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Park J, Cho YG, Kim JK, Kim HH. STS and PUDP Deletion Identified by Targeted Panel Sequencing with CNV Analysis in X-Linked Ichthyosis: A Case Report and Literature Review. Genes (Basel) 2023; 14:1925. [PMID: 37895274 PMCID: PMC10606178 DOI: 10.3390/genes14101925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
X-linked recessive ichthyosis (XLI) is clinically characterized by dark brown, widespread dryness with polygonal scales. We describe the identification of STS and PUDP deletions using targeted panel sequencing combined with copy-number variation (CNV) analysis in XLI. A 9-month-old infant was admitted for genetic counseling. Since the second day after birth, the infant's skin tended to be dry and polygonal scales had accumulated over the abdomen and upper extremities. The infant's maternal uncle and brother (who had also exhibited similar skin symptoms from birth) presented with polygonal scales on their trunks. CNV analysis revealed a hemizygous deletion spanning 719.3 Kb on chromosome Xp22 (chrX:7,108,996-7,828,312), which included a segment of the STS gene and exhibited a Z ratio of -2 in the proband. Multiplex ligation-dependent probe amplification (MLPA) confirmed this interstitial Xp22.31 deletion. Our report underscores the importance of implementing CNV screening techniques, including sequencing data analysis and gene dosage assays such as MLPA, to detect substantial deletions that encompass the STS gene region of Xq22 in individuals suspected of having XLI.
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Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea; (J.P.); (Y.G.C.)
| | - Yong Gon Cho
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea; (J.P.); (Y.G.C.)
| | - Jin Kyu Kim
- Department of Pediatrics, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
| | - Hyun Ho Kim
- Department of Pediatrics, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
- Research Institute of Clinical Medicine, Jeonbuk National University-Biomedical Research Institute, Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
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Wu Y, Wu D, Lan Y, Lan S, Li D, Zheng Z, Wang H, Ma L. Case report: Sex-specific characteristics of epilepsy phenotypes associated with Xp22.31 deletion: a case report and review. Front Genet 2023; 14:1025390. [PMID: 37347056 PMCID: PMC10280017 DOI: 10.3389/fgene.2023.1025390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/23/2023] [Indexed: 06/23/2023] Open
Abstract
Deletion in the Xp22.31 region is increasingly suggested to be involved in the etiology of epilepsy. Little is known regarding the genomic and clinical delineations of X-linked epilepsy in the Chinese population or the sex-stratified difference in epilepsy characteristics associated with deletions in the Xp22.31 region. In this study, we reported two siblings with a 1.69 Mb maternally inherited microdeletion at Xp22.31 involving the genes VCX3A, HDHD1, STS, VCX, VCX2, and PNPLA4 presenting with easily controlled focal epilepsy and language delay with mild ichthyosis in a Chinese family with a traceable 4-generation history of skin ichthyosis. Both brain magnetic resonance imaging results were normal, while EEG revealed epileptic abnormalities. We further performed an exhaustive literature search, documenting 25 patients with epilepsy with gene defects in Xp22.31, and summarized the epilepsy heterogeneities between sexes. Males harboring the Xp22.31 deletion mainly manifested with child-onset, easily controlled focal epilepsy accompanied by X-linked ichthyosis; the deletions were mostly X-linked recessive, with copy number variants (CNVs) in the classic region of deletion (863.38 kb-2 Mb). In contrast, epilepsy in females tended to be earlier-onset, and relatively refractory, with pathogenic CNV sizes varying over a larger range (859 kb-56.36 Mb); the alterations were infrequently inherited and almost combined with additional CNVs. A candidate region encompassing STS, HDHD1, and MIR4767 was the likely pathogenic epilepsy-associated region. This study filled in the knowledge gap regarding the genomic and clinical delineations of X-linked recessive epilepsy in the Chinese population and extends the understanding of the sex-specific characteristics of Xp22.31 deletion in regard to epilepsy.
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Affiliation(s)
- Yi Wu
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Dan Wu
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
- Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Yulong Lan
- Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Department of Cardiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Shaocong Lan
- Department of clinical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Duo Li
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Zexin Zheng
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Hongwu Wang
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Lian Ma
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Hematology and Oncology, Shenzhen Children’s Hospital of China Medical University, Shenzhen, China
- Shenzhen Public Service Platform of Molecular Medicine in Pediatric Hematology and Oncology, Shenzhen, China
- Department of Pediatrics, The Third Affiliated Hospital of Guangzhou Medical University (The Women and Children’s Hospital of Guangzhou Medical University), Guangzhou, China
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Hu H, Huang Y, Hou R, Xu H, Liu Y, Liao X, Xu J, Jiang L, Wang D. Xp22.31 copy number variations in 87 fetuses: refined genotype-phenotype correlations by prenatal and postnatal follow-up. BMC Med Genomics 2023; 16:69. [PMID: 37013593 PMCID: PMC10069036 DOI: 10.1186/s12920-023-01493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Xp22.31 deletion and duplication have been described in various studies, but different laboratories interpret pathogenicity differently. OBJECTIVES Our study aimed to refine the genotype-phenotype associations between Xp22.31 copy number variants in fetuses, with the aim of providing data support to genetic counseling. METHODS We retrospectively analyzed karyotyping and single nucleotide polymorphism array results from 87 fetuses and their family members. Phenotypic data were obtained through follow-up visits. RESULTS The percentage of fetuses carrying the Xp22.31 deletions (9 females, 12 males) was 24.1% (n = 21), while duplications (38 females, 28 males) accounted for 75.9% (n = 66). Here, we noted that the typical region (from 6.4 to 8.1 Mb, hg19) was detected in the highest ratio, either in the fetuses with deletions (76.2%, 16 of 21) or duplications (69.7%, 46 of 66). In female deletion carriers, termination of pregnancy was chosen for two fetuses, and the remaining seven were born without distinct phenotypic abnormalities. In male deletion carriers, termination of pregnancy was chosen for four fetuses, and the remaining eight of them displayed ichthyosis without neurodevelopmental anomalies. In two of these cases, the chromosomal imbalance was inherited from the maternal grandfathers, who also only had ichthyosis phenotypes. Among the 66 duplication carriers, two cases were lost at follow-up, and pregnancy was terminated for eight cases. There were no other clinical findings in the rest of the 56 fetuses, including two with Xp22.31 tetrasomy, for either male or female carriers. CONCLUSION Our observations provide support for genetic counseling in male and female carriers of Xp22.31 copy number variants. Most of them are asymptomatic in male deletion carriers, except for skin findings. Our study is consistent with the view that the Xp22.31 duplication may be a benign variant in both sexes.
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Affiliation(s)
- Huamei Hu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yulin Huang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Renke Hou
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Huanhuan Xu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yalan Liu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xueqian Liao
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Juchun Xu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Lupin Jiang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
| | - Dan Wang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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Bertini V, Milone R, Cristofani P, Cambi F, Bosetti C, Barbieri F, Bertelloni S, Cioni G, Valetto A, Battini R. Enhancing DLG2 Implications in Neuropsychiatric Disorders: Analysis of a Cohort of Eight Patients with 11q14.1 Imbalances. Genes (Basel) 2022; 13:genes13050859. [PMID: 35627244 PMCID: PMC9140951 DOI: 10.3390/genes13050859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 11/20/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are considered synaptopathies, as they are due to anomalies in neuronal connectivity during development. DLG2 is a gene involved insynaptic function; the phenotypic effect of itsalterations in NDDs has been underestimated since few cases have been thoroughly described.We report on eight patients with 11q14.1 imbalances involving DLG2, underlining its potential effects on clinical presentation and its contribution to NDD comorbidity by accurate neuropsychiatric data collection. DLG2 is a very large gene in 11q14.1, extending over 2.172 Mb, with alternative splicing that gives rise to numerous isoforms differentially expressed in brain tissues. A thorough bioinformatic analysis of the altered transcripts was conducted for each patient. The different expression profiles of the isoforms of this gene and their influence on the excitatory–inhibitory balance in crucial brain structures could contribute to the phenotypic variability related to DLG2 alterations. Further studies on patients would be helpful to enrich clinical and neurodevelopmental findings and elucidate the molecular mechanisms subtended to NDDs.
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Affiliation(s)
- Veronica Bertini
- Cytogenetic Unit, Department of Laboratory Medicine, Azienda Ospedaliero-Univeristaria Pisana, Via Roma 57, 56100 Pisa, Italy; (V.B.); (F.C.)
| | - Roberta Milone
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
| | - Paola Cristofani
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
| | - Francesca Cambi
- Cytogenetic Unit, Department of Laboratory Medicine, Azienda Ospedaliero-Univeristaria Pisana, Via Roma 57, 56100 Pisa, Italy; (V.B.); (F.C.)
| | - Chiara Bosetti
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
| | - Filippo Barbieri
- Mental Health Department, ASL Toscana Nordovest, 56100 Pisa, Italy;
| | - Silvano Bertelloni
- Pediatric Endocrinology, Department of Obstetrics, Gynecology and Pediatrics, Azienda Ospedaliero-Universitaria Pisana, Via Roma 57, 56100 Pisa, Italy;
| | - Giovanni Cioni
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56100 Pisa, Italy
| | - Angelo Valetto
- Cytogenetic Unit, Department of Laboratory Medicine, Azienda Ospedaliero-Univeristaria Pisana, Via Roma 57, 56100 Pisa, Italy; (V.B.); (F.C.)
- Correspondence:
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56100 Pisa, Italy
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6
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Wu X, Dong W, Li H, Yang X, Jin Y, Zhang Z, Jiang Y. CYP2C9*3/*3 Gene Expression Affects the Total and Free Concentrations of Valproic Acid in Pediatric Patients with Epilepsy. Pharmgenomics Pers Med 2021; 14:417-430. [PMID: 33859491 PMCID: PMC8043849 DOI: 10.2147/pgpm.s301893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/16/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose To perform therapeutic drug monitoring (TDM) of total and free plasma valproic acid (VPA) concentrations in pediatric patients with epilepsy and to analyze related factors. Patients and Methods Pediatric epileptic patients treated in 2015-2019 in our hospital were assessed. Total and free plasma VPA concentrations were obtained by UPLC and LC-MS/MS, respectively. Regression analysis was performed to examine the associations of free plasma VPA with total plasma VPA and plasma protein binding rate. The impacts of individual situation, CYP2C9 genotype, and drug combination on VPA concentration were examined. Results Of the 251 patients, 81 had lower total concentrations than effective therapeutic levels; 86 and 31 patients had infections and central nervous system dysplasia, respectively. VPA's daily doses and free drug concentrations were significantly lower in the CYP2C9 *3/*3 genotype group versus the CYP2C9 *1/*3 and CYP2C9 *1/*1 groups (P<0.05). Free and total VPA concentrations were linked by Y = 0.0004 X2 + 0.042 X + 0.3035 (r=0.6981); VPA plasma protein binding rate and free VPA concentration were related by Y = 0.0003 X2 - 0.0127 X + 0.9777 (r=0.8136). Both total and free VPA concentrations were significantly decreased in patients simultaneously administered phenobarbital, meropenem and biapenem (P<0.05), with therapeutic failure after meropenem/biapenem co-administration. Conclusion Free VPA amounts have nonlinear relationships with total VPA amounts and plasma protein binding rate in epileptic children. Additionally, CYP2C9 *3/*3 expression affects VPA metabolism. Since phenobarbital affects VPA metabolism, TDM is recommended. Meanwhile, carbapenem-co-administration with VPA should be prohibited.
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Affiliation(s)
- Xikun Wu
- The Second Hospital of Hebei Medical University, Shijiazhuang City, People's Republic of China
| | - Weichong Dong
- The Second Hospital of Hebei Medical University, Shijiazhuang City, People's Republic of China
| | - Haoran Li
- The Second Hospital of Hebei Medical University, Shijiazhuang City, People's Republic of China
| | - Xiuling Yang
- The Second Hospital of Hebei Medical University, Shijiazhuang City, People's Republic of China
| | - Yiran Jin
- The Second Hospital of Hebei Medical University, Shijiazhuang City, People's Republic of China
| | - Zhiqing Zhang
- The Second Hospital of Hebei Medical University, Shijiazhuang City, People's Republic of China
| | - Ye Jiang
- Pharmacy College, Hebei Medical University, Shijiazhuang City, People's Republic of China
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Albuz B, Ozdemir O, Silan F. The high frequency of chromosomal copy number variations and candidate genes in epilepsy patients. Clin Neurol Neurosurg 2021; 202:106487. [PMID: 33484953 DOI: 10.1016/j.clineuro.2021.106487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/29/2020] [Accepted: 01/07/2021] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Epilepsy is a chronic brain disease and is estimated to affect more than 50 million people worldwide.Epilepsy is a polygenic and multifactorial disease.Genetic causes play a major role in 40-60 % of all epilepsies.Copy number variations(CNVs) have been reported in approximately 5-12 % of patients with different types of epilepsy.Here we aimed to determine the diagnostic yield of the aCGH in epilepsy and to reveal new candidate genes and CNVs by analyzing aCGH data retrospectively. METHODS The clinical data of 80 patients with the diagnosis of epilepsy were examined retrospectively and the raw data of aCGH of these patients were reanalyzed in the light of current literature. RESULTS Pathogenic/likely pathogenic CNVs were detected in 14 of 80 patients and 12 of these CNVs (15 %) were associated with epilepsy phenotype. In addition, 18 CNVs in 16 different chromosomal loci that were evaluated as the variant of unknown clinical significance(VOUS). In four cases (5%), CNVs associated with epilepsy were less than 100 kb and these accounted for 13.3 % of all epilepsy associated CNVs. CONCLUSION The diagnostic yield of aCGH in epilepsy patients was found to be higher than most studies in the literature. MACROD2,ADGRB3(BAI3),SOX8,HIP1,PARK2 and TAFA2 genes were evaluated as potential epilepsy-related genes and NEDD9,RASAL2 and TNR genes thought to be the candidate genes for epilepsy. Our study showed that the diagnostic efficiency of aCGH in epilepsy is high and with more comprehensive studies, it will contribute to the elucidation of genes involved in genetic etiology in epilepsy patients.
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Affiliation(s)
- Burcu Albuz
- Department of Medical Genetics, Faculty of Medicine, Canakkale Onsekiz Mart University, 17020, Canakkale, Turkey.
| | - Ozturk Ozdemir
- Department of Medical Genetics, Faculty of Medicine, Canakkale Onsekiz Mart University, 17020, Canakkale, Turkey.
| | - Fatma Silan
- Department of Medical Genetics, Faculty of Medicine, Canakkale Onsekiz Mart University, 17020, Canakkale, Turkey.
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Sanders SS, Hernandez LM, Soh H, Karnam S, Walikonis RS, Tzingounis AV, Thomas GM. The palmitoyl acyltransferase ZDHHC14 controls Kv1-family potassium channel clustering at the axon initial segment. eLife 2020; 9:56058. [PMID: 33185190 PMCID: PMC7685708 DOI: 10.7554/elife.56058] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 11/12/2020] [Indexed: 01/02/2023] Open
Abstract
The palmitoyl acyltransferase (PAT) ZDHHC14 is highly expressed in the hippocampus and is the only PAT predicted to bind Type-I PDZ domain-containing proteins. However, ZDHHC14’s neuronal roles are unknown. Here, we identify the PDZ domain-containing Membrane-associated Guanylate Kinase (MaGUK) PSD93 as a direct ZDHHC14 interactor and substrate. PSD93, but not other MaGUKs, localizes to the axon initial segment (AIS). Using lentiviral-mediated shRNA knockdown in rat hippocampal neurons, we find that ZDHHC14 controls palmitoylation and AIS clustering of PSD93 and also of Kv1 potassium channels, which directly bind PSD93. Neurodevelopmental expression of ZDHHC14 mirrors that of PSD93 and Kv1 channels and, consistent with ZDHHC14’s importance for Kv1 channel clustering, loss of ZDHHC14 decreases outward currents and increases action potential firing in hippocampal neurons. To our knowledge, these findings identify the first neuronal roles and substrates for ZDHHC14 and reveal a previously unappreciated role for palmitoylation in control of neuronal excitability.
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Affiliation(s)
- Shaun S Sanders
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, United States
| | - Luiselys M Hernandez
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, United States
| | - Heun Soh
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, United States
| | - Santi Karnam
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, United States
| | - Randall S Walikonis
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, United States
| | | | - Gareth M Thomas
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, United States.,Department of Anatomy and Cell Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, United States
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Díaz-Casado E, Gómez-Nieto R, de Pereda JM, Muñoz LJ, Jara-Acevedo M, López DE. Analysis of gene variants in the GASH/Sal model of epilepsy. PLoS One 2020; 15:e0229953. [PMID: 32168507 PMCID: PMC7069730 DOI: 10.1371/journal.pone.0229953] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Epilepsy is a complex neurological disorder characterized by sudden and recurrent seizures, which are caused by various factors, including genetic abnormalities. Several animal models of epilepsy mimic the different symptoms of this disorder. In particular, the genetic audiogenic seizure hamster from Salamanca (GASH/Sal) animals exhibit sound-induced seizures similar to the generalized tonic seizures observed in epileptic patients. However, the genetic alterations underlying the audiogenic seizure susceptibility of the GASH/Sal model remain unknown. In addition, gene variations in the GASH/Sal might have a close resemblance with those described in humans with epilepsy, which is a prerequisite for any new preclinical studies that target genetic abnormalities. Here, we performed whole exome sequencing (WES) in GASH/Sal animals and their corresponding controls to identify and characterize the mutational landscape of the GASH/Sal strain. After filtering the results, moderate- and high-impact variants were validated by Sanger sequencing, assessing the possible impact of the mutations by “in silico” reconstruction of the encoded proteins and analyzing their corresponding biological pathways. Lastly, we quantified gene expression levels by RT-qPCR. In the GASH/Sal model, WES showed the presence of 342 variations, in which 21 were classified as high-impact mutations. After a full bioinformatics analysis to highlight the high quality and reliable variants, the presence of 3 high-impact and 15 moderate-impact variants were identified. Gene expression analysis of the high-impact variants of Asb14 (ankyrin repeat and SOCS Box Containing 14), Msh3 (MutS Homolog 3) and Arhgef38 (Rho Guanine Nucleotide Exchange Factor 38) genes showed a higher expression in the GASH/Sal than in control hamsters. In silico analysis of the functional consequences indicated that those mutations in the three encoded proteins would have severe functional alterations. By functional analysis of the variants, we detected 44 significantly enriched pathways, including the glutamatergic synapse pathway. The data show three high-impact mutations with a major impact on the function of the proteins encoded by these genes, although no mutation in these three genes has been associated with some type of epilepsy until now. Furthermore, GASH/Sal animals also showed gene variants associated with different types of epilepsy that has been extensively documented, as well as mutations in other genes that encode proteins with functions related to neuronal excitability, which could be implied in the phenotype of the GASH/Sal. Our findings provide valuable genetic and biological pathway data associated to the genetic burden of the audiogenic seizure susceptibility and reinforce the need to validate the role of each key mutation in the phenotype of the GASH/Sal model.
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Affiliation(s)
- Elena Díaz-Casado
- Institute of Neurosciences of Castilla y León, University of Salamanca, Salamanca, Spain
- Salamanca Institute for Biomedical Research, Salamanca, Spain
| | - Ricardo Gómez-Nieto
- Institute of Neurosciences of Castilla y León, University of Salamanca, Salamanca, Spain
- Salamanca Institute for Biomedical Research, Salamanca, Spain
- Department of Cell Biology and Pathology, School Medicine, University of Salamanca, Salamanca, Spain
| | - José M. de Pereda
- Institute of Molecular and Cellular Biology of Cancer, CSIC.—University of Salamanca, Salamanca, Spain
| | - Luis J. Muñoz
- Animal facilities, University of Salamanca, Salamanca, Spain
| | | | - Dolores E. López
- Institute of Neurosciences of Castilla y León, University of Salamanca, Salamanca, Spain
- Salamanca Institute for Biomedical Research, Salamanca, Spain
- Department of Cell Biology and Pathology, School Medicine, University of Salamanca, Salamanca, Spain
- * E-mail:
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10
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Yan H, Shi Z, Wu Y, Xiao J, Gu Q, Yang Y, Li M, Gao K, Chen Y, Yang X, Ji H, Cao B, Duan R, Jiang Y, Wang J. Targeted next generation sequencing in 112 Chinese patients with intellectual disability/developmental delay: novel mutations and candidate gene. BMC MEDICAL GENETICS 2019; 20:80. [PMID: 31088393 PMCID: PMC6518638 DOI: 10.1186/s12881-019-0794-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/27/2019] [Indexed: 11/27/2022]
Abstract
Background Intellectual disability/developmental delay is a complex condition with extraordinary heterogeneity. A large proportion of patients lacks a specific diagnosis. Next generation sequencing, enabling identification of genetic variations in multiple genes, has become an efficient strategy for genetic analysis in intellectual disability/developmental delay. Methods Clinical data of 112 Chinese families with unexplained intellectual disability/developmental delay was collected. Targeted next generation sequencing of 454 genes related to intellectual disability/developmental delay was performed for all 112 index patients. Patients with promising variants and their other family members underwent Sanger sequencing to validate the authenticity and segregation of the variants. Results Fourteen promising variants in genes EFNB1, MECP2, ATRX, NAA10, ANKRD11, DHCR7, LAMA1, NFIX, UBE3A, ARID1B and PTPRD were identified in 11 of 112 patients (11/112, 9.82%). Of 14 variants, eight arose de novo, and 13 are novel. Nine patients (9/112, 8.03%) got definite molecular diagnoses. It is the first time to report variants in EFNB1, NAA10, DHCR7, LAMA1 and NFIX in Chinese intellectual disability/developmental delay patients and first report about variants in NAA10 and LAMA1 in affected individuals of Asian ancestry. Conclusions Targeted next generation sequencing of 454 genes is an effective test strategy for patients with unexplained intellectual disability/developmental delay. Genetic heterogenicity is significant in this Chinese cohort and de novo variants play an important role in the diagnosis. Findings of this study further delineate the corresponding phenotypes, expand the mutation spectrum and support the involvement of PTPRD in the disease. Electronic supplementary material The online version of this article (10.1186/s12881-019-0794-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huifang Yan
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing, China
| | - Zhen Shi
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing, China
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing, China
| | - Jiangxi Xiao
- Department of Radiology, Peking University First Hospital, Beijing, China
| | - Qiang Gu
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing, China
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing, China
| | - Ming Li
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing, China
| | - Kai Gao
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing, China
| | - Yinyin Chen
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Department of Neurology, First Hospital of Shanxi Medical University, Taiyuan, China.,VIP Ward, Affiliated Hospital of Hebei University, Baoding, China
| | - Xiaoping Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Department of Neurology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Haoran Ji
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Binbin Cao
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Ruoyu Duan
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China. .,Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing, China. .,Key Laboratory for Neuroscience, Ministry of education/National Health and Family Planning Commission, Peking University, Beijing, China.
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China. .,Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Peking University First Hospital, Beijing, China. .,Key Laboratory for Neuroscience, Ministry of education/National Health and Family Planning Commission, Peking University, Beijing, China.
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