene co-expression and co-methylation network analyses identified co-regulated networks in maternally inherited Ube3a deletion offspring enriched in postnatal developmental processes including Wnt signaling, synaptic regulation, neuronal and glial functions, epigenetic regulation, ubiquitin, circadian entrainment and splicing. Furthermore, we showed that loss of the paternal Ube3a antisense transcript resulted in both unique and overlapping dysregulated gene pathways with maternal loss, predominantly at the level of differential methylation. Together, these results provide a holistic examination of the molecular impacts of UBE3A loss in brain, supporting the existence of interactive epigenetic networks between maternal and paternal transcripts at the Ube3a locus.
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Affiliation(s)
- S Jesse Lopez
- Medical Immunology and Microbiology, University of California (UC) Davis School of Medicine, Davis, CA 95616, USA.,Genome Center, UC Davis, Davis, CA, USA.,Integrative Genetics and Genomics, UC Davis, Davis, CA 95616, USA.,Biochemistry and Molecular Medicine, UC Davis School of Medicine, Davis, CA 95616, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
| | - Benjamin I Laufer
- Medical Immunology and Microbiology, University of California (UC) Davis School of Medicine, Davis, CA 95616, USA.,Genome Center, UC Davis, Davis, CA, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
| | - Ulrika Beitnere
- Genome Center, UC Davis, Davis, CA, USA.,Biochemistry and Molecular Medicine, UC Davis School of Medicine, Davis, CA 95616, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
| | - Elizabeth L Berg
- Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA.,Psychiatry and Behavioral Sciences, UC Davis School of Medicine, Sacromento, CA 95817, USA
| | - Jill L Silverman
- Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA.,Psychiatry and Behavioral Sciences, UC Davis School of Medicine, Sacromento, CA 95817, USA
| | - Henriette O'Geen
- Genome Center, UC Davis, Davis, CA, USA.,Biochemistry and Molecular Medicine, UC Davis School of Medicine, Davis, CA 95616, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
| | - David J Segal
- Genome Center, UC Davis, Davis, CA, USA.,Integrative Genetics and Genomics, UC Davis, Davis, CA 95616, USA.,Biochemistry and Molecular Medicine, UC Davis School of Medicine, Davis, CA 95616, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
| | - Janine M LaSalle
- Medical Immunology and Microbiology, University of California (UC) Davis School of Medicine, Davis, CA 95616, USA.,Genome Center, UC Davis, Davis, CA, USA.,Integrative Genetics and Genomics, UC Davis, Davis, CA 95616, USA.,Medical Investigation of Neurodevelopmental Disorders Institute, UC Davis Health, Sacramento, CA 95817, USA
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26
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Role of Non-Coding RNAs in Lung Circadian Clock Related Diseases. Int J Mol Sci 2020; 21:ijms21083013. [PMID: 32344623 PMCID: PMC7215637 DOI: 10.3390/ijms21083013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
Circadian oscillations are regulated at both central and peripheral levels to maintain physiological homeostasis. The central circadian clock consists of a central pacemaker in the suprachiasmatic nucleus that is entrained by light dark cycles and this, in turn, synchronizes the peripheral clock inherent in other organs. Circadian dysregulation has been attributed to dysregulation of peripheral clock and also associated with several diseases. Components of the molecular clock are disrupted in lung diseases like chronic obstructive pulmonary disease (COPD), asthma and IPF. Airway epithelial cells play an important role in temporally organizing magnitude of immune response, DNA damage response and acute airway inflammation. Non-coding RNAs play an important role in regulation of molecular clock and in turn are also regulated by clock components. Dysregulation of these non-coding RNAs have been shown to impact the expression of core clock genes as well as clock output genes in many organs. However, no studies have currently looked at the potential impact of these non-coding RNAs on lung molecular clock. This review focuses on the ways how these non-coding RNAs regulate and in turn are regulated by the lung molecular clock and its potential impact on lung diseases.
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27
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Bratkovič T, Božič J, Rogelj B. Functional diversity of small nucleolar RNAs. Nucleic Acids Res 2020; 48:1627-1651. [PMID: 31828325 PMCID: PMC7038934 DOI: 10.1093/nar/gkz1140] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/17/2019] [Accepted: 12/05/2019] [Indexed: 12/22/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are short non-protein-coding RNAs with a long-recognized role in tuning ribosomal and spliceosomal function by guiding ribose methylation and pseudouridylation at targeted nucleotide residues of ribosomal and small nuclear RNAs, respectively. SnoRNAs are increasingly being implicated in regulation of new types of post-transcriptional processes, for example rRNA acetylation, modulation of splicing patterns, control of mRNA abundance and translational efficiency, or they themselves are processed to shorter stable RNA species that seem to be the principal or alternative bioactive isoform. Intriguingly, some display unusual cellular localization under exogenous stimuli, or tissue-specific distribution. Here, we discuss the new and unforeseen roles attributed to snoRNAs, focusing on the presumed mechanisms of action. Furthermore, we review the experimental approaches to study snoRNA function, including high resolution RNA:protein and RNA:RNA interaction mapping, techniques for analyzing modifications on targeted RNAs, and cellular and animal models used in snoRNA biology research.
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Affiliation(s)
- Tomaž Bratkovič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, SI1000 Ljubljana, Slovenia
| | - Janja Božič
- Jozef Stefan Institute, Department of Biotechnology, Jamova cesta 39, SI1000 Ljubljana, Slovenia.,Biomedical Research Institute BRIS, Puhova ulica 10, SI1000 Ljubljana, Slovenia
| | - Boris Rogelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, SI1000 Ljubljana, Slovenia.,Jozef Stefan Institute, Department of Biotechnology, Jamova cesta 39, SI1000 Ljubljana, Slovenia.,Biomedical Research Institute BRIS, Puhova ulica 10, SI1000 Ljubljana, Slovenia.,University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI1000 Ljubljana, Slovenia
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28
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Salminen I, Read S, Hurd P, Crespi B. Does SNORD116 mediate aspects of psychosis in Prader-Willi syndrome? Evidence from a non-clinical population. Psychiatry Res 2020; 286:112858. [PMID: 32065983 DOI: 10.1016/j.psychres.2020.112858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/27/2022]
Abstract
The paternally expressed gene SNORD116 encodes a set of short nucleolar RNAs that affect the expression of hundreds of other genes via epigenetic interactions. Lack of expression for SNORD116 has been implicated in major phenotypes of Prader-Willi Syndrome (PWS). Rates of psychosis and autism spectrum disorders are greatly increased in PWS, but the genetic and epigenetic causes of these increases remain unknown. We genotyped a large population of typical individuals for five SNPs within SNORD116 and phenotyped them for variation in schizotypal and autism spectrum traits. SNORD116 SNP and haplotype variation mediated variation exclusively in the Schizotypal Personality Questionnaire - Ideas of Reference subscale, which reflects variation in aspects of paranoia. The effect was restricted to females. SNORD116 represents, in addition to UBE3A and NDN-MAGEL2, a third, independent locus in the 15q11-q13 imprinted region that preferentially or exclusively affects levels of paranoia. This convergent pattern may reflect a common neural pathway affected by multiple genes, or an effect of interactions between the imprinted loci.
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Affiliation(s)
- Iiro Salminen
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Silven Read
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Pete Hurd
- Department of Psychology and Centre for Neuroscience, University of Alberta, Edmonton, Canada
| | - Bernard Crespi
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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29
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Yao RW, Liu CX, Chen LL. Linking RNA Processing and Function. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:67-82. [PMID: 32019863 DOI: 10.1101/sqb.2019.84.039495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA processing is critical for eukaryotic mRNA maturation and function. It appears there is no exception for other types of RNAs. Long noncoding RNAs (lncRNAs) represent a subclass of noncoding RNAs, have sizes of >200 nucleotides (nt), and participate in various aspects of gene regulation. Although many lncRNAs are capped, polyadenylated, and spliced just like mRNAs, others are derived from primary transcripts of RNA polymerase II and stabilized by forming circular structures or by ending with small nucleolar RNA-protein complexes. Here we summarize the recent progress in linking the processing and function of these unconventionally processed lncRNAs; we also discuss how directional RNA movement is achieved using the radial flux movement of nascent precursor ribosomal RNA (pre-rRNA) in the human nucleolus as an example.
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Affiliation(s)
- Run-Wen Yao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chu-Xiao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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30
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Yi T, Wang T, Shi Y, Peng X, Tang S, Zhong L, Chen Y, Li Y, He K, Wang M, Zhao H, Li Q. Long noncoding RNA 91H overexpression contributes to the growth and metastasis of HCC by epigenetically positively regulating IGF2 expression. Liver Int 2020; 40:456-467. [PMID: 31724285 DOI: 10.1111/liv.14300] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Long noncoding RNA 91H is transcribed from the H19/IGF2 locus and contributes to the development of breast and oesophagus cancers by regulating the expression of IGF2, but the regulation mechanism remains poorly characterized. Here, we explored the role of 91H in hepatocellular carcinoma (HCC) and the mechanism of IGF2 expression regulation by 91H. METHODS Firstly, the expression of 91H was analysed in HCC by quantitative RT-PCR, the association of 91H with survival was evaluated by the Kaplan-Meier method and the effect of 91H on the growth and invasion of HCC was investigated by the in vitro and in vivo studies. Then, the association of 91H with the expression of IGF2 was evaluated in HCC tissues, and the effect of 91H on the expression of IGF2 was investigated by 91H knockdown. Finally, the binding of RBBP5 to 91H and the binding of RBBP5, activating H3K4me3 mark and repressive H3K27me3 mark to the P3 and P4 promoters of IGF2 gene were studied by RIP and ChIP respectively. RESULTS The overexpression of 91H was found in HCC and in association with the growth, metastasis and shorter survival time of HCC. The knockdown of 91H down-regulated the IGF2 expression in HCC, and the mechanism was correlated with the decreased enrichment of RBBP5 and H3K4me3 and increased enrichment of H3K27me3 at the bivalent P3 and P4 promoters. CONCLUSIONS The overexpression of 91H promotes tumour growth and metastasis, and is associated with a poor prognosis of HCC at least partially by positively regulating the expression of IGF2 through bivalent histone modification changes characterized by H3K4me3 and H3K27me3 at the P3 and P4 promoters.
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Affiliation(s)
- Tingzhuang Yi
- Internal Medicine, The First Affiliated Hospital, Jinan University, Guangzhou, P. R. China.,Department of Gastroenterology, Affiliated Hospital of Youjiang Medical University for Nationalities, BaiSe, P. R. China
| | - Tonghua Wang
- Department of Gastroenterology, Affiliated Hospital of Youjiang Medical University for Nationalities, BaiSe, P. R. China.,Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, P. R. China
| | - Ying Shi
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, P. R. China
| | - Xiaojuan Peng
- Department of Endocrinology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, P. R. China
| | - Shaohui Tang
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, P. R. China
| | - Lu Zhong
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, P. R. China
| | - Yanfang Chen
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, P. R. China
| | - Yuting Li
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, P. R. China
| | - Kaiyin He
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, P. R. China
| | - Min Wang
- Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, P. R. China
| | - Hailiang Zhao
- Department of Gastroenterology, Affiliated Hospital of Youjiang Medical University for Nationalities, BaiSe, P. R. China.,Department of Gastroenterology, The First Affiliated Hospital, Jinan University, Guangzhou, P. R. China
| | - Qing Li
- Department of Interventional vascular surgery, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, P. R. China
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31
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32
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Thamban T, Agarwaal V, Khosla S. Role of genomic imprinting in mammalian development. J Biosci 2020; 45:20. [PMID: 31965998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-mendelian inheritance refers to the group of phenomena and observations related to the inheritance of genetic information that cannot be merely explained by Mendel's laws of inheritance. Phenomenon including Genomic imprinting, X-chromosome Inactivation, Paramutations are some of the best studied examples of non-mendelian inheritance. Genomic imprinting is a process that reversibly marks one of the two homologous loci, chromosome or chromosomal sets during development, resulting in functional non-equivalence of gene expression. Genomic imprinting is known to occur in a few insect species, plants, and placental mammals. Over the years, studies on imprinted genes have contributed immensely to highlighting the role of epigenetic modifications and the epigenetic circuitry during gene expression and development. In this review, we discuss the phenomenon of genomic imprinting in mammals and the role it plays especially during fetoplacental growth and early development.
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Affiliation(s)
- Thushara Thamban
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
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33
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Zhao Y, Zhou J, He L, Li Y, Yuan J, Sun K, Chen X, Bao X, Esteban MA, Sun H, Wang H. MyoD induced enhancer RNA interacts with hnRNPL to activate target gene transcription during myogenic differentiation. Nat Commun 2019; 10:5787. [PMID: 31857580 PMCID: PMC6923398 DOI: 10.1038/s41467-019-13598-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Emerging evidence supports roles of enhancer RNAs (eRNAs) in regulating target gene. Here, we study eRNA regulation and function during skeletal myoblast differentiation. We provide a panoramic view of enhancer transcription and categorization of eRNAs. Master transcription factor MyoD is crucial in activating eRNA production. Super enhancer (se) generated seRNA-1 and -2 promote myogenic differentiation in vitro and in vivo. seRNA-1 regulates expression levels of two nearby genes, myoglobin (Mb) and apolipoprotein L6 (Apol6), by binding to heterogeneous nuclear ribonucleoprotein L (hnRNPL). A CAAA tract on seRNA-1 is essential in mediating seRNA-1/hnRNPL binding and function. Disruption of seRNA-1-hnRNPL interaction attenuates Pol II and H3K36me3 deposition at the Mb locus, in coincidence with the reduction of its transcription. Furthermore, analyses of hnRNPL binding transcriptome-wide reveal its association with eRNAs is a general phenomenon in multiple cells. Collectively, we propose that eRNA-hnRNPL interaction represents a mechanism contributing to target mRNA activation.
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Affiliation(s)
- Yu Zhao
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Liangqiang He
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kun Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518000, China
| | - Xiaona Chen
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xichen Bao
- Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Miguel A Esteban
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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34
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Lithium alters expression of RNAs in a type-specific manner in differentiated human neuroblastoma neuronal cultures, including specific genes involved in Alzheimer's disease. Sci Rep 2019; 9:18261. [PMID: 31797941 PMCID: PMC6892907 DOI: 10.1038/s41598-019-54076-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/08/2019] [Indexed: 02/08/2023] Open
Abstract
Lithium (Li) is a medication long-used to treat bipolar disorder. It is currently under investigation for multiple nervous system disorders, including Alzheimer's disease (AD). While perturbation of RNA levels by Li has been previously reported, its effects on the whole transcriptome has been given little attention. We, therefore, sought to determine comprehensive effects of Li treatment on RNA levels. We cultured and differentiated human neuroblastoma (SK-N-SH) cells to neuronal cells with all-trans retinoic acid (ATRA). We exposed cultures for one week to lithium chloride or distilled water, extracted total RNA, depleted ribosomal RNA and performed whole-transcriptome RT-sequencing. We analyzed results by RNA length and type. We further analyzed expression and protein interaction networks between selected Li-altered protein-coding RNAs and common AD-associated gene products. Lithium changed expression of RNAs in both non-specific (inverse to sequence length) and specific (according to RNA type) fashions. The non-coding small nucleolar RNAs (snoRNAs) were subject to the greatest length-adjusted Li influence. When RNA length effects were taken into account, microRNAs as a group were significantly less likely to have had levels altered by Li treatment. Notably, several Li-influenced protein-coding RNAs were co-expressed or produced proteins that interacted with several common AD-associated genes and proteins. Lithium's modification of RNA levels depends on both RNA length and type. Li activity on snoRNA levels may pertain to bipolar disorders while Li modification of protein coding RNAs may be relevant to AD.
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Dhawan A, Harris AL, Buffa FM, Scott JG. Endogenous miRNA sponges mediate the generation of oscillatory dynamics for a non-coding RNA network. J Theor Biol 2019; 481:54-60. [PMID: 30385313 DOI: 10.1016/j.jtbi.2018.10.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 10/28/2022]
Abstract
Oscillations are crucial to the normal function of living organisms, across a wide variety of biological processes. In eukaryotes, oscillatory dynamics are thought to arise from interactions at the protein and RNA levels; however, the role of non-coding RNA in regulating these dynamics remains understudied. In this work, we show how non-coding RNA acting as microRNA (miRNA) sponges in a conserved miRNA - transcription factor feedback motif, can give rise to oscillatory behaviour, and how to test for this experimentally. Control of these non-coding RNA can dynamically create oscillations or stability, and we show how this behaviour predisposes to oscillations in the stochastic limit. These results, supported by emerging evidence for the role of miRNA sponges in development, point towards key roles of different species of miRNA sponges, such as circular RNA, potentially in the maintenance of yet unexplained oscillatory behaviour. These results help to provide a paradigm for understanding functional differences between the many redundant, but distinct RNA species thought to act as miRNA sponges in nature, such as long non-coding RNA, pseudogenes, competing mRNA, circular RNA, and3' UTRs.
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Affiliation(s)
- Andrew Dhawan
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Adrian L Harris
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Francesca M Buffa
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Jacob G Scott
- Departments of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, United States.
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36
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Crutcher E, Pal R, Naini F, Zhang P, Laugsch M, Kim J, Bajic A, Schaaf CP. mTOR and autophagy pathways are dysregulated in murine and human models of Schaaf-Yang syndrome. Sci Rep 2019; 9:15935. [PMID: 31685878 PMCID: PMC6828689 DOI: 10.1038/s41598-019-52287-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/11/2019] [Indexed: 11/09/2022] Open
Abstract
MAGEL2 is a maternally imprinted, paternally expressed gene, located in the Prader-Willi region of human chromosome 15. Pathogenic variants in the paternal copy of MAGEL2 cause Schaaf-Yang syndrome (SHFYNG), a neurodevelopmental disorder related to Prader-Willi syndrome (PWS). Patients with SHFYNG, like PWS, manifest neonatal hypotonia, feeding difficulties, hypogonadism, intellectual disability and sleep apnea. However, individuals with SHFYNG have joint contractures, greater cognitive impairment, and higher prevalence of autism than seen in PWS. Additionally, SHFYNG is associated with a lower prevalence of hyperphagia and obesity than PWS. Previous studies have shown that truncating variants in MAGEL2 lead to SHFYNG. However, the molecular pathways involved in manifestation of the SHFYNG disease phenotype are still unknown. Here we show that a Magel2 null mouse model and fibroblast cell lines from individuals with SHFYNG exhibit increased expression of mammalian target of rapamycin (mTOR) and decreased autophagy. Additionally, we show that SHFYNG induced pluripotent stem cell (iPSC)-derived neurons exhibit impaired dendrite formation. Alterations in SHFYNG patient fibroblast lines and iPSC-derived neurons are rescued by treatment with the mTOR inhibitor rapamycin. Collectively, our findings identify mTOR as a potential target for the development of pharmacological treatments for SHFYNG.
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Affiliation(s)
- Emeline Crutcher
- Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Rituraj Pal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Fatemeh Naini
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Neural Differentiation Core, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Ping Zhang
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Stem Cell Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Magdalena Laugsch
- Institute of Human Genetics, Heidelberg University, 69120, Heidelberg, Germany
| | - Jean Kim
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Stem Cell Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Aleksandar Bajic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Neural Differentiation Core, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Christian P Schaaf
- Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.
- Institute of Human Genetics, Heidelberg University, 69120, Heidelberg, Germany.
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Adhikari A, Copping NA, Onaga B, Pride MC, Coulson RL, Yang M, Yasui DH, LaSalle JM, Silverman JL. Cognitive deficits in the Snord116 deletion mouse model for Prader-Willi syndrome. Neurobiol Learn Mem 2019; 165:106874. [PMID: 29800646 PMCID: PMC6520209 DOI: 10.1016/j.nlm.2018.05.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/24/2018] [Accepted: 05/16/2018] [Indexed: 01/12/2023]
Abstract
Prader-Willi syndrome (PWS) is an imprinted neurodevelopmental disease caused by a loss of paternal genes on chromosome 15q11-q13. It is characterized by cognitive impairments, developmental delay, sleep abnormalities, and hyperphagia often leading to obesity. Clinical research has shown that a lack of expression of SNORD116, a paternally expressed imprinted gene cluster that encodes multiple copies of a small nucleolar RNA (snoRNA) in both humans and mice, is most likely responsible for many PWS symptoms seen in humans. The majority of previous research using PWS preclinical models focused on characterization of the hyperphagic and metabolic phenotypes. However, a crucial understudied clinical phenotype is cognitive impairments and thus we investigated the learning and memory abilities using a model of PWS, with a heterozygous deletion in Snord116. We utilized the novel object recognition task, which doesn't require external motivation, or exhaustive swim training. Automated findings were further confirmed with manual scoring by a highly trained blinded investigator. We discovered deficits in Snord116+/- mutant mice in the novel object recognition, location memory and tone cue fear conditioning assays when compared to age-, sex- matched, littermate control Snord116+/+ mice. Further, we confirmed that despite physical neo-natal developmental delays, Snord116+/- mice had normal exploratory and motor abilities. These results show that the Snord116+/- deletion murine model is a valuable preclinical model for investigating learning and memory impairments in individuals with PWS without common confounding phenotypes.
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Affiliation(s)
- Anna Adhikari
- MIND Institute, University of California, Davis School of Medicine, Department of Psychiatry and Behavioral Sciences, Sacramento, CA, USA
| | - Nycole A Copping
- MIND Institute, University of California, Davis School of Medicine, Department of Psychiatry and Behavioral Sciences, Sacramento, CA, USA
| | - Beth Onaga
- MIND Institute, University of California, Davis School of Medicine, Department of Psychiatry and Behavioral Sciences, Sacramento, CA, USA
| | - Michael C Pride
- MIND Institute, University of California, Davis School of Medicine, Department of Psychiatry and Behavioral Sciences, Sacramento, CA, USA
| | - Rochelle L Coulson
- MIND Institute, Genome Center, UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Davis, CA, USA
| | - Mu Yang
- Department of Psychiatry and Institute for Genomic Medicine, New York, NY, USA
| | - Dag H Yasui
- MIND Institute, Genome Center, UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Davis, CA, USA
| | - Janine M LaSalle
- MIND Institute, Genome Center, UC Davis School of Medicine, Department of Medical Microbiology and Immunology, Davis, CA, USA
| | - Jill L Silverman
- MIND Institute, University of California, Davis School of Medicine, Department of Psychiatry and Behavioral Sciences, Sacramento, CA, USA.
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38
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Long Noncoding RNAs in Atherosclerosis: JACC Review Topic of the Week. J Am Coll Cardiol 2019; 72:2380-2390. [PMID: 30384894 DOI: 10.1016/j.jacc.2018.08.2161] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/10/2018] [Accepted: 08/07/2018] [Indexed: 01/14/2023]
Abstract
Atherosclerosis is a complex and chronic disease characterized by lipid deposition in the vessel wall that leads to an inflammatory and proliferative cascade involving smooth muscle, endothelial, and immune cells. Despite substantial improvements in our understanding of mechanisms contributing to atherosclerosis and overall reduction in cardiovascular mortality, the absolute disease burden remains substantially high. The recent discovery of a new group of mediators known as long noncoding ribonucleic acids (lncRNAs) offers a unique opportunity for the development of novel diagnostic and therapeutic tools in atherothrombotic disease. A number of studies suggest that lncRNAs are important mediators in health and disease, and rapidly accumulating evidence implicates lncRNAs in regulatory circuits controlling atherosclerosis. In this review, the authors outline important contributions of lncRNAs to atherosclerosis and its associated risk factors, including hypercholesterolemia, diabetes, hypertension, and obesity.
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Wang J, Gao X, Liu J, Wang J, Zhang Y, Zhang T, Zhang H. Effect of intravitreal conbercept treatment on the expression of Long Noncoding RNAs and mRNAs in Proliferative Diabetic Retinopathy Patients. Acta Ophthalmol 2019; 97:e902-e912. [PMID: 30900812 DOI: 10.1111/aos.14083] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/16/2019] [Indexed: 01/03/2023]
Abstract
PURPOSE To evaluate the effect of conbercept on the expression of long noncoding RNAs (lncRNAs) and mRNAs in the fibrovascular membranes of proliferative diabetic retinopathy (PDR) patients. METHODS Twenty patients, diagnosed with PDR, who underwent pars plana vitrectomy (PPV), were recruited for this study. Ten patients were treated for PPV alone (Control Group), and the others received conbercept injections before PPV (Treated Group). The fibrovascular membranes were harvested during surgery. Expression of lncRNAs and mRNAs in the membranes was tested using lncRNA Arrays. Bioinformatics analyses were performed to identify the related biological modules and pathways of the differentially expressed genes. A lncRNA/mRNA coexpression network was built to identify the correlations between lncRNAs and mRNAs. Real-time PCR was conducted to verify the microarray results. RESULTS We identified 427 differentially expressed lncRNAs, of which 263 were upregulated and 164 were downregulated. Gene ontology (GO) analysis indicated that these lncRNAs-coexpressed mRNAs targeted various metabolic processes, especially the gluconeogenesis. Kyoto Encyclopaedia of Genes and Genomes (KEGG) results indicated that 16 pathways had significant differences in gene expression, including gluconeogenesis, HIF-1 signalling pathway, NOD-like receptor pathway, etc. The lncRNA/mRNA coexpression network revealed that many differentially expressed lncRNAs were enriched in the HIF-1, TNF-α and NOD-like receptor pathways. LincRNAs were the largest category and further bioinformatics analysis implied that these lincRNAs-coexpressed mRNAs were mainly involved in PDR-related biological processes and pathological pathways. CONCLUSION Conbercept treatment can change the expression profiles of lncRNAs and mRNAs in the fibrovascular membranes of PDR patients. A complete understanding of the relationship between lncRNAs and anti-VEGF drugs may contribute to new therapeutic regimen for PDR.
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Affiliation(s)
- Jiawei Wang
- Eye Center of Shandong University The Second Hospital of Shandong University Jinan People's Republic of China
| | - Xue Gao
- Eye Center of Shandong University The Second Hospital of Shandong University Jinan People's Republic of China
| | - Jing Liu
- Eye Center of Shandong University The Second Hospital of Shandong University Jinan People's Republic of China
| | - Jing Wang
- Eye Center of Shandong University The Second Hospital of Shandong University Jinan People's Republic of China
| | - Yue Zhang
- Department of surgery The Second Hospital of Shandong University Jinan People's Republic of China
| | - Tonghe Zhang
- Department of ophthalmology The second people's Hospital of Jinan 148# Jingyi Road Jinan People's Republic of China
| | - Han Zhang
- Eye Center of Shandong University The Second Hospital of Shandong University Jinan People's Republic of China
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Li P, Chen X, Chang X, Tang T, Qi K. A preliminary study on the differential expression of long noncoding RNAs and messenger RNAs in obese and control mice. J Cell Biochem 2019; 121:1126-1143. [PMID: 31464023 DOI: 10.1002/jcb.29348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 08/13/2019] [Indexed: 12/21/2022]
Abstract
Obesity has become one of the public health problems that threatens children's health, but its specific etiology and pathogenesis are still unclear. Recently, many long noncoding RNAs (lncRNAs) have been shown to be involved in the occurrence of obesity. However, their roles are still poorly understood. Thus, the aim of this study was to discover the profiles of the lncRNAs and messenger RNAs (mRNAs) altered in obesity. Epididymal fat samples were collected from mice fed with control and high-fat diets (HFD) for 16 weeks to investigate the differentially expressed lncRNAs and mRNAs by lncRNA microarray, after which seven lncRNAs and nine mRNAs were validated using reverse-transcription polymerase chain reaction (RT-PCR). Bioinformatics analysis and predictions were used to determine the potential biofunctions of these differentially expressed lncRNAs. Then a coexpression network was constructed to determine the transcriptional regulatory relationship of the differentially expressed lncRNAs and mRNAs between the control and HFD groups. The body weight of the HFD group was much higher than that of the control group, as a result of the increased energy intake. In total, 8421 differentially expressed lncRNAs and 6840 mRNAs were profiled using the lncRNAs microarray. Bioinformatics predictions and the coexpression network all indicated that the occurrence of obesity was attributed to those differentially expressed lncRNAs and mRNAs associated with energy metabolism, cell differentiation, and oxidative phosphorylation. The expression levels of Cyp2e1, Atp5b, Hibch, Cnbp, Frmd6, Ptchd3, ENSMUST00000155948, AK140152, ENSMUST00000135194, and ENSMUST00000180861 were significantly different between the control and HFD groups. All these Results suggested that obesity was partially attributed to those lncRNAs associated with energy metabolism, cell differentiation, and oxidative phosphorylation.
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Affiliation(s)
- Ping Li
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaoyu Chen
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xuelian Chang
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Tiantian Tang
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Kemin Qi
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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41
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Atkinson SP. A Preview of Selected Articles. Stem Cells Transl Med 2019. [PMCID: PMC6646695 DOI: 10.1002/sctm.19-0198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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42
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Akella A, Bhattarai S, Dharap A. Long Noncoding RNAs in the Pathophysiology of Ischemic Stroke. Neuromolecular Med 2019; 21:474-483. [DOI: 10.1007/s12017-019-08542-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/09/2019] [Indexed: 12/24/2022]
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43
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Guinovart M, Coronas R, Caixàs A. Psychopathological disorders in Prader-Willi syndrome. ACTA ACUST UNITED AC 2019; 66:579-587. [PMID: 31006652 DOI: 10.1016/j.endinu.2019.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/27/2019] [Accepted: 03/02/2019] [Indexed: 01/07/2023]
Abstract
Prader-Willi syndrome is a genetic disorder caused by chromosomal changes in segment 15q11-q13 including cognitive, mental, and behavioral symptoms, as well as a specific physical phenotype. Both the most common psychopathological changes (intellectual disability, obsessions, impulsivity, autism spectrum disorders, self-injuries) and the main psychiatric comorbidities (affective disorders, psychosis, obsessive-compulsive disorder, autism spectrum disorder) are characterized by a great heterogeneity, which warrants the need for better identification of their frequency and clinical signs. In addition to its effects on body compositionand hypotony, growth hormone has been shown to be useful for regulating patient behavior, and psychoactive drugs are also an option. Other alternatives have shown promising results in experimental trials. Adequate understanding of the psychopathology associated to Prader-Willi syndrome would allow for improving clinical approach, symptom identification, detection of comorbidities, and administration of more effective treatments, leading to better clinical outcomes.
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Affiliation(s)
- Martí Guinovart
- Servicio de Salud Mental, Hospital Universitari Parc Taulí, Universidad Autónoma de Barcelona, Sabadell (Barcelona), España
| | - Ramón Coronas
- Servicio de Salud Mental, Hospital Universitari Parc Taulí, Universidad Autónoma de Barcelona, Sabadell (Barcelona), España; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, España
| | - Assumpta Caixàs
- Servicio de Endocrinología y Nutrición, Hospital Universitari Parc Taulí, Universidad Autónoma de Barcelona, Sabadell (Barcelona), España.
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44
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Carias KV, Wevrick R. Preclinical Testing in Translational Animal Models of Prader-Willi Syndrome: Overview and Gap Analysis. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 13:344-358. [PMID: 30989085 PMCID: PMC6447752 DOI: 10.1016/j.omtm.2019.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Prader-Willi syndrome (PWS) is a rare neurodevelopmental disorder causing endocrine, musculoskeletal, and neurological dysfunction. PWS is caused by the inactivation of contiguous genes, complicating the development of targeted therapeutics. Clinical trials are now underway in PWS, with more trials to be implemented in the next few years. PWS-like endophenotypes are recapitulated in gene-targeted mice in which the function of one or more PWS genes is disrupted. These animal models can guide priorities for clinical trials or provide information about efficacy of a compound within the context of the specific disease. We now review the current status of preclinical studies that measure the effect of therapeutics on PWS-like endophenotypes. Seven categories of therapeutics (oxytocin and related compounds, K+-ATP channel agonists, melanocortin 4 receptor agonists, incretin mimetics and/or GLP-1 receptor agonists, cannabinoids, ghrelin agents, and Caralluma fimbriata [cactus] extract) have been tested for their effect on endophenotypes in both PWS animal models and clinical trials. Many other therapeutics have been tested in clinical trials, but not preclinical models of PWS or vice versa. Fostering dialogs among investigators performing preclinical validation of animal models and those implementing clinical studies will accelerate the discovery and translation of therapies into clinical practice in PWS.
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Affiliation(s)
- K Vanessa Carias
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
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45
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Machyna M, Simon MD. Catching RNAs on chromatin using hybridization capture methods. Brief Funct Genomics 2019; 17:96-103. [PMID: 29126220 DOI: 10.1093/bfgp/elx038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The growing appreciation of the importance of long noncoding RNAs (lncRNAs), together with the awareness that some of these RNAs are associated with chromatin, has inspired the development of methods to detect their sites of interaction on a genome-wide scale at high resolution. Hybridization capture methods combine antisense oligonucleotide hybridization with enrichment of RNA from cross-linked chromatin extracts. These techniques have provided insight into lncRNA localization and the interactions of lncRNAs with protein to better understand biological roles of lncRNAs. Here, we review the core principles of hybridization capture methods, focusing on the three most commonly used protocols: capture hybridization analysis of RNA targets (CHART), chromatin isolation by RNA purification (ChIRP) and RNA affinity purification (RAP). We highlight the general principles of these techniques and discuss how differences in experimental procedures present distinct challenges to help researchers using these protocols or, more generally, interpreting the results of hybridization capture experiments.
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46
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Matsubara K, Itoh M, Shimizu K, Saito S, Enomoto K, Nakabayashi K, Hata K, Kurosawa K, Ogata T, Fukami M, Kagami M. Exploring the unique function of imprinting control centers in the PWS/AS-responsible region: finding from array-based methylation analysis in cases with variously sized microdeletions. Clin Epigenetics 2019; 11:36. [PMID: 30819260 PMCID: PMC6396496 DOI: 10.1186/s13148-019-0633-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 02/14/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Human 15q11-13 is responsible for Prader-Willi syndrome (PWS) and Angelman syndrome (AS) and includes several imprinted genes together with bipartite elements named AS-IC (imprinting center) and PWS-IC. These concertedly confer allele specificity on 15q11-13. Here, we report DNA methylation status of 15q11-13 and other autosomal imprinted differentially methylated regions (iDMRs) in cases with various deletions within the PWS/AS-responsible region. METHODS We performed array-based methylation analysis and examined the methylation status of CpG sites in 15q11-13 and in 71 iDMRs in six cases with various microdeletions, eight cases with conventional deletions within 15q11-13, and healthy controls. RESULTS We detected 89 CpGs in 15q11-13 showing significant methylation changes in our cases. Of them, 14 CpGs in the SNORD116s cluster presented slight hypomethylation in the PWS cases and hypermethylation in the AS cases. No iDMRs at regions other than 15q11-13 showed abnormal methylation. CONCLUSIONS We identified CpG sites and regions in which methylation status is regulated by AS-IC and PWS-IC. This result indicated that each IC had unique functions and coordinately regulated the DNA methylation of respective alleles. In addition, only aberrant methylation at iDMRs in 15q11-13 leads to the development of the phenotypes in our cases.
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Affiliation(s)
- Keiko Matsubara
- Department of Molecular Endocrinology, National Center for Child Health and Development, 2-10-1 Ohkura, Setagaya-ku, Tokyo, 157-8535, Japan.
| | - Masatsune Itoh
- Department of Pediatrics, Kanazawa Medical University, Kanazawa, 920-1192, Japan
| | - Kenji Shimizu
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, 330-8777, Japan
| | - Shinji Saito
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
| | - Keisuke Enomoto
- Enomoto Children's Clinic, Moriya, 302-0127, Japan.,Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University Graduate School, Tokyo, 113-8510, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, 232-8555, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Center for Child Health and Development, 2-10-1 Ohkura, Setagaya-ku, Tokyo, 157-8535, Japan.,Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Center for Child Health and Development, 2-10-1 Ohkura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Center for Child Health and Development, 2-10-1 Ohkura, Setagaya-ku, Tokyo, 157-8535, Japan.
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47
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Genomic imprinting and the control of sleep in mammals. Curr Opin Behav Sci 2019. [DOI: 10.1016/j.cobeha.2018.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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48
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49
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Salminen II, Crespi BJ, Mokkonen M. Baby food and bedtime: Evidence for opposite phenotypes from different genetic and epigenetic alterations in Prader-Willi and Angelman syndromes. SAGE Open Med 2019; 7:2050312118823585. [PMID: 30728968 PMCID: PMC6350130 DOI: 10.1177/2050312118823585] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/14/2018] [Indexed: 12/22/2022] Open
Abstract
Prader–Willi and Angelman syndromes are often referred to as a sister pair of
neurodevelopmental disorders, resulting from different genetic and epigenetic
alterations to the same chromosomal region, 15q11-q13. Some of the primary
phenotypes of the two syndromes have been suggested to be opposite to one
another, but this hypothesis has yet to be tested comprehensively, and it
remains unclear how opposite effects could be produced by changes to different
genes in one syndrome compared to the other. We evaluated the evidence for
opposite effects on sleep and eating phenotypes in Prader–Willi syndrome and
Angelman syndrome, and developed physiological–genetic models that represent
hypothesized causes of these differences. Sleep latency shows opposite
deviations from controls in Prader–Willi and Angelman syndromes, with shorter
latency in Prader–Willi syndrome by meta-analysis and longer latency in Angelman
syndrome from previous studies. These differences can be accounted for by the
effects of variable gene dosages of UBE3A and MAGEL2, interacting with clock
genes, and leading to acceleration (in Prader–Willi syndrome) or deceleration
(in Angelman syndrome) of circadian rhythms. Prader–Willi and Angelman syndromes
also show evidence of opposite alterations in hyperphagic food selectivity, with
more paternally biased subtypes of Angelman syndrome apparently involving
increased preference for complementary foods (“baby foods”); hedonic reward from
eating may also be increased in Angelman syndrome and decreased in Prader–Willi
syndrome. These differences can be explained in part under a model whereby
hyperphagia and food selectivity are mediated by the effects of the genes
SNORD-116, UBE3A and MAGEL2, with outcomes depending upon the genotypic cause of
Angelman syndrome. The diametric variation observed in sleep and eating
phenotypes in Prader–Willi and Angelman syndromes is consistent with predictions
from the kinship theory of imprinting, reflecting extremes of higher resource
demand in Angelman syndrome and lower demand in Prader–Willi syndrome, with a
special emphasis on social–attentional demands and attachment associated with
bedtime, and feeding demands associated with mother-provided complementary foods
compared to offspring-foraged family-type foods.
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Langouët M, Glatt-Deeley HR, Chung MS, Dupont-Thibert CM, Mathieux E, Banda EC, Stoddard CE, Crandall L, Lalande M. Zinc finger protein 274 regulates imprinted expression of transcripts in Prader-Willi syndrome neurons. Hum Mol Genet 2019; 27:505-515. [PMID: 29228278 DOI: 10.1093/hmg/ddx420] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/01/2017] [Indexed: 01/09/2023] Open
Abstract
Prader-Willi syndrome (PWS) is characterized by neonatal hypotonia, developmental delay and hyperphagia/obesity and is caused by the absence of paternal contribution to chromosome 15q11-q13. Using induced pluripotent stem cell (iPSC) models of PWS, we previously discovered an epigenetic complex that is comprised of the zinc-finger protein ZNF274 and the SET domain bifurcated 1 (SETDB1) histone H3 lysine 9 (H3K9) methyltransferase and that silences the maternal alleles at the PWS locus. Here, we have knocked out ZNF274 and rescued the expression of silent maternal alleles in neurons derived from PWS iPSC lines, without affecting DNA methylation at the PWS-Imprinting Center (PWS-IC). This suggests that the ZNF274 complex is a separate imprinting mark that represses maternal PWS gene expression in neurons and is a potential target for future therapeutic applications to rescue the PWS phenotype.
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Affiliation(s)
- Maéva Langouët
- Department of Genetics and Genome Sciences, School of Medicine
| | | | - Michael S Chung
- Department of Genetics and Genome Sciences, School of Medicine
| | | | - Elodie Mathieux
- Department of Genetics and Genome Sciences, School of Medicine
| | - Erin C Banda
- Department of Genetics and Genome Sciences, School of Medicine
| | | | - Leann Crandall
- Department of Genetics and Genome Sciences, School of Medicine
| | - Marc Lalande
- Department of Genetics and Genome Sciences, School of Medicine.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030-6403, USA
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