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Maden Bedel F, Balasar Ö, Şimşek A, Tokgöz H, Çaksen H. Could the 14q23.2 microdeletion or AKAP5 haploinsufficiency be a potential cause of intellectual disability? Psychiatr Genet 2024; 34:71-73. [PMID: 38690958 DOI: 10.1097/ypg.0000000000000368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Intellectual disability is characterized by impairment in at least two of the following areas: social skills, communication skills, self-care tasks, and academic skills. These impairments are evaluated in relation to the expected standards based on the individual's age and cultural levels. Additionally, intellectual disability is typically defined by a measurable level of intellectual functioning, represented by an intelligence quotients core of 70 or below. Autism spectrum disorder is a developmental disability resulting from differences in the brain, often characterized by problems in social communication and interaction, and limited or repetitive behaviors or interests. Hereditary spherocytosis is a disease characterized by anemia, jaundice, and splenomegaly as a result of increased tendency to hemolysis with morphological transformation of erythrocytes from biconcave disc-shaped cells with central pallor to spherocytes lacking central pallor due to hereditary injury of cellular membrane proteins. An 11-year-old female patient was referred to Pediatric Genetics Subdivision due to the presence of growth retardation and a diagnosis of hereditary spherocytosis. Since she also had dysmorphic facial features, such as frontal bossing, broad and prominent forehead, tubular nasal structure, and thin vermillion, genetic tests were performed. Chromosomal microarray analysis revealed a 2.5 Mb deletion in the 14q23.2q23.3 region. Deletion was also identified in the same region in her father, who had the same phenotypic characteristics, including hereditary spherocytosis and learning difficulties. We propose that the PLEKHG3 and AKAP5 genes, which are located in this region, may contribute to the development of intellectual disability.
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Affiliation(s)
- Fayize Maden Bedel
- Department of Pediatric Genetics, Faculty of Medicine, Necmettin Erbakan University
| | | | - Ayşe Şimşek
- Department of Pediatric Hematology, Konya City Hospital
| | - Hüseyin Tokgöz
- Department of Pediatric Hematology, Faculty of Medicine, Necmettin Erbakan University, Konya, Turkey
| | - Hüseyin Çaksen
- Department of Pediatric Genetics, Faculty of Medicine, Necmettin Erbakan University
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2
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White M, Arif-Pardy J, Connor KL. Identification of novel nutrient-sensitive gene regulatory networks in amniocytes from fetuses with spina bifida. Reprod Toxicol 2023; 116:108333. [PMID: 36584796 DOI: 10.1016/j.reprotox.2022.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/14/2022] [Accepted: 12/26/2022] [Indexed: 12/28/2022]
Abstract
Neural tube defects (NTDs) remain among the most common congenital anomalies. Contributing risk factors include genetics and nutrient deficiencies, however, a comprehensive assessment of nutrient-gene interactions in NTDs is lacking. We applied a nutrient-focused gene expression analysis pipeline to identify nutrient-sensitive gene regulatory networks in amniocyte gene expression data (GSE4182) from fetuses with NTDs (cases; n = 3) and fetuses with no congenital anomalies (controls; n = 5). Differentially expressed genes (DEGs) were screened for having nutrient cofactors. Nutrient-dependent transcriptional regulators (TRs) that regulated DEGs, and nutrient-sensitive miRNAs with a previous link to NTDs, were identified. Of the 880 DEGs in cases, 10% had at least one nutrient cofactor. DEG regulatory network analysis revealed that 39% and 52% of DEGs in cases were regulated by 22 nutrient-sensitive miRNAs and 10 nutrient-dependent TRs, respectively. Zinc- and B vitamin-dependent gene regulatory networks (Zinc: 10 TRs targeting 50.6% of DEGs; B vitamins: 4 TRs targeting 37.7% of DEGs, 9 miRNAs targeting 17.6% of DEGs) were dysregulated in cases. We identified novel, nutrient-sensitive gene regulatory networks not previously linked to NTDs, which may indicate new targets to explore for NTD prevention or to optimise fetal development.
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Affiliation(s)
- Marina White
- Health Sciences, Carleton University, 1125 Colonel By Dr, Ottawa K1S 5B6, ON, Canada
| | - Jayden Arif-Pardy
- Health Sciences, Carleton University, 1125 Colonel By Dr, Ottawa K1S 5B6, ON, Canada
| | - Kristin L Connor
- Health Sciences, Carleton University, 1125 Colonel By Dr, Ottawa K1S 5B6, ON, Canada.
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3
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Galán-Vidal J, Socuéllamos PG, Baena-Nuevo M, Contreras L, González T, Pérez-Poyato MS, Valenzuela C, González-Lamuño D, Gandarillas A. A novel loss-of-function mutation of the voltage-gated potassium channel Kv10.2 involved in epilepsy and autism. Orphanet J Rare Dis 2022; 17:345. [PMID: 36068614 PMCID: PMC9446776 DOI: 10.1186/s13023-022-02499-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Background Novel developmental mutations associated with disease are a continuous challenge in medicine. Clinical consequences caused by these mutations include neuron and cognitive alterations that can lead to epilepsy or autism spectrum disorders. Often, it is difficult to identify the physiological defects and the appropriate treatments. Results We have isolated and cultured primary cells from the skin of a patient with combined epilepsy and autism syndrome. A mutation in the potassium channel protein Kv10.2 was identified. We have characterised the alteration of the mutant channel and found that it causes loss of function (LOF). Primary cells from the skin displayed a very striking growth defect and increased differentiation. In vitro treatment with various carbonic anhydrase inhibitors with various degrees of specificity for potassium channels, (Brinzolamide, Acetazolamide, Retigabine) restored the activation capacity of the mutated channel. Interestingly, the drugs also recovered in vitro the expansion capacity of the mutated skin cells. Furthermore, treatment with Acetazolamide clearly improved the patient regarding epilepsy and cognitive skills. When the treatment was temporarily halted the syndrome worsened again. Conclusions By in vitro studying primary cells from the patient and the activation capacity of the mutated protein, we could first, find a readout for the cellular defects and second, test pharmaceutical treatments that proved to be beneficial. The results show the involvement of a novel LOF mutation of a Potassium channel in autism syndrome with epilepsy and the great potential of in vitro cultures of primary cells in personalised medicine of rare diseases.
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Affiliation(s)
- Jesús Galán-Vidal
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Institute for Research Marqués de Valdecilla (IDIVAL), 39011, Santander, Spain
| | - Paula G Socuéllamos
- Instituto de Investigaciones Biomédicas Alberto Sols, IIBM, CSIC-UAM, Madrid, Spain.,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - María Baena-Nuevo
- Instituto de Investigaciones Biomédicas Alberto Sols, IIBM, CSIC-UAM, Madrid, Spain.,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Lizbeth Contreras
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Institute for Research Marqués de Valdecilla (IDIVAL), 39011, Santander, Spain
| | - Teresa González
- Instituto de Investigaciones Biomédicas Alberto Sols, IIBM, CSIC-UAM, Madrid, Spain.,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - María S Pérez-Poyato
- Neuropediatric, University Hospital Marqués de Valdecilla, 39008, Santander, Spain
| | - Carmen Valenzuela
- Instituto de Investigaciones Biomédicas Alberto Sols, IIBM, CSIC-UAM, Madrid, Spain. .,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain.
| | - Domingo González-Lamuño
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Institute for Research Marqués de Valdecilla (IDIVAL), 39011, Santander, Spain. .,Paediatric Department, University of Cantabria University, Marqués de Valdecilla Hospital, 39008, Santander, Spain.
| | - Alberto Gandarillas
- Cell Cycle, Stem Cell Fate and Cancer Laboratory, Institute for Research Marqués de Valdecilla (IDIVAL), 39011, Santander, Spain. .,INSERM, Occitanie Méditerranée, 34394, Montpellier, France.
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Kouchi Z, Kojima M. Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis. Sci Rep 2022; 12:4325. [PMID: 35279680 PMCID: PMC8918327 DOI: 10.1038/s41598-022-08147-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 03/02/2022] [Indexed: 11/21/2022] Open
Abstract
Recent investigations of neurological developmental disorders have revealed the Rho-family modulators such as Syde and its interactors as the candidate genes. Although the mammalian Syde proteins are reported to possess GTPase-accelerating activity for RhoA-family proteins, diverse species-specific substrate selectivities and binding partners have been described, presumably based on their evolutionary variance in the molecular organization. A comprehensive in silico analysis of Syde family proteins was performed to elucidate their molecular functions and neurodevelopmental networks. Predicted structural modeling of the RhoGAP domain may account for the molecular constraints to substrate specificity among Rho-family proteins. Deducing conserved binding motifs can extend the Syde interaction network and highlight diverse but Syde isoform-specific signaling pathways in neuronal homeostasis, differentiation, and synaptic plasticity from novel aspects of post-translational modification and proteolysis.
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A genotype-first analysis in a cohort of Mullerian anomaly. J Hum Genet 2022; 67:347-352. [PMID: 35022528 DOI: 10.1038/s10038-021-00996-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/08/2022]
Abstract
Müllerian anomaly (M.A.) is a group of congenital anatomic abnormalities caused by aberrations of the development process of the Müllerian duct. M.A. can either be isolated or be involved in Mendelian syndromes, such as Dandy-Walker syndrome, Holt-Oram syndrome and Bardet-Biedl syndrome, which are often associated with both uterus and kidney malformations. In this study, we applied a genotype-first approach to analyze the whole-exome sequencing data of 492 patients with M.A. Six potential pathogenic variants were found in five genes previously related to female urogenital deformities (PKD1, SON, SALL1, BMPR1B, ITGA8), which are partially overlapping with our patients' phenotypes. We further identified eight incidental findings in seven genes related to Mendelian syndromes without known association with reproductive anomalies (TEK, COL11A1, ANKRD11, LEMD3, DLG5, SPTB, BMP2), which represent potential phenotype expansions of these genes.
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Xie F, Lei L, Cai B, Gan L, Gao Y, Liu X, Zhou L, Jiang J. Clinical manifestation and phenotypic analysis of novel gene mutation in 28 Chinese children with hereditary spherocytosis. Mol Genet Genomic Med 2021; 9:e1577. [PMID: 33620149 PMCID: PMC8123760 DOI: 10.1002/mgg3.1577] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/02/2020] [Accepted: 11/24/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose Objective to summarize the clinical features and laboratory findings of 28 Chinese children with hereditary spherocytosis (HS), and analyze these mutations. Method Collected and analyzed the clinical data of all children and their parents, and completed the relevant laboratory examinations of all children. Analyzed the sequence of related genes by second‐generation sequencing technology, and verified the suspected mutations by Sanger sequencing method. Analyzed all biological information using the Single Nucleotide Polymorphism database, the 1000 Human Genome Project, and the Exosome Aggregation Consortium. Result New mutations were detected in the HS coding region of 28 children. Among them, there were 13 cases (46.4%) with ANK1 mutation, 10 cases (35.7%) with SPTB mutation, three cases (10.7%) with SLC4A1 mutation, and two cases (7.2%) with SPTA1 mutation. All mutations cause amino acid changes in the coding gene, as well as subsequent changes in protein structure or loss of function. Conclusion All the newly discovered gene coding region mutation sites detected are the suspected pathogenic causes of the 28 Chinese children. At the same time, the second‐generation gene sequencing technology is an effective means to diagnose HS. Different mutation types and different mutation regions have no significant correlation with the severity of anemia. The novel gene mutation sites in 28 children studied in this paper have not yet been included in the human genome database, dbSNP (v138), or ExAC database. The new gene mutations found in HS children can provide a theoretical basis for further exploring the genetic causes of HS in Chinese children.
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Affiliation(s)
- Fei Xie
- Department of Pediatrics, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Lei Lei
- Department of Pediatrics, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Bin Cai
- Department of Pediatrics, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Lu Gan
- Department of Pediatrics, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Yu Gao
- Department of Pediatrics, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xiaoying Liu
- Department of Pediatrics, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Lin Zhou
- Department of Pediatrics, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Jinjin Jiang
- Department of Pediatrics, Changhai Hospital, Naval Military Medical University, Shanghai, China
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Morrow JS, Stankewich MC. The Spread of Spectrin in Ataxia and Neurodegenerative Disease. JOURNAL OF EXPERIMENTAL NEUROLOGY 2021; 2:131-139. [PMID: 34528024 PMCID: PMC8439443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Experimental and hereditary defects in the ubiquitous scaffolding proteins of the spectrin gene family cause an array of neuropathologies. Most recognized are ataxias caused by missense, deletions, or truncations in the SPTBN2 gene that encodes beta III spectrin. Such mutations disrupt the organization of post-synaptic receptors, their active transport through the secretory pathway, and the organization and dynamics of the actin-based neuronal skeleton. Similar mutations in SPTAN1 that encodes alpha II spectrin cause severe and usually lethal neurodevelopmental defects including one form of early infantile epileptic encephalopathy type 5 (West syndrome). Defects in these and other spectrins are implicated in degenerative and psychiatric conditions. In recent published work, we describe in mice a novel variant of alpha II spectrin that results in a progressive ataxia with widespread neurodegenerative change. The action of this variant is distinct, in that rather than disrupting a constitutive ligand-binding function of spectrin, the mutation alters its response to calcium and calmodulin-regulated signaling pathways including its response to calpain activation. As such, it represents a novel spectrinopathy that targets a key regulatory pathway where calcium and tyrosine kinase signals converge. Here we briefly discuss the various roles of spectrin in neuronal processes and calcium activated regulatory inputs that control its participation in neuronal growth, organization, and remodeling. We hypothesize that damage to the neuronal spectrin scaffold may be a common final pathway in many neurodegenerative disorders. Targeting the pathways that regulate spectrin function may thus offer novel avenues for therapeutic intervention.
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Affiliation(s)
- Jon S. Morrow
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA,Molecular & Cellular Developmental Biology, Yale University, New Haven, CT 06520, USA,Correspondence should be addressed to Jon S. Morrow; , Michael Stankewich;
| | - Michael C. Stankewich
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA,Correspondence should be addressed to Jon S. Morrow; , Michael Stankewich;
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8
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Beta-Spectrin Deletion Responsible for Hereditary Spherocytosis: When New Technologies Are Not the Key to Success. J Pediatr Hematol Oncol 2020; 42:e686-e688. [PMID: 32079985 DOI: 10.1097/mph.0000000000001742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Hereditary spherocytosis arises from alterations in the genes encoding red blood cell membrane proteins. Although its diagnosis is mostly clinical, recent advances in next-generation sequencing (NGS) technologies have allowed for a faster cost-effective gene-based diagnosis. We report the case of a boy with spherocytic anemia and development delay in whom a de novo 2.84-Mb deletion at chromosome 14 including SPTB (ß-spectrin gene) was identified by array-based comparative genomic hybridization. This alteration, consistent with de novo spherocytosis, was missed by a NGS gene panel. When associated with other symptoms, especially neurologic, NGS may not be appropriate to genetically diagnose spherocytic anemia.
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9
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Meglic A, Debeljak M, Kovac J, Trampus Bakija A, Rajic V, Kojc N, Trebusak Podkrajsek K. SPTB related spherocytosis in a three-generation family presenting with kidney failure in adulthood due to co-occurrence of UMOD disease causing variant. Nefrologia 2020; 40:421-428. [PMID: 32113667 DOI: 10.1016/j.nefro.2019.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/14/2019] [Accepted: 10/27/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Hereditary spherocytosis is clinically and genetically heterogeneous disorder and its clinical characteristics are spherocytosis, anaemia, jaundice and splenomegaly. The aetiology is associated to the genes encoding proteins involved in the interaction between the erythrocyte membrane and the lipid bilayer. Causative variants in βI-spectrin (SPTB) gene presenting as mild to moderately severe disease are responsible for approximately 25% cases in the USA and Europe. Among kidney disease, isolated cases of nephrotic syndrome due to membranoproliferative glomerulonephritis and macroscopic haematuria with proteinuria due to IgA nephropathy were previously reported in patients with SPTB deficiency. OBJECTIVE Seven patients from the same family with spherocytosis were evaluated to assess the kidney failure presented in all affected adult patients. METHODS Clinical, radiological and laboratory investigations were issued to evaluate the spherocytosis and kidney disease. In selected patients, we also performed genetics testing with next generation sequencing of genes related to hereditary spherocytosis, inherited glomerular disorders and tubulo-interstitial kidney disease. RESULTS Among the family members with spherocytosis, two adults had end-stage kidney disease and one chronic kidney disease stage 4 with unspecific histopathological findings of interstitial fibrosis/tubular atrophy and glomerulosclerosis. At the time, there were no signs of kidney disease present in four paediatric patients. Novel nonsense variant in SPTB gene (NM_001024858; c.4796G>A; p.Trp1599Ter) was detected in all family members with spherocytosis and was predicted to be disease causing. Furthermore, all adult patients with kidney failure and two paediatric cousins of the index patients were heterozygous for the UMOD gene variant (NM_003361.3:c.552G>C, NP_003352.2:p.Trp184Cys) previously reported in patients with tubulo-interstitial kidney disease. UMOD variant was not present in the index patients. CONCLUSIONS The co-occurrence of any two rare inherited disorders is extremely rare, while to our knowledge the co-occurrence of genetically confirmed HS and autosomal dominant tubulo-interstitial kidney disease (ADTKD) has previously not been reported. It is not possibly to evaluate whether the haemolytic crises due to HS are influencing the progression of the UMOD related renal disease, since the UMOD related ADTKD characteristics in general and in here presented family are extremely variable. Nevertheless, the observed kidney disease in the family is warranting the regular nephrological examinations in UMOD positive paediatric patients in the family in order to recognise hyperuricemia and treat it as early as possible. This is emphasising the importance of serum uric acid detection in routine laboratory screening of paediatric patients in order to identify early signs of tubular injury indicating possible ADTKD.
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Affiliation(s)
- Anamarija Meglic
- University Medical Centre Ljubljana, University Children's Hospital, Department of Nephrology, Ljubljana, Slovenia
| | - Marusa Debeljak
- University Medical Centre Ljubljana, University Children's Hospital, Institute for Special Laboratory Diagnostics, Ljubljana, Slovenia
| | - Jernej Kovac
- University Medical Centre Ljubljana, University Children's Hospital, Institute for Special Laboratory Diagnostics, Ljubljana, Slovenia
| | - Alenka Trampus Bakija
- University Medical Centre Ljubljana, University Children's Hospital, Institute for Special Laboratory Diagnostics, Ljubljana, Slovenia
| | - Vladan Rajic
- University Medical Centre Ljubljana, University Children's Hospital, Department of Haematology and Oncology, Ljubljana, Slovenia
| | - Nika Kojc
- University of Ljubljana, Faculty of Medicine, Institute of Pathology, Ljubljana, Slovenia
| | - Katarina Trebusak Podkrajsek
- University Medical Centre Ljubljana, University Children's Hospital, Institute for Special Laboratory Diagnostics, Ljubljana, Slovenia; University of Ljubljana, Faculty of Medicine, Institute of Biochemistry, Ljubljana, Slovenia.
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Kotar A, Kocman V, Plavec J. Intercalation of a Heterocyclic Ligand between Quartets in a G-Rich Tetrahelical Structure. Chemistry 2020; 26:814-817. [PMID: 31750579 PMCID: PMC7004031 DOI: 10.1002/chem.201904923] [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] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/20/2019] [Indexed: 11/20/2022]
Abstract
YES G‐rich oligonucleotide VK2 folds into an AGCGA‐quadruplex tetrahelical structure distinct and significantly different from G‐quadruplexes, even though it contains four G3 tracts. Herein, a bis‐quinolinium ligand 360A with high affinity for G‐quadruplex structures and selective telomerase inhibition is shown to strongly bind to VK2. Upon binding, 360A does not induce a conformational switch from VK2 to an expected G‐quadruplex. In contrast, NMR structural study revealed formation of a well‐defined VK2–360A complex with a 1:1 binding stoichiometry, in which 360A intercalates between GAGA‐ and GCGC‐quartets in the central cavity of VK2. This is the first high‐resolution structure of a G‐quadruplex ligand intercalating into a G‐rich tetrahelical fold. This unique mode of ligand binding into tetrahelical DNA architecture offers insights into the stabilization of an AGCGA‐quadruplex by a heterocyclic ligand and provides guidelines for rational design of novel VK2 binding molecules with selectivity for different DNA secondary structures.
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Affiliation(s)
- Anita Kotar
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Vojč Kocman
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia.,EN-FIST Center of Excellence, Trg Osvobodilne fronte 13, 1000, Ljubljana, Slovenia
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11
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Jang W, Kim J, Chae H, Kim M, Koh KN, Park CJ, Kim Y. Hereditary spherocytosis caused by copy number variation in SPTB gene identified through targeted next-generation sequencing. Int J Hematol 2019; 110:250-254. [DOI: 10.1007/s12185-019-02630-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
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12
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Andolfo I, Russo R, Gambale A, Iolascon A. New insights on hereditary erythrocyte membrane defects. Haematologica 2016; 101:1284-1294. [PMID: 27756835 PMCID: PMC5394881 DOI: 10.3324/haematol.2016.142463] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/16/2016] [Indexed: 01/02/2023] Open
Abstract
After the first proposed model of the red blood cell membrane skeleton 36 years ago, several additional proteins have been discovered during the intervening years, and their relationship with the pathogenesis of the related disorders have been somewhat defined. The knowledge of erythrocyte membrane structure is important because it represents the model for spectrin-based membrane skeletons in all cells and because defects in its structure underlie multiple hemolytic anemias. This review summarizes the main features of erythrocyte membrane disorders, dividing them into structural and altered permeability defects, focusing particularly on the most recent advances. New proteins involved in alterations of the red blood cell membrane permeability were recently described. The mechanoreceptor PIEZO1 is the largest ion channel identified to date, the fundamental regulator of erythrocyte volume homeostasis. Missense, gain-of-function mutations in the PIEZO1 gene have been identified in several families as causative of dehydrated hereditary stomatocytosis or xerocytosis. Similarly, the KCNN4 gene, codifying the so called Gardos channel, has been recently identified as a second causative gene of hereditary xerocytosis. Finally, ABCB6 missense mutations were identified in different pedigrees of familial pseudohyperkalemia. New genomic technologies have improved the quality and reduced the time of diagnosis of these diseases. Moreover, they are essential for the identification of the new causative genes. However, many questions remain to solve, and are currently objects of intensive studies.
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Affiliation(s)
- Immacolata Andolfo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy
- CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Roberta Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy
- CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Antonella Gambale
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy
- CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy
- CEINGE Biotecnologie Avanzate, Napoli, Italy
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Adi A, Tawil B, Aldosari M, Shinwari J, Nester M, Aldhalaan H, Alshamrani H, Ghannam M, Meyer B, Al Tassan N. Homozygosity analysis in subjects with autistic spectrum disorder. Mol Med Rep 2015; 12:2307-12. [PMID: 25901489 DOI: 10.3892/mmr.2015.3663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 03/23/2015] [Indexed: 11/06/2022] Open
Abstract
Autistic spectrum disorder (ASD) is a complex neurodevelopmental disorder that results in social and communication impairments, as well as repetitive and stereotyped patterns. Genetically, ASD has been described as a multifactorial genetic disorder. The aim of the present study was to investigate possible susceptibility loci of ASD, utilizing the highly consanguineous and inbred nature of numerous families within the population of Saudi Arabia. A total of 13 multiplex families and 27 affected individuals were recruited and analyzed using Affymetrix GeneChip(®) Mapping 250K and 6.0 arrays as well as Axiom arrays. Numerous regions of homozygosity were identified, including regions in genes associated with synaptic function and neurotransmitters, as well as energy and mitochondria-associated genes, and developmentally-associated genes. The loci identified in the present study represent regions that may be further investigated, which could reveal novel changes and variations associated with ASD, reinforcing the complex inheritance of the disease.
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Affiliation(s)
- Ahmad Adi
- Behavioral Genetics Unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Basma Tawil
- Behavioral Genetics Unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Mohammed Aldosari
- Center for Autism Research, King Faisal Specialist Hospital, Riyadh 11211, Saudi Arabia
| | - Jameela Shinwari
- Behavioral Genetics Unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Michael Nester
- Center for Autism Research, King Faisal Specialist Hospital, Riyadh 11211, Saudi Arabia
| | - Hisham Aldhalaan
- Center for Autism Research, King Faisal Specialist Hospital, Riyadh 11211, Saudi Arabia
| | - Hussain Alshamrani
- Center for Autism Research, King Faisal Specialist Hospital, Riyadh 11211, Saudi Arabia
| | - Manar Ghannam
- Center for Autism Research, King Faisal Specialist Hospital, Riyadh 11211, Saudi Arabia
| | - Brian Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Nada Al Tassan
- Behavioral Genetics Unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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Manor O, Segal E. GenoExp: a web tool for predicting gene expression levels from single nucleotide polymorphisms. ACTA ACUST UNITED AC 2015; 31:1848-50. [PMID: 25637557 DOI: 10.1093/bioinformatics/btv050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 01/26/2015] [Indexed: 12/16/2022]
Abstract
UNLABELLED Understanding the effect of single nucleotide polymorphisms (SNPs) on the expression level of genes is an important goal. We recently published a study in which we devised a multi-SNP predictive model for gene expression in Lymphoblastoid cell lines (LCL), and showed that it can robustly predict the expression of a small number of genes in test individuals. Here, we validate the generality of our models by predicting expression profiles for genes in LCL in an independent study, and extend the pool of predictable genes for which we are able to explain more than 25% of their expression variability to 232 genes across 14 different cell types. As the number of people who obtained their SNP profiles through companies such as 23andMe is rising rapidly, we developed GenoExp, a web-based tool in which users can upload their individual SNP data and obtain predicted expression levels for the set of predictable genes across the 14 different cell types. Our tool thus allows users with biological knowledge to study the possible effects that their set of SNPs might have on these genes and predict their cell-specific expression levels relative to the population average. AVAILABILITY AND IMPLEMENTATION GenoExp is freely available at http://genie.weizmann.ac.il/pubs/GenoExp/.
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Affiliation(s)
- Ohad Manor
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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15
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A tetrahelical DNA fold adopted by tandem repeats of alternating GGG and GCG tracts. Nat Commun 2014; 5:5831. [PMID: 25500730 PMCID: PMC4275592 DOI: 10.1038/ncomms6831] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 11/12/2014] [Indexed: 01/21/2023] Open
Abstract
DNA can form diverse higher-order structures, whose details are greatly dependent on nucleotide sequence. G-rich sequences containing four or more repeats of three guanines are expected to form G-quadruplexes. Here we show that DNA sequences with GGGAGCG repeats found in the regulatory region of the PLEKHG3 gene are capable of forming tetrahelical DNA structures that are distinct from G-quadruplexes. The d(GGGAGCGAGGGAGCG) sequence, VK1, forms a dimer. Two VK1 sequences connected by an adenine residue, VK2, fold into a monomer, which shares identical structural characteristics with the VK1 fold. Their four-stranded architectures are stabilized by four G-C, four G-A and six G-G base pairs. No G-quartets or Hoogsteen-type hydrogen-bonded guanine residues are present and the overall topology is conserved in the presence of Li(+), Na(+), K(+) and NH4(+) ions. Unique structural features include two edgewise loops on each side of the structure stabilized by three G-G base pairs in N1-carbonyl symmetric geometry.
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16
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Miller NLG, Kleinschmidt EG, Schlaepfer DD. RhoGEFs in cell motility: novel links between Rgnef and focal adhesion kinase. Curr Mol Med 2014; 14:221-34. [PMID: 24467206 DOI: 10.2174/1566524014666140128110339] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 07/08/2013] [Accepted: 12/02/2013] [Indexed: 11/22/2022]
Abstract
Rho guanine exchange factors (GEFs) are a large, diverse family of proteins defined by their ability to catalyze the exchange of GDP for GTP on small GTPase proteins such as Rho family members. GEFs act as integrators from varied intra- and extracellular sources to promote spatiotemporal activity of Rho GTPases that control signaling pathways regulating cell proliferation and movement. Here we review recent studies elucidating roles of RhoGEF proteins in cell motility. Emphasis is placed on Dbl-family GEFs and connections to development, integrin signaling to Rho GTPases regulating cell adhesion and movement, and how these signals may enhance tumor progression. Moreover, RhoGEFs have additional domains that confer distinctive functions or specificity. We will focus on a unique interaction between Rgnef (also termed Arhgef28 or p190RhoGEF) and focal adhesion kinase (FAK), a non-receptor tyrosine kinase that controls migration properties of normal and tumor cells. This Rgnef-FAK interaction activates canonical GEF-dependent RhoA GTPase activity to govern contractility and also functions as a scaffold in a GEF-independent manner to enhance FAK activation. Recent studies have also brought to light the importance of specific regions within the Rgnef pleckstrin homology (PH) domain for targeting the membrane. As revealed by ongoing Rgnef-FAK investigations, exploring GEF roles in cancer will yield fundamental new information on the molecular mechanisms promoting tumor spread and metastasis.
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Affiliation(s)
| | | | - D D Schlaepfer
- University of California San Diego, Moores Cancer Center, Department of Reproductive Medicine, MC 0803, 3855 Health Sciences Dr., La Jolla, CA 92093 USA.
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17
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A meta-analysis of gene expression quantitative trait loci in brain. Transl Psychiatry 2014; 4:e459. [PMID: 25290266 PMCID: PMC4350525 DOI: 10.1038/tp.2014.96] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 07/15/2014] [Accepted: 08/21/2014] [Indexed: 12/18/2022] Open
Abstract
Current catalogs of brain expression quantitative trait loci (eQTL) are incomplete and the findings do not replicate well across studies. All existing cortical eQTL studies are small and emphasize the need for a meta-analysis. We performed a meta-analysis of 424 brain samples across five studies to identify regulatory variants influencing gene expression in human cortex. We identified 3584 genes in autosomes and chromosome X with false discovery rate q<0.05 whose expression was significantly associated with DNA sequence variation. Consistent with previous eQTL studies, local regulatory variants tended to occur symmetrically around transcription start sites and the effect was more evident in studies with large sample sizes. In contrast to random SNPs, we observed that significant eQTLs were more likely to be near 5'-untranslated regions and intersect with regulatory features. Permutation-based enrichment analysis revealed that SNPs associated with schizophrenia and bipolar disorder were enriched among brain eQTLs. Genes with significant eQTL evidence were also strongly associated with diseases from OMIM (Online Mendelian Inheritance in Man) and the NHGRI (National Human Genome Research Institute) genome-wide association study catalog. Surprisingly, we found that a large proportion (28%) of ~1000 autosomal genes encoding proteins needed for mitochondrial structure or function were eQTLs (enrichment P-value=1.3 × 10(-9)), suggesting a potential role for common genetic variation influencing the robustness of energy supply in brain and a possible role in the etiology of some psychiatric disorders. These systematically generated eQTL information should be a valuable resource in determining the functional mechanisms of brain gene expression and the underlying biology of associations with psychiatric disorders.
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18
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Hsu WCJ, Nilsson CL, Laezza F. Role of the axonal initial segment in psychiatric disorders: function, dysfunction, and intervention. Front Psychiatry 2014; 5:109. [PMID: 25191280 PMCID: PMC4139700 DOI: 10.3389/fpsyt.2014.00109] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/06/2014] [Indexed: 12/22/2022] Open
Abstract
The progress of developing effective interventions against psychiatric disorders has been limited due to a lack of understanding of the underlying cellular and functional mechanisms. Recent research findings focused on exploring novel causes of psychiatric disorders have highlighted the importance of the axonal initial segment (AIS), a highly specialized neuronal structure critical for spike initiation of the action potential. In particular, the role of voltage-gated sodium channels, and their interactions with other protein partners in a tightly regulated macromolecular complex has been emphasized as a key component in the regulation of neuronal excitability. Deficits and excesses of excitability have been linked to the pathogenesis of brain disorders. Identification of the factors and regulatory pathways involved in proper AIS function, or its disruption, can lead to the development of novel interventions that target these mechanistic interactions, increasing treatment efficacy while reducing deleterious off-target effects for psychiatric disorders.
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Affiliation(s)
- Wei-Chun Jim Hsu
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Graduate Program in Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- M.D.–Ph.D. Combined Degree Program, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Carol Lynn Nilsson
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Sealy Center for Molecular Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Fernanda Laezza
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Center for Addiction Research, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Center for Biomedical Engineering, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Mitchell Center for Neurodegenerative Diseases, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
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19
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Lehalle D, Sanlaville D, Guimier A, Plouvier E, Leblanc T, Galmiche L, Radford I, Romana S, Colleaux L, de Pontual L, Lyonnet S, Amiel J. Multiple congenital anomalies-intellectual disability (MCA-ID) and neuroblastoma in a patient harboring a de novo 14q23.1q23.3 deletion. Am J Med Genet A 2014; 164A:1310-7. [DOI: 10.1002/ajmg.a.36452] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 12/15/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Daphné Lehalle
- Département de Génétique Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
- INSERM U781; Université Sorbonne Paris Cité, Institut IMAGINE; Paris France
| | - Damien Sanlaville
- Hospices Civils de Lyon; Service de Génétique and CRNL; CNRS UMR 5292; INSERM U1028, Université Claude Bernard Lyon I; Lyon France
| | - Anne Guimier
- Département de Génétique Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
- INSERM U781; Université Sorbonne Paris Cité, Institut IMAGINE; Paris France
| | - Emmanuel Plouvier
- Service d'Onco-Hématologie Pédiatrique; Centre Hospitalo-Universitaire de Besançon; Paris France
| | - Thierry Leblanc
- Département d'Hématologie Pédiatrique; Hôpitaux Robert Debré et Université Paris Diderot; Paris France
| | - Louise Galmiche
- Département d'Anatomo-Pathologie; Hôpital Necker-Enfants Malades; Paris France
| | - Isabelle Radford
- Département de Génétique Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
| | - Serge Romana
- Département de Génétique Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
| | - Laurence Colleaux
- INSERM U781; Université Sorbonne Paris Cité, Institut IMAGINE; Paris France
| | - Loïc de Pontual
- INSERM U781; Université Sorbonne Paris Cité, Institut IMAGINE; Paris France
| | - Stanislas Lyonnet
- Département de Génétique Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
- INSERM U781; Université Sorbonne Paris Cité, Institut IMAGINE; Paris France
| | - Jeanne Amiel
- Département de Génétique Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
- INSERM U781; Université Sorbonne Paris Cité, Institut IMAGINE; Paris France
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20
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Integrative biological analysis for neuropsychopharmacology. Neuropsychopharmacology 2014; 39:5-23. [PMID: 23800968 PMCID: PMC3857644 DOI: 10.1038/npp.2013.156] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 01/24/2023]
Abstract
Although advances in psychotherapy have been made in recent years, drug discovery for brain diseases such as schizophrenia and mood disorders has stagnated. The need for new biomarkers and validated therapeutic targets in the field of neuropsychopharmacology is widely unmet. The brain is the most complex part of human anatomy from the standpoint of number and types of cells, their interconnections, and circuitry. To better meet patient needs, improved methods to approach brain studies by understanding functional networks that interact with the genome are being developed. The integrated biological approaches--proteomics, transcriptomics, metabolomics, and glycomics--have a strong record in several areas of biomedicine, including neurochemistry and neuro-oncology. Published applications of an integrated approach to projects of neurological, psychiatric, and pharmacological natures are still few but show promise to provide deep biological knowledge derived from cells, animal models, and clinical materials. Future studies that yield insights based on integrated analyses promise to deliver new therapeutic targets and biomarkers for personalized medicine.
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21
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Tajeran M, Baghbani F, Hassanzadeh-Nazarabadi M. A Case of Autism with Ring Chromosome 14. IRANIAN JOURNAL OF PUBLIC HEALTH 2013; 42:1316-20. [PMID: 26171345 PMCID: PMC4499074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 09/21/2013] [Indexed: 10/27/2022]
Abstract
BACKGROUND Autism is a complex neuropsychiatric disorder that manifests in early childhood. Although the etiology is unknown yet but, new hypothesis focused on identifying the key genes related to autism may elucidate its etiology. The main objective of the present study was to verify the value of karyotyping in autistic children and identifying association between chromosome abnormalities and autism. METHODS We examined the peripheral blood lymphocytes cell culture for cytogenetic alterations by GTG-banding technique. The investigation was carried out on 50 autistic patients referred by Pediatric neurologist to Cytogenetic Laboratory in Khorasan-e-razavi Province, Iran. RESULTS Using GTG-banding technique, the chromosome analysis of patients identified an unbalanced male karyotype with a r (14) in all 50 metaphaseswere examined. CONCLUSION Since structural abnormalities may have a critical role in the etiology of autism, according to the region where is affected and number of related genes, therefore an outcome with wide spectrum of clinical manifestations could be expected. Furthermore by considering of recent study, the results indicated that there is an association between chromosome 14 with brain development and neurological disorders, but, in conclusion, it could not be suggested that in order to postulate cytogenetic testing in idiopathic autism patients, specifically screening for chromosome 14 which might has diagnostic value.
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Affiliation(s)
- Massoumeh Tajeran
- Dept. of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences (MUMS), Mashhad, Iran
| | - Fatemeh Baghbani
- Dept. of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences (MUMS), Mashhad, Iran
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22
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Rattazzi L, Piras G, Ono M, Deacon R, Pariante CM, D'Acquisto F. CD4⁺ but not CD8⁺ T cells revert the impaired emotional behavior of immunocompromised RAG-1-deficient mice. Transl Psychiatry 2013; 3:e280. [PMID: 23838891 PMCID: PMC3731786 DOI: 10.1038/tp.2013.54] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 04/08/2013] [Accepted: 05/23/2013] [Indexed: 12/21/2022] Open
Abstract
An imbalanced immune system has long been known to influence a variety of mood disorders including anxiety, obsessive-compulsive disorders and depression. In this study, we sought to model the impact of an immunocompromised state on these emotional behaviors using RAG-1⁻/⁻ mice, which lack T and B cells. We also investigated the relative contribution of CD4⁺ or CD8⁺ T cells to these manifestations using RAG-1⁻/⁻/OT-II and RAG-1⁻/⁻/OT-I transgenic mice, respectively. Our results show that RAG-1⁻/⁻ mice present a significant increase in digging and marble-burying activities compared with wild-type mice. Surprisingly, these anxiety-like behaviors were significantly reverted in RAG-1⁻/⁻/OT-II but not RAG-1⁻/⁻/OT-I transgenic mice. Immunodepletion experiments with anti-CD4 or anti-CD8 in C57/BL6 mice or repopulation studies in RAG-1⁻/⁻ mice did not reproduce these findings. Microarray analysis of the brain of RAG-1⁻/⁻ and RAG-1⁻/⁻/OT-II mice revealed a significantly different gene fingerprint, with the latter being more similar to wild-type mice than the former. Further analysis revealed nine main signaling pathways as being significantly modulated in RAG-1⁻/⁻ compared with wild-type mice. Taken together, these results suggest that life-long rather than transient immunodeficient conditions influence the emotional behaviors in mice. Most interestingly, these effects seem to correlate with a specific absence of CD4⁺ rather than CD8⁺ T cells. Validation of these findings in man might provide new clues on the mechanism by which early life immune modulation might impact mood response in adults and provide a further link between immune and emotional well-being.
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Affiliation(s)
- L Rattazzi
- Centre for Biochemical Pharmacology, The William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - G Piras
- Centre for Biochemical Pharmacology, The William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - M Ono
- Institute of Child Health, University College London, London, UK
| | - R Deacon
- Department of Experimental Psychology, University of Oxford, Oxford, UK
| | - C M Pariante
- Department of Psychological Medicine, Institute of Psychiatry, King's College London, London, UK
| | - F D'Acquisto
- Centre for Biochemical Pharmacology, The William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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23
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A discovery resource of rare copy number variations in individuals with autism spectrum disorder. G3-GENES GENOMES GENETICS 2012; 2:1665-85. [PMID: 23275889 PMCID: PMC3516488 DOI: 10.1534/g3.112.004689] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 10/24/2012] [Indexed: 12/15/2022]
Abstract
The identification of rare inherited and de novo copy number variations (CNVs) in human subjects has proven a productive approach to highlight risk genes for autism spectrum disorder (ASD). A variety of microarrays are available to detect CNVs, including single-nucleotide polymorphism (SNP) arrays and comparative genomic hybridization (CGH) arrays. Here, we examine a cohort of 696 unrelated ASD cases using a high-resolution one-million feature CGH microarray, the majority of which were previously genotyped with SNP arrays. Our objective was to discover new CNVs in ASD cases that were not detected by SNP microarray analysis and to delineate novel ASD risk loci via combined analysis of CGH and SNP array data sets on the ASD cohort and CGH data on an additional 1000 control samples. Of the 615 ASD cases analyzed on both SNP and CGH arrays, we found that 13,572 of 21,346 (64%) of the CNVs were exclusively detected by the CGH array. Several of the CGH-specific CNVs are rare in population frequency and impact previously reported ASD genes (e.g., NRXN1, GRM8, DPYD), as well as novel ASD candidate genes (e.g., CIB2, DAPP1, SAE1), and all were inherited except for a de novo CNV in the GPHN gene. A functional enrichment test of gene-sets in ASD cases over controls revealed nucleotide metabolism as a potential novel pathway involved in ASD, which includes several candidate genes for follow-up (e.g., DPYD, UPB1, UPP1, TYMP). Finally, this extensively phenotyped and genotyped ASD clinical cohort serves as an invaluable resource for the next step of genome sequencing for complete genetic variation detection.
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24
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Griswold AJ, Ma D, Cukier HN, Nations LD, Schmidt MA, Chung RH, Jaworski JM, Salyakina D, Konidari I, Whitehead PL, Wright HH, Abramson RK, Williams SM, Menon R, Martin ER, Haines JL, Gilbert JR, Cuccaro ML, Pericak-Vance MA. Evaluation of copy number variations reveals novel candidate genes in autism spectrum disorder-associated pathways. Hum Mol Genet 2012; 21:3513-23. [PMID: 22543975 DOI: 10.1093/hmg/dds164] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Autism spectrum disorders (ASDs) are highly heritable, yet relatively few associated genetic loci have been replicated. Copy number variations (CNVs) have been implicated in autism; however, the majority of loci contribute to <1% of the disease population. Therefore, independent studies are important to refine associated CNV regions and discover novel susceptibility genes. In this study, a genome-wide SNP array was utilized for CNV detection by two distinct algorithms in a European ancestry case-control data set. We identify a significantly higher burden in the number and size of deletions, and disrupting more genes in ASD cases. Moreover, 18 deletions larger than 1 Mb were detected exclusively in cases, implicating novel regions at 2q22.1, 3p26.3, 4q12 and 14q23. Case-specific CNVs provided further evidence for pathways previously implicated in ASDs, revealing new candidate genes within the GABAergic signaling and neural development pathways. These include DBI, an allosteric binder of GABA receptors, GABARAPL1, the GABA receptor-associated protein, and SLC6A11, a postsynaptic GABA transporter. We also identified CNVs in COBL, deletions of which cause defects in neuronal cytoskeleton morphogenesis in model vertebrates, and DNER, a neuron-specific Notch ligand required for cerebellar development. Moreover, we found evidence of genetic overlap between ASDs and other neurodevelopmental and neuropsychiatric diseases. These genes include glutamate receptors (GRID1, GRIK2 and GRIK4), synaptic regulators (NRXN3, SLC6A8 and SYN3), transcription factor (ZNF804A) and RNA-binding protein FMR1. Taken together, these CNVs may be a few of the missing pieces of ASD heritability and lead to discovering novel etiological mechanisms.
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Affiliation(s)
- Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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