1
|
Proske M, Janowski R, Bacher S, Kang HS, Monecke T, Koehler T, Hutten S, Tretter J, Crois A, Molitor L, Varela-Rial A, Fino R, Donati E, De Fabritiis G, Dormann D, Sattler M, Niessing D. PURA syndrome-causing mutations impair PUR-domain integrity and affect P-body association. eLife 2024; 13:RP93561. [PMID: 38655849 DOI: 10.7554/elife.93561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
Mutations in the human PURA gene cause the neurodevelopmental PURA syndrome. In contrast to several other monogenetic disorders, almost all reported mutations in this nucleic acid-binding protein result in the full disease penetrance. In this study, we observed that patient mutations across PURA impair its previously reported co-localization with processing bodies. These mutations either destroyed the folding integrity, RNA binding, or dimerization of PURA. We also solved the crystal structures of the N- and C-terminal PUR domains of human PURA and combined them with molecular dynamics simulations and nuclear magnetic resonance measurements. The observed unusually high dynamics and structural promiscuity of PURA indicated that this protein is particularly susceptible to mutations impairing its structural integrity. It offers an explanation why even conservative mutations across PURA result in the full penetrance of symptoms in patients with PURA syndrome.
Collapse
Affiliation(s)
- Marcel Proske
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Robert Janowski
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Sabrina Bacher
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
- Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of Munich, Mainz, Germany
| | - Thomas Monecke
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Tony Koehler
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Saskia Hutten
- Biocenter, Institute of Molecular Physiology, Johannes Gutenberg-Universität (JGU), Mainz, Germany
| | - Jana Tretter
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Anna Crois
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Lena Molitor
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | | | | | | | | | - Dorothee Dormann
- Biocenter, Institute of Molecular Physiology, Johannes Gutenberg-Universität (JGU), Mainz, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
- Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of Munich, Mainz, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| |
Collapse
|
2
|
Chen F, Zhang W, Xu S, Zhang H, Chen L, Chen C, Zhu Z, Zhao Y. Discovery and validation of PURA as a transcription target of 20(S)-protopanaxadiol: Implications for the treatment of cognitive dysfunction. J Ginseng Res 2023; 47:662-671. [PMID: 37720572 PMCID: PMC10499581 DOI: 10.1016/j.jgr.2023.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/23/2023] [Accepted: 04/24/2023] [Indexed: 09/19/2023] Open
Abstract
Background 20(S)-protopanaxadiol (PPD), a ginsenoside metabolite, has prominent benefits for the central nervous system, especially in improving learning and memory. However, its transcriptional targets in brain tissue remain unknown. Methods In this study, we first used mass spectrometry-based drug affinity responsive target stability (DARTS) to identify the potential proteins of ginsenosides and intersected them with the transcription factor library. Second, the transcription factor PURA was confirmed as a target of PPD by biolayer interferometry (BLI) and molecular docking. Next, the effect of PPD on the transcriptional levels of target genes of PURA in brain tissues was determined by qRT-PCR. Finally, bioinformatics analysis was used to analyze the potential biological features of these target proteins. Results The results showed three overlapping transcription factors between the proteomics of DARTS and transcription factor library. BLI analysis further showed that PPD had a higher direct interaction with PURA than parent ginsenosides. Subsequently, BLI kinetic analysis, molecular docking, and mutations in key amino acids of PURA indicated that PPD specifically bound to PURA. The results of qRT-PCR showed that PPD could increase the transcription levels of PURA target genes in brain. Finally, bioinformatics analysis showed that these target proteins were involved in learning and memory function. Conclusion The above-mentioned findings indicate that PURA is a transcription target of PPD in brain, and PPD upregulate the transcription levels of target genes related to cognitive dysfunction by binding PURA, which could provide a chemical and biological basis for the study of treating cognitive impairment by targeting PURA.
Collapse
Affiliation(s)
- Feiyan Chen
- Research and Innovation Center, College of Traditional Chinese Medicine·Integrated Chinese and Western Medicine College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenjing Zhang
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shuyi Xu
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hantao Zhang
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Lin Chen
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Cuihua Chen
- Research and Innovation Center, College of Traditional Chinese Medicine·Integrated Chinese and Western Medicine College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhu Zhu
- Department of Pathology and Pathophysiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yunan Zhao
- Department of Pathology and Pathophysiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| |
Collapse
|
3
|
Noda Y, Kido J, Misumi Y, Sugawara K, Ohori S, Fujita A, Matsumoto N, Ueda M, Nakamura K. Heterozygous c.175C>T variant in PURA gene causes severe developmental delay. Clin Case Rep 2023; 11:e7779. [PMID: 37692153 PMCID: PMC10483498 DOI: 10.1002/ccr3.7779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 09/12/2023] Open
Abstract
Key Clinical Message This case report presents a child with PURA-related neurodevelopmental disorder, caused by the heterozygous pathogenic variant c.175C>T (p.Gln59*). The clinical symptoms included microcephaly, brachygnathia, central and peripheral hypotonia, and developmental delay (non-verbal), among others. On comparison with published literature, even patients with the same mutation present different clinical symptoms. Abstract This case report presents a child with PURA-related neurodevelopmental disorder, caused by the heterozygous pathogenic variant c.175C>T (p.Gln59*), whose symptoms included microcephaly, brachygnathia, the development of a high anterior hairline, hip dysplasia, strabismus, severe hypotonia, developmental delay (non-meaningful verbal), feeding difficulties, and respiratory difficulties. His development ceased with age, such that his development at 10 years corresponded to an infant of 6 months. Moreover, even patients with the same variant can have different clinical symptoms, such as the presence or absence of epilepsy or congenital malformations. Therefore, we should follow his long-term clinical course and provide medical support as necessary.
Collapse
Affiliation(s)
- Yusuke Noda
- Department of PediatricsKumamoto University HospitalKumamotoJapan
- Department of Pediatrics Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Jun Kido
- Department of PediatricsKumamoto University HospitalKumamotoJapan
- Department of Pediatrics Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Yohei Misumi
- Department of NeurologyKumamoto University HospitalKumamotoJapan
| | - Keishin Sugawara
- Department of Pediatrics Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Sachiko Ohori
- Department of Human GeneticsYokohama City University Graduate School of MedicineYokohamaJapan
| | - Atsushi Fujita
- Department of Human GeneticsYokohama City University Graduate School of MedicineYokohamaJapan
| | - Naomichi Matsumoto
- Department of Human GeneticsYokohama City University Graduate School of MedicineYokohamaJapan
| | - Mitsuharu Ueda
- Department of NeurologyKumamoto University HospitalKumamotoJapan
| | - Kimitoshi Nakamura
- Department of PediatricsKumamoto University HospitalKumamotoJapan
- Department of Pediatrics Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| |
Collapse
|
4
|
Iyadurai S, Geller T, Wyrebek R, Crenshaw M, Brooks S, DiBartolomeo M, Mroczek M. PURA syndrome: Neuromuscular junction manifestations with potential therapeutic implications. Neuromuscul Disord 2023; 33:699. [PMID: 36631330 DOI: 10.1016/j.nmd.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Stanley Iyadurai
- Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA.
| | - Thomas Geller
- Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Rita Wyrebek
- Cardinal Glennon Children's Hospital, Saint Louis University, St. Louis, MO 63103, USA
| | - Melissa Crenshaw
- Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Sandra Brooks
- Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Mara DiBartolomeo
- Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Magdalena Mroczek
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich 8952, Switzerland.
| |
Collapse
|
5
|
Ben Issa A, Ben Ayed I, Jallouli O, Souissi A, Bouchaalla W, Ben Said M, Mallouli S, Masmoudi S, Charfi Triki C, Hadj Kacem H, Kammoun F. A new case with the recurrent PURA p.(Phe233del) pathogenic variant: Expansion of the phenotype and review of the literature. Int J Dev Neurosci 2023. [PMID: 37204304 DOI: 10.1002/jdn.10266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/19/2023] [Accepted: 04/28/2023] [Indexed: 05/20/2023] Open
Abstract
In the process of neuronal development, the protein Purα (encoded by the PURA gene) is essential for neuronal proliferation, dendritic maturation, and the transportation of mRNA to translation sites. Mutations in the PURA gene may alter normal brain development and impair neuronal function, contributing to developmental delays and seizures. Recently, PURA syndrome is described as developmental encephalopathy with or without epilepsy, neonatal hypotonia, feeding difficulties, global developmental delay, and severe intellectual disability. In our study, we aimed to perform a genetic analysis by whole exome sequencing (WES) in a Tunisian patient presented with developmental and epileptic encephalopathy to provide a molecular explanation for the developed phenotype. We collected, also, clinical data of all PURA p.(Phe233del) patients reported yet and compared the clinical features with those of our patient. Results revealed the presence of the known PURA c.697_699del, p.(Phe233del) variant. Our studied case shares some clinical features including hypotonia, feeding difficulties, severe developmental delay, epilepsy, and language delay (nonverbal) but presents a radiological finding undescribed before. Our finding defines and expands the phenotypic and genotypic spectrum of the PURA syndrome supporting the absence of reliable genotype-phenotype correlations and the existence of a highly variable, wide-ranging clinical spectrum.
Collapse
Affiliation(s)
- Abir Ben Issa
- Research Laboratory "Neuropédiatrie" (LR19ES15), Sfax Faculty of Medicine, Sfax University, Sfax, Tunisia
- Child Neurology Department, Hedi Chaker Sfax University Hospital, Sfax, Tunisia
| | - Ikhlas Ben Ayed
- Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
- Medical Genetic Department, Hédi Chaker Sfax University Hospital, Sfax, Tunisia
| | - Olfa Jallouli
- Research Laboratory "Neuropédiatrie" (LR19ES15), Sfax Faculty of Medicine, Sfax University, Sfax, Tunisia
- Child Neurology Department, Hedi Chaker Sfax University Hospital, Sfax, Tunisia
- Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
| | - Wafa Bouchaalla
- Research Laboratory "Neuropédiatrie" (LR19ES15), Sfax Faculty of Medicine, Sfax University, Sfax, Tunisia
- Child Neurology Department, Hedi Chaker Sfax University Hospital, Sfax, Tunisia
- Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
| | - Salma Mallouli
- Research Laboratory "Neuropédiatrie" (LR19ES15), Sfax Faculty of Medicine, Sfax University, Sfax, Tunisia
- Child Neurology Department, Hedi Chaker Sfax University Hospital, Sfax, Tunisia
- Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Sfax University, Sfax, Tunisia
| | - Chahnez Charfi Triki
- Research Laboratory "Neuropédiatrie" (LR19ES15), Sfax Faculty of Medicine, Sfax University, Sfax, Tunisia
- Child Neurology Department, Hedi Chaker Sfax University Hospital, Sfax, Tunisia
- Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Hassen Hadj Kacem
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Fatma Kammoun
- Research Laboratory "Neuropédiatrie" (LR19ES15), Sfax Faculty of Medicine, Sfax University, Sfax, Tunisia
- Child Neurology Department, Hedi Chaker Sfax University Hospital, Sfax, Tunisia
- Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| |
Collapse
|
6
|
Choi SA, Lee HS, Park TJ, Park S, Ko YJ, Kim SY, Lim BC, Kim KJ, Chae JH. Expanding the clinical phenotype and genetic spectrum of PURA-related neurodevelopmental disorders. Brain Dev 2021; 43:912-918. [PMID: 34116881 DOI: 10.1016/j.braindev.2021.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/28/2021] [Accepted: 05/16/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND PURA-related neurodevelopmental disorders (PURA-NDDs) include 5q31.3 deletion syndrome and PURA syndrome. PURA-NDDs are characterized by neonatal hypotonia, moderate to severe global developmental delay/intellectual disability (GDD/ID), facial dysmorphism, epileptic seizures, nonepileptic movement disorders, and ophthalmological problems. PURA-NDDs have recently been identified and underestimated in neurodevelopmental cohorts, but their diagnosis is still challenging. METHODS We retrospectively reviewed the clinical characteristics, genetic spectrum, and diagnostic journey of patients with PURA-NDDs. RESULTS We report 2 patients with 5q31.3 microdeletion and 5 with PURA pathogenic variants. They demonstrated hypotonia (7/7, 100%), feeding difficulties (4/5, 80%), and respiratory problems (4/7, 57%) in the neonatal period. All of them had severe GDD/ID and could not achieve independent walking and verbal responses. Distinctive facial features of open-tented upper vermilion, long philtrum, and anteverted nares and poor visual fixation and tracking with or without nystagmus were most commonly found (5/7, 71.4%). There were no significant differences in clinical phenotypes between 5q31.3 microdeletion syndrome and PURA syndrome. PURA-NDDs need to be considered as a differential diagnosis in individuals who show severe hypotonia, including feeding difficulties since birth and severe developmental retardation with distinctive facial and ophthalmological features. CONCLUSIONS Our data expands the phenotypic and genetic spectrum of PURA-NDD. Next-generation sequencing methods based on the detailed phenotypic evaluation would shorten the diagnostic delay and would help this rare disorder become a recognizable cause of neurodevelopmental delay.
Collapse
Affiliation(s)
- Sun Ah Choi
- Department of Pediatrics, Ewha Womans University Medical Center, Ewha Womans University College of Medicine, Seoul, Republic of Korea
| | - Heun-Sik Lee
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Republic of Korea
| | - Tae-Joon Park
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Republic of Korea
| | - Soojin Park
- Department of Medicine, Seoul National University College of Medicine Graduate School, Seoul, Republic of Korea; Division of Pediatric Neurology, Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Young Jun Ko
- Division of Pediatric Neurology, Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Soo Yeon Kim
- Division of Pediatric Neurology, Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Rare Disease Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Byung Chan Lim
- Division of Pediatric Neurology, Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Rare Disease Center, Seoul National University Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ki Joong Kim
- Division of Pediatric Neurology, Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jong-Hee Chae
- Division of Pediatric Neurology, Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Rare Disease Center, Seoul National University Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
7
|
Boczek NJ, Macke EL, Kemppainen J, Klee EW, Renaud DL, Gavrilova RH. Expansion of PURA-Related Phenotypes and Discovery of a Novel PURA Variant: A Case Report. Child Neurol Open 2020; 7:2329048X20955003. [PMID: 33117858 PMCID: PMC7573717 DOI: 10.1177/2329048x20955003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/08/2020] [Accepted: 07/30/2020] [Indexed: 11/17/2022] Open
Abstract
Variants in PURA have recently been associated with an autosomal dominant form of PURA-related neurodevelopmental disorders. Using whole exome sequencing, patients with neurological phenotypes including hypotonia, developmental delay, learning disabilities, and seizures were identified to have de novo variants in PURA. We describe a proband with features similar to the previously described cases with PURA variants, but including additional features, such as short stature, delayed bone age, and delayed puberty. Exome sequencing revealed a novel pathogenic nonsense variant, c.190A>T (p.Lys64*; NM_005859), in PURA that was not inherited from the proband’s mother. In the recent literature, a significant number of patients with variants in PURA have been described, but to our knowledge, none of these patients have the delayed bone age and growth plateau observed in the proband. It is therefore possible that the above PURA variant may be responsible for the novel features and thus expands the PURA-related phenotype spectrum.
Collapse
Affiliation(s)
- Nicole J Boczek
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jennifer Kemppainen
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Biomedical Informatics, Mayo Clinic, Rochester, MN, USA
| | - Deborah L Renaud
- Department of Neurology, Mayo Clinic, Rochester, MN, USA.,Department of Pediatrics, Mayo Clinic, Rochester, MN, USA
| | - Ralitza H Gavrilova
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Neurology, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
8
|
Abstract
RNA- and DNA-binding domains are essential building blocks for specific regulation of gene expression. While a number of canonical nucleic acid binding domains share sequence and structural conservation, others are less obviously linked by evolutionary traits. In this review, we describe a protein fold of about 150 aa in length, bearing a conserved β-β-β-β-α-linker-β-β-β-β-α topology and similar nucleic acid binding properties but no apparent sequence conservation. The same overall fold can also be achieved by dimerization of two proteins, each bearing a β-β-β-β-α topology. These proteins include but are not limited to the transcription factors PC4 and P24 from humans and plants, respectively, the human RNA-transport factor Pur-α (also termed PURA), as well as the ssDNA-binding SP_0782 protein from Streptococcus pneumonia and the bacteriophage coat proteins PP7 and MS2. Besides their common overall topology, these proteins share common nucleic acids binding surfaces and thus functional similarity. We conclude that these PC4-like domains include proteins from all kingdoms of life and are much more abundant than previously known.
Collapse
Affiliation(s)
- Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University , Ulm, Germany
| |
Collapse
|
9
|
Jezela-Stanek A, Ciara E, Jurkiewicz D, Kucharczyk M, Jędrzejowska M, Chrzanowska KH, Krajewska-Walasek M, Żemojtel T. The phenotype-driven computational analysis yields clinical diagnosis for patients with atypical manifestations of known intellectual disability syndromes. Mol Genet Genomic Med 2020; 8:e1263. [PMID: 32337850 PMCID: PMC7507388 DOI: 10.1002/mgg3.1263] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/24/2020] [Accepted: 03/01/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Due to extensive clinical and genetic heterogeneity of intellectual disability (ID) syndromes, the process of diagnosis is very challenging even for expert clinicians. Despite recent advancements in molecular diagnostics methodologies, a significant fraction of ID patients remains without a clinical diagnosis. METHODS, RESULTS, AND CONCLUSIONS Here, in a prospective study on a cohort of 21 families (trios) with a child presenting with ID of unknown etiology, we executed phenotype-driven bioinformatic analysis method, PhenIX, utilizing targeted next-generation sequencing (NGS) data and Human Phenotype Ontology (HPO)-encoded phenotype data. This approach resulted in clinical diagnosis for eight individuals presenting with atypical manifestations of Rubinstein-Taybi syndrome 2 (MIM 613684), Spastic Paraplegia 50 (MIM 612936), Wiedemann-Steiner syndrome (MIM 605130), Cornelia de Lange syndrome 2 (MIM 300590), Cerebral creatine deficiency syndrome 1 (MIM 300352), Glass Syndrome (MIM 612313), Mental retardation, autosomal dominant 31 (MIM 616158), and Bosch-Boonstra-Schaaf optic atrophy syndrome (MIM 615722).
Collapse
Affiliation(s)
- Aleksandra Jezela-Stanek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland.,Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Elżbieta Ciara
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Dorota Jurkiewicz
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marzena Kucharczyk
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Maria Jędrzejowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland.,Mossakowski Medical Research Centre, Neuromuscular Unit, Polish Academy of Sciences, Warsaw, Poland
| | - Krystyna H Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Tomasz Żemojtel
- Genomics Platform, Berlin Institute of Health, Berlin, Germany.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| |
Collapse
|
10
|
Abstract
Esophageal cancer (EC) is a highly complex disease with high incidence and mortality rates. Recent studies have shown that miRNAs play critical roles in diverse biological processes including oncogenesis, and we previously reported significantly increased expression of tissue and circulating miR-144 in EC. This study evaluates the functional significance of miR-144 in esophageal squamous cell carcinoma. Herein, we analysed the role of miR-144 in ESCC by silencing it in KYSE-410 cells, and followed this with cell cycle analysis and the following assays; MTT, annexin, colony formation, scratch and matrigel invasion assay. The miR-144 knockdown significantly suppressed ESCC cell proliferation at 72 hours post transfection (p=0.029). Silencing of miR-144 significantly decreased the migration, invasion and colony formation potential of KYSE-410 cells compared to cells treated with negative control (NC). Potential targets of miR-144 were predicted by the in silico approach followed by in vitro validation in real time PCR and luciferase reporter assay. The PURA and Spred1 in silico predicted miR-144 targets were validated by qRT-PCR and luciferase reporter assay. Over-expression of miR-144 significantly decreased PURA mRNA expression by 58.85% at 24 hours post transfection (p=0.009). Further validation by dual-luciferase reporter assay confirmed it is a direct targets of miR-144. Our overall study suggests the oncogenic role of miR-144 in EC by promoting proliferation and migration of ESCC cells. To the best of our knowledge, this is the first report showing PURA as a direct miR-144 downstream target and suggests its potential as a novel therapeutic target for this disease.
Collapse
Affiliation(s)
- P Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - R Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| |
Collapse
|
11
|
Qiao Y, Bagheri H, Tang F, Badduke C, Martell S, Lewis SME, Robinson W, Connolly MB, Arbour L, Rajcan-Separovic E. Exome sequencing identified a de novo mutation of PURA gene in a patient with familial Xp22.31 microduplication. Eur J Med Genet 2018; 62:103-108. [PMID: 29908350 DOI: 10.1016/j.ejmg.2018.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 06/08/2018] [Accepted: 06/10/2018] [Indexed: 11/28/2022]
Abstract
The clinical significance of Xp22.31 microduplication is controversial as it is reported in subjects with developmental delay (DD), their unaffected relatives and unrelated controls. We performed multifaceted studies in a family of a boy with hypotonia, dysmorphic features and DD who carried a 600 Kb Xp22.31 microduplication (7515787-8123310bp, hg19) containing two genes, VCX and PNPLA4. The duplication was transmitted from his cognitively normal maternal grandfather. We found no evidence of the duplication causing the proband's DD and congenital anomalies based on unaltered expression of PNPLA4 in the proband and his mother in comparison to controls and preferential activation of the paternal chromosome X with Xp22.31 duplication in proband's mother. However, a de novo, previously reported deleterious, missense mutation in Pur-alpha gene (PURA) (5q31.2), with a role in neuronal differentiation was detected in the proband by exome sequencing. We propose that the variability in the phenotype in carriers of Xp22.31 microduplication can be due to a second and more deleterious genetic mutation in more severely affected carriers. Widespread use of whole genome next generation sequencing in families with Xp22.31 CNV could help identify such cases.
Collapse
Affiliation(s)
- Ying Qiao
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Hani Bagheri
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | - Flamingo Tang
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | | | - Sally Martell
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | - Suzanne M E Lewis
- BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medical Genetics, UBC, Vancouver, BC, Canada
| | - Wendy Robinson
- Department of Medical Genetics, UBC, Vancouver, BC, Canada
| | - Mary B Connolly
- Division of Pediatric Neurology, Department of Pediatrics, UBC and BC Children's Hospital, Vancouver, BC, Canada
| | - Laura Arbour
- Department of Medical Genetics, University of Victoria, Victoria, BC, Canada.
| | - Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada.
| |
Collapse
|
12
|
Mayorga L, Gamboni B, Mampel A, Roqué M. A frame-shift deletion in the PURA gene associates with a new clinical finding: Hypoglycorrhachia. Is GLUT1 a new PURA target? Mol Genet Metab 2018; 123:331-336. [PMID: 29307761 DOI: 10.1016/j.ymgme.2017.12.436] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/29/2017] [Accepted: 12/30/2017] [Indexed: 12/24/2022]
Abstract
PURA is a DNA/RNA-binding protein known to have an important role as a transcriptional and translational regulator. Mutations in the PURA gene have been documented to cause mainly a neurologic phenotype including hypotonia, epilepsy, development delay and respiratory alterations. We report here a patient with a frame-shift deletion in the PURA gene that apart from the classical PURA deficiency phenotype had marked hypoglycorrhachia, overlapping the clinical findings with a GLUT1 deficiency syndrome. SLC2A1 (GLUT1) mutations were discarded, so we hypothesized that GLUT1 could be downregulated in this PURA deficient scenario. We confirmed reduced GLUT1 expression in the patient's peripheral blood cells compared to controls predicting that this could also be happening in the blood-brain barrier and in this way explain the hypoglycorrhachia. Based on PURA's known functions as a transcriptional and translational regulator, we propose GLUT1 as a new PURA target. Further in vitro and in vivo studies are needed to confirm this and to uncover the underlying molecular mechanisms.
Collapse
Affiliation(s)
- Lía Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM), Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina.
| | - Beatriz Gamboni
- Instituto de Neurología Infanto Juvenil (Neuroinfan), Mendoza, Argentina
| | - Alejandra Mampel
- Instituto de Genética, Hospital Universitario, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - María Roqué
- Instituto de Histología y Embriología de Mendoza (IHEM), Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
| |
Collapse
|
13
|
Lee BH, Reijnders MRF, Abubakare O, Tuttle E, Lape B, Minks KQ, Stodgell C, Bennetto L, Kwon J, Fong CT, Gripp KW, Marsh ED, Smith WE, Huq AM, Coury SA, Tan WH, Solis O, Mehta RI, Leventer RJ, Baralle D, Hunt D, Paciorkowski AR. Expanding the neurodevelopmental phenotype of PURA syndrome. Am J Med Genet A 2017; 176:56-67. [PMID: 29150892 DOI: 10.1002/ajmg.a.38521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/04/2017] [Accepted: 10/08/2017] [Indexed: 01/07/2023]
Abstract
PURA syndrome is a recently described developmental encephalopathy presenting with neonatal hypotonia, feeding difficulties, global developmental delay, severe intellectual disability, and frequent apnea and epilepsy. We describe 18 new individuals with heterozygous sequence variations in PURA. A neuromotor disorder starting with neonatal hyptonia, but ultimately allowing delayed progression to walking, was present in nearly all individuals. Congenital apnea was present in 56% during infancy, but all cases in this cohort resolved during the first year of life. Feeding difficulties were frequently reported, with gastrostomy tube placement required in 28%. Epilepsy was present in 50% of the subjects, including infantile spasms and Lennox-Gastaut syndrome. Skeletal complications were found in 39%. Disorders of gastrointestinal motility and nystagmus were also recurrent features. Autism was diagnosed in one individual, potentially expanding the neurodevelopmental phenotype associated with this syndrome. However, we did not find additional PURA sequence variations in a cohort of 120 subjects with autism. We also present the first neuropathologic studies of PURA syndrome, and describe chronic inflammatory changes around the arterioles within the deep white matter. We did not find significant correlations between mutational class and severity, nor between location of the sequence variation in PUR repeat domains. Further studies are required in larger cohorts of subjects with PURA syndrome to clarify these genotype-phenotype associations.
Collapse
Affiliation(s)
- Bo Hoon Lee
- Department of Neurology, University of Rochester Medical Center, Rochester, New York
| | - Margot R F Reijnders
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Oluwatobi Abubakare
- Center for Neural Development and Disease, University of Rochester Medical Center, Rochester, New York
| | - Emily Tuttle
- Center for Neural Development and Disease, University of Rochester Medical Center, Rochester, New York
| | - Brynn Lape
- Center for Neural Development and Disease, University of Rochester Medical Center, Rochester, New York
| | - Kelly Q Minks
- Department of Neurology, University of Rochester Medical Center, Rochester, New York
| | - Christopher Stodgell
- Department of Obstetrics and Gynecology, University of Rochester Medical Center, Rochester, New York
| | - Loisa Bennetto
- Department of Clinical and Social Sciences in Psychology, University of Rochester, Rochester, New York
| | - Jennifer Kwon
- Department of Neurology, University of Rochester Medical Center, Rochester, New York.,Department of Pediatrics, University of Rochester Medical Center, Rochester, New York.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Karen W Gripp
- A.I. du Pont Hospital for Children/Nemours, Wilmington, Delaware
| | - Eric D Marsh
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, and Pediatric Regional Epilepsy Program, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Wendy E Smith
- Department of Pediatrics, Maine Medical Center, Portland, Maine
| | - Ahm M Huq
- Departments of Pediatrics and Neurology, Wayne State University, Children's Hospital of Michigan, Detroit, Michigan
| | - Stephanie A Coury
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Wen-Hann Tan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Orestes Solis
- Center for Neural Development and Disease, University of Rochester Medical Center, Rochester, New York
| | - Rupal I Mehta
- Center for Neural Development and Disease, University of Rochester Medical Center, Rochester, New York.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York
| | - Richard J Leventer
- The Royal Children's Hospital Department of Neurology, University of Melbourne, Department of Pediatrics and the Murdoch Children's Hospital Institute, Melbourne, Victoria, Australia
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK.,Faculty of Medicine, Wessex Clinical Genetics Service, Princess Anne Hospital, University of Southampton, Southampton, Hampshire, UK
| | - David Hunt
- Faculty of Medicine, Wessex Clinical Genetics Service, Princess Anne Hospital, University of Southampton, Southampton, Hampshire, UK
| | - Alex R Paciorkowski
- Department of Neurology, University of Rochester Medical Center, Rochester, New York.,Center for Neural Development and Disease, University of Rochester Medical Center, Rochester, New York.,Department of Pediatrics, University of Rochester Medical Center, Rochester, New York.,Departments of Neuroscience and Biomedical Genetics, University of Rochester Medical Center, Rochester, New York
| |
Collapse
|
14
|
Barbe MF, Krueger JJ, Loomis R, Otte J, Gordon J. Memory deficits, gait ataxia and neuronal loss in the hippocampus and cerebellum in mice that are heterozygous for Pur-alpha. Neuroscience 2016; 337:177-190. [PMID: 27651147 DOI: 10.1016/j.neuroscience.2016.09.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/07/2016] [Accepted: 09/09/2016] [Indexed: 01/21/2023]
Abstract
Pur-alpha is a highly conserved sequence-specific DNA and RNA binding protein with established roles in DNA replication, RNA translation, cell cycle regulation, and maintenance of neuronal differentiation. Prior studies have shown that mice lacking Pur-alpha (-/-) display decreased neurogenesis and impaired neuronal differentiation. We sought to examine for the first time, the behavioral phenotype and brain histopathology of mice that are heterozygous (+/-) for Pur-alpha. Standardized behavioral phenotyping revealed a decreased escape response to touch, limb and abdominal hypotonia, and gait abnormalities in heterozygous Pur-alpha (+/-) mice, compared to wild-type (+/+) littermates. Footprint pattern analyses showed wider-based steps, increased missteps and more outwardly rotated hindpaws in heterozygous Pur-alpha (+/-) mice, suggestive of cerebellar pathology. The Barnes maze and novel object location testing revealed significant memory deficits in heterozygous Pur-alpha mice, suggestive of hippocampal pathology. Quantitative immunohistochemical assays of the vermal region of the cerebellum and CA1-3 regions of the hippocampus revealed reduced numbers of neurons in general, as well as reduced numbers of Pur-alpha+-immunopositive neurons and dendrites in heterozygous Pur-alpha mice, compared to wild-type littermates. Past studies have implicated mutations in Pur-alpha in several diseases of brain development and neurodegeneration. When combined with these new findings, the Pur-alpha heterozygous knockout mice may provide an animal model to study mechanisms of and treatments for Pur-alpha-related cognitive deficiencies and neuropathology.
Collapse
Affiliation(s)
- Mary F Barbe
- Department of Anatomy and Cell Biology, Temple University School of Medicine, Philadelphia, PA, USA; Comprehensive NeuroAIDS Center, Temple University School of Medicine, Philadelphia, PA, USA.
| | - Jessica J Krueger
- Comprehensive NeuroAIDS Center, Temple University School of Medicine, Philadelphia, PA, USA
| | - Regina Loomis
- Comprehensive NeuroAIDS Center, Temple University School of Medicine, Philadelphia, PA, USA
| | - Jessica Otte
- Department of Neuroscience and Center for Neurovirology, Temple University School of Medicine, Philadelphia, PA, USA; Comprehensive NeuroAIDS Center, Temple University School of Medicine, Philadelphia, PA, USA
| | - Jennifer Gordon
- Department of Neuroscience and Center for Neurovirology, Temple University School of Medicine, Philadelphia, PA, USA; Comprehensive NeuroAIDS Center, Temple University School of Medicine, Philadelphia, PA, USA
| |
Collapse
|