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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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Almazroea A, Ijaz A, Aziz A, Mushtaq Yasinzai M, Rafiullah R, Rehman FU, Daud S, Shaikh R, Ayub M, Wali A. Identification and In Silico Analysis of a Homozygous Nonsense Variant in TGM1 Gene Segregating with Congenital Ichthyosis in a Consanguineous Family. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:103. [PMID: 36676727 PMCID: PMC9866252 DOI: 10.3390/medicina59010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/25/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
Background and Objectives: Lamellar ichthyosis is a rare skin disease characterized by large, dark brown plate-like scales on the entire body surface with minimum or no erythema. This phenotype is frequently associated with a mutation in the TGM1 gene, encoding the enzyme transglutaminase 1 which plays a catalytic role in the formation of the cornified cell envelop. The present study aimed to carry out clinical and genetic characterization of the autosomal recessive lamellar ichthyosis family from Balochistan. Materials and Methods: A consanguineous family with lamellar ichthyosis was enrolled from Balochistan, Pakistan. PCR amplification of all the exons and splice site junctions of the TGM1 gene followed by Sanger sequencing was performed on the genomic DNA. The identified variant was checked by In silico prediction tools to evaluate the effect of the variant on protein. Results: Sanger sequencing identified a homozygous nonsense variant c.131G >A (p.Trp44*) in the TGM1 gene that segregated in the autosomal recessive mode of inheritance in the family. The identified variant results in premature termination of transcribed mRNA and is predicted to cause a truncated or absent translation product transglutaminase-1 (TGase-1) accompanied by loss of catalytic activity, causing a severe clinical phenotype of lamellar ichthyosis in the patients. Conclusions: Here, we report a consanguineous lamellar ichthyosis family with a homozygous nonsense variant in the TGM1 gene. The variant is predicted as pathogenic by different In silico prediction tools.
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Affiliation(s)
- Abdulhadi Almazroea
- Pediatrician, Associate Professor at College of Medicine, Taibah University, Madinah 41477, Saudi Arabia
| | - Ambreen Ijaz
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta 87300, Pakistan
- Department of Zoology, SBK Women’s University, Quetta 87500, Pakistan
| | - Abdul Aziz
- Department of Computer Sciences and Bioinformatics, Khushal Khan Khattak University, Karak 27200, Pakistan
| | - Muhammad Mushtaq Yasinzai
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta 87300, Pakistan
| | - Rafiullah Rafiullah
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta 87300, Pakistan
| | - Fazal Ur Rehman
- Department of Microbiology, University of Balochistan, Quetta 87550, Pakistan
| | - Shakeela Daud
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta 87300, Pakistan
| | - Rozeena Shaikh
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta 87300, Pakistan
| | - Muhammad Ayub
- Institute of Biochemistry, University of Balochistan, Quetta 87550, Pakistan
| | - Abdul Wali
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta 87300, Pakistan
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Wren GH, Davies W. X-linked ichthyosis: New insights into a multi-system disorder. SKIN HEALTH AND DISEASE 2022; 2:e179. [PMID: 36479267 PMCID: PMC9720199 DOI: 10.1002/ski2.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/09/2022] [Indexed: 11/07/2022]
Abstract
Background X-linked ichthyosis (XLI) is a rare genetic condition almostexclusively affecting males; it is characterised by abnormal desquamation and retentionhyperkeratosis, and presents with polygonal brown scales. Most cases resultfrom genetic deletions within Xp22.31 spanning the STS (steroid sulfatase)gene, with the remaining cases resulting from STS-specific mutations. For manyyears it has been recognised that individuals with XLI are at increased risk ofcryptorchidism and corneal opacities. Methods We discuss emerging evidence that such individuals are alsomore likely to be affected by a range of neurodevelopmental and psychiatrictraits, by cardiac arrhythmias, and by rare fibrotic and bleeding-relatedconditions. We consider candidate mechanisms that may confer elevatedlikelihood of these individual conditions, and propose a novel commonbiological risk pathway. Results Understanding the prevalence, nature and co-occurrence ofcomorbidities associated with XLI is critical for ensuring early identificationof symptoms and for providing the most effective genetic counselling andmultidisciplinary care for affected individuals. Conclusion Future work in males with XLI, and in new preclinical andcellular model systems, should further clarify underlying pathophysiologicalmechanisms amenable to therapeutic intervention.
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Affiliation(s)
| | - William Davies
- School of Psychology Cardiff University Cardiff UK.,School of Medicine Cardiff University Cardiff UK.,Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff UK.,Neuroscience and Mental Health Innovation Institute Cardiff University Cardiff UK
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Park SJ, Park KH, Bae MH, Kim YM. Developmental Delay in Children with X-Linked Ichthyosis: A Case Series. ANNALS OF CHILD NEUROLOGY 2021. [DOI: 10.26815/acn.2021.00402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Labonne JDJ, Driessen TM, Harris ME, Kong IK, Brakta S, Theisen J, Sangare M, Layman LC, Kim CH, Lim J, Kim HG. Comparative Genomic Mapping Implicates LRRK2 for Intellectual Disability and Autism at 12q12, and HDHD1, as Well as PNPLA4, for X-Linked Intellectual Disability at Xp22.31. J Clin Med 2020; 9:jcm9010274. [PMID: 31963867 PMCID: PMC7019335 DOI: 10.3390/jcm9010274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/28/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023] Open
Abstract
We report a genomic and phenotypic delineation for two chromosome regions with candidate genes for syndromic intellectual disability at 12q12 and Xp22.31, segregating independently in one family with four affected members. Fine mapping of three affected members, along with six unreported small informative CNVs, narrowed down the candidate chromosomal interval to one gene LRRK2 at 12q12. Expression studies revealed high levels of LRRK2 transcripts in the whole human brain, cerebral cortex and hippocampus. RT-qPCR assays revealed that LRRK2 transcripts were dramatically reduced in our microdeletion patient DGDP289A compared to his healthy grandfather with no deletion. The decreased expression of LRRK2 may affect protein–protein interactions between LRRK2 and its binding partners, of which eight have previously been linked to intellectual disability. These findings corroborate with a role for LRRK2 in cognitive development, and, thus, we propose that intellectual disability and autism, displayed in the 12q12 microdeletions, are likely caused by LRRK2. Using another affected member, DGDP289B, with a microdeletion at Xp22.31, in this family, we performed the genomic and clinical delineation with six published and nine unreported cases. We propose HDHD1 and PNPLA4 for X-linked intellectual disability in this region, since their high transcript levels in the human brain substantiate their role in intellectual functioning.
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Affiliation(s)
- Jonathan D. J. Labonne
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - Terri M. Driessen
- Department of Genetics, Yale University, New Haven, CT 06510, USA; (T.M.D.); (J.L.)
| | - Marvin E. Harris
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science (BK21plus), Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea;
| | - Soumia Brakta
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - John Theisen
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - Modibo Sangare
- Faculty of Medicine and Odontostomatology (FMOS), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali;
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA 30912, USA
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Korea;
| | - Janghoo Lim
- Department of Genetics, Yale University, New Haven, CT 06510, USA; (T.M.D.); (J.L.)
- Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale Stem Cell Center, Yale University, New Haven, CT 06510, USA
| | - Hyung-Goo Kim
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar
- Correspondence:
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Zhuang J, Wang Y, Zeng S, Lv C, Lin Y, Jiang Y. A prenatal diagnosis and genetics study of five pedigrees in the Chinese population with Xp22.31 microduplication. Mol Cytogenet 2019; 12:50. [PMID: 31857824 PMCID: PMC6907354 DOI: 10.1186/s13039-019-0461-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/26/2019] [Indexed: 11/16/2022] Open
Abstract
Background Copy number variations (CNVs) can contribute to human phenotype, phenotypic diversity and disease susceptibility, while others may benign. In the current study, an attempt to investigate the pathogenicity of CNVs in chromosome Xp22.31 was explored. Methods G-banding and SNP-array techniques were used to analyze chromosome karyotypes and CNVs in fetuses. Parents associate with five different pedigrees possessing high risk factors in pregnancy were considered with such parameters as advanced age, high risk of serological screening and ultrasound abnormalities. Results The fetuses’ amniotic fluid karyotypes were 46, XX and those of their parents with the five pedigrees revealed no abnormalities. Here, we noticed a series of individuals with Xp22.31 duplications ranging from 534.6 kb to 1.6 Mb. It was detected through SNP array that the fetuses in Pedigree 1 and 2 had ~ 600 kb duplications in the Xp22.31 region of their X chromosomes which contained two OMIM genes, HDHD1 (OMIM: 306480) and part of STS (OMIM: 300747). The fetuses of Pedigrees 3, 4 and 5 had 1.6 Mb duplication in the same chromosome which contained four OMIM genes: HDHD1 (OMIM: 306480), STS (OMIM: 300747), PNPLA4 (OMIM: 300102) and VCX (OMIM: 300229). The duplications in the fetuses of Pedigrees 1 and 5 were inherited from the non-phenotypic parents. Pedigrees 3 and 4 refused to perform parental verification. Finally, four of the five pedigrees continue towards pregnancy with no abnormalities being observed during followed-ups. Conclusion Our study first showed duplications of Xp22.31 in Chinese population. Clinical and genetic investigation on five different pedigrees, we consider the duplication of these fragments as likely benign copy number variants (CNVs). We suggest that the duplications of Xp22.31 with recurrent duplication as a benign CNVs .
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Yuanbai Wang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Shuhong Zeng
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Chunling Lv
- Zhejiang Biosan technology Co., Ltd, Zhejiang, People's Republic of China
| | - Yiming Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
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Bai J, Qu Y, Cao Y, Li Y, Zhang W, Jin Y, Wang H, Song F. X-linked ichthyosis and Crigler-Najjar syndrome I: Coexistence in a male patient with two copy number variable regions of 2q37.1 and Xp22.3. Mol Med Rep 2015; 13:1135-40. [PMID: 26676689 PMCID: PMC4732863 DOI: 10.3892/mmr.2015.4674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 11/18/2015] [Indexed: 11/06/2022] Open
Abstract
X-linked ichthyosis (XLI) is an X-linked recessive skin disorder generally restricted to males, which arises from mutations in the steroid sulfatase (STS) gene located on Xp22.3. Crigler-Najjar syndrome (CN-I) is a rare autosomal recessive disease caused by the homozygous or compound heterozygous mutations in the UPD-glucuronosyltransferase 1 family, polypeptide A1 (UGT1A1) gene on chromosome 2q37. A male patient was referred to the Department of Medical Genetics with of severe icterus and ichthyosis. The patient and his family members underwent genetic tests related to XLI and CN-I. Quantitative polymerase chain reaction on genomic DNA was performed to determine the gene copy number, while single nucleotide polymorphism array analysis was conducted to identify deletion mutations. Family pedigree analysis showed that the patient and his two cousins were all affected by ichthyosis, which was in accordance with the inheritance pattern of an X-linked recessive disease. In addition, the patient's serum bilirubin concentration (>340 mmol/l) was markedly greater than the normal level. The patient presented with kernicterus and phenobarbital treatment was ineffective. The clinical diagnosis of XLI was confirmed molecularly by laboratory evidence of a maternal 1.61 M deletion (including the STS gene) on ChrXp22.31. Coincidentally, the male patient was also confirmed to carry a rare maternal inherited microdeletion (374 Kb) comprising the entire UGT1A1 gene combined with a paternal UGT1A1 mutation (c.1253delT), a causative event of CN-I. To the best of our knowledge, this study reported for the first time the comorbidity of XLI and CN-I in a male patient. The results suggested that co-occurrence of these two recessive diseases in a patient may be incidental.
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Affiliation(s)
- Jinli Bai
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, P.R. China
| | - Yujin Qu
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, P.R. China
| | - Yanyan Cao
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, P.R. China
| | - Yan Li
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, P.R. China
| | - Wenhui Zhang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, P.R. China
| | - Yuwei Jin
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, P.R. China
| | - Hong Wang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, P.R. China
| | - Fang Song
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, P.R. China
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Hand JL, Runke CK, Hodge JC. The phenotype spectrum of X-linked ichthyosis identified by chromosomal microarray. J Am Acad Dermatol 2015; 72:617-27. [DOI: 10.1016/j.jaad.2014.12.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 11/29/2022]
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Elias PM, Williams ML, Choi EH, Feingold KR. Role of cholesterol sulfate in epidermal structure and function: lessons from X-linked ichthyosis. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:353-61. [PMID: 24291327 DOI: 10.1016/j.bbalip.2013.11.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 11/13/2013] [Accepted: 11/20/2013] [Indexed: 02/07/2023]
Abstract
X-linked ichthyosis is a relatively common syndromic form of ichthyosis most often due to deletions in the gene encoding the microsomal enzyme, steroid sulfatase, located on the short area of the X chromosome. Syndromic features are mild or unapparent unless contiguous genes are affected. In normal epidermis, cholesterol sulfate is generated by cholesterol sulfotransferase (SULT2B1b), but desulfated in the outer epidermis, together forming a 'cholesterol sulfate cycle' that potently regulates epidermal differentiation, barrier function and desquamation. In XLI, cholesterol sulfate levels my exceed 10% of total lipid mass (≈1% of total weight). Multiple cellular and biochemical processes contribute to the pathogenesis of the barrier abnormality and scaling phenotype in XLI. This article is part of a Special Issue entitled The Important Role of Lipids in the Epidermis and their Role in the Formation and Maintenance of the Cutaneous Barrier. Guest Editors: Kenneth R. Feingold and Peter Elias.
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Affiliation(s)
- Peter M Elias
- Dermatology Service, Department of Veterans Affairs Medical Center, and Department of Dermatology, University of California, San Francisco, CA USA.
| | - Mary L Williams
- Departments of Dermatology and Pediatrics, University of California, San Francisco, CA USA
| | - Eung-Ho Choi
- Department of Dermatology, Yonsei University, Wonju College of Medicine, Wonju, South Korea
| | - Kenneth R Feingold
- Medical Service, Department of Veterans Affairs Medical Center, and Department of Medicine, University of California, San Francisco, CA, USA
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Xp22.3 interstitial deletion: A recognizable chromosomal abnormality encompassing VCX3A and STS genes in a patient with X-linked ichthyosis and mental retardation. Gene 2013; 527:578-83. [DOI: 10.1016/j.gene.2013.06.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 06/06/2013] [Accepted: 06/07/2013] [Indexed: 12/18/2022]
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Trent S, Davies W. Cognitive, behavioural and psychiatric phenotypes associated with steroid sulfatase deficiency. World J Transl Med 2013; 2:1-12. [DOI: 10.5528/wjtm.v2.i1.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/24/2013] [Accepted: 02/08/2013] [Indexed: 02/05/2023] Open
Abstract
The enzyme steroid sulfatase (STS) desulfates a variety of steroid compounds thereby altering their activity. STS is expressed in the skin, and its deficiency in this tissue has been linked to the dermatological condition X-linked ichthyosis. STS is also highly expressed in the developing and adult human brain, and in a variety of steroidogenic organs (including the placenta and gonads); therefore it has the potential to influence brain development and function directly and/or indirectly (through influencing the hormonal milieu). In this review, we first discuss evidence from human and animal model studies suggesting that STS deficiency might predispose to neurobehavioural abnormalities and certain psychiatric disorders. We subsequently discuss potential mechanisms that may underlie these vulnerabilities. The data described herein have potential implications for understanding the complete spectrum of clinical phenotypes associated with X-linked ichthyosis, and may indicate novel pathogenic mechanisms underlying psychological dysfunction in developmental disorders such as attention deficit hyperactivity disorder and Turner syndrome.
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Bardoni B, Abekhoukh S, Zongaro S, Melko M. Intellectual disabilities, neuronal posttranscriptional RNA metabolism, and RNA-binding proteins: three actors for a complex scenario. PROGRESS IN BRAIN RESEARCH 2012; 197:29-51. [PMID: 22541287 DOI: 10.1016/b978-0-444-54299-1.00003-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intellectual disability (ID) is the most frequent cause of serious handicap in children and young adults and interests 2-3% of worldwide population, representing a serious problem from the medical, social, and economic points of view. The causes are very heterogeneous. Genes involved in ID have various functions altering different pathways important in neuronal function. Regulation of mRNA metabolism is particularly important in neurons for synaptic structure and function. Here, we review ID due to alteration of mRNA metabolism. Functional absence of some RNA-binding proteins--namely, FMRP, FMR2P, PQBP1, UFP3B, VCX-A--causes different forms of ID. These proteins are involved in different steps of RNA metabolism and, even if a detailed analysis of their RNA targets has been performed so far only for FMRP, it appears clear that they modulate some aspects (translation, stability, transport, and sublocalization) of a subset of RNAs coding for proteins, whose function must be relevant for neurons. Two other proteins, DYRK1A and CDKL5, involved in Down syndrome and Rett syndrome, respectively, have been shown to have an impact on splicing efficiency of specific mRNAs. Both proteins are kinases and their effect is indirect. Interestingly, both are localized in nuclear speckles, the nuclear domains where splicing factors are assembled, stocked, and recycled and influence their biogenesis and/or their organization.
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Affiliation(s)
- Barbara Bardoni
- Institute of Molecular and Cellular Pharmacology, CNRS-UMR6097, Université de Nice Sophia-Antipolis,Valbonne, France.
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Yuan ZQ, Zhao BS, Zhang JY. Expression patterns of the STAG gene in intact and regenerating planarians (Dugesia japonica). GENETICS AND MOLECULAR RESEARCH 2011; 10:410-8. [PMID: 21425091 DOI: 10.4238/vol10-1gmr1042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We examined the spatial and temporal expression of the planarian Dugesia japonica STAG-related gene (DjStag), in both intact and regenerating planarians, by whole-mount in situ hybridization and relative quantitative real-time PCR. The first localized transcripts of DjStag were detected in the blastemas three days after amputation, in all regenerates including those from head, tail and trunk pieces. The maximum level of expression of DjStag transcripts occurred at five days after cutting. After regeneration for seven days, DjStag was weakly expressed. A similar decrease occurs regardless of the orientation of the cut. The expression pattern did not differ significantly in the different types of regeneration. Relative quantitative real-time PCR analysis of DjStag mRNA indicated that the expression of DjStag mRNA was increased after amputation compared to that in normal intact planarians, and the maximum level of expression of DjStag transcripts occurred at five days after amputation. All results suggest that DjStag, implicated in planarian regeneration, plays a role in maintaining the ability of pluripotent stem cells to regenerate lost tissue in planarians.
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Affiliation(s)
- Z Q Yuan
- Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo, PR China
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Colak D, Al-Dhalaan H, Nester M, Albakheet A, Al-Younes B, Al-Hassnan Z, Al-Dosari M, Chedrawi A, Al-Owain M, Abudheim N, Al-Alwan L, Al-Odaib A, Ozand P, Inan MS, Kaya N. Genomic and transcriptomic analyses distinguish classic Rett and Rett-like syndrome and reveals shared altered pathways. Genomics 2010; 97:19-28. [PMID: 20934504 DOI: 10.1016/j.ygeno.2010.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/20/2010] [Accepted: 09/24/2010] [Indexed: 11/24/2022]
Abstract
Rett syndrome (RTT) is an X-linked neurodevelopmental disorder characterized by derangements in nervous system especially in cognition and behavior. The present study aims to understand the molecular underpinnings of two subtypes of RTT, classic RTT and Rett-like, and to elucidate common pathways giving rise to common RTT phenotype using genomic and transcriptomic approaches. Mutation screening on selected nuclear genes revealed only MECP2 mutations in a subset of classic RTT patients. MLPA assays and mtDNA screenings were all negative. Genome-wide copy number analysis indicated a novel duplication on X chromosome. Transcriptional profiling revealed blood gene signatures that clearly distinguish classic RTT and RTT-like patients, as well as shared altered pathways in interleukin-4 and NF-κB signaling pathways in both subtypes of the syndrome. To our knowledge, this is the first report on investigating common regulatory mechanisms/signaling pathways that may be relevant to the pathobiology of the "common RTT" phenotype.
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Affiliation(s)
- Dilek Colak
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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Li Y, Kiledjian M. Regulation of mRNA decapping. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:253-65. [PMID: 21935889 DOI: 10.1002/wrna.15] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Decapping is a critical step in the control of mRNA stability and the regulation of gene expression. Two major decapping enzymes involved in mRNA turnover have been identified, each functioning in one of the two exonucleolytic mRNA decay pathways in eukaryotic cells. The Dcp2 protein cleaves capped mRNA and initiates 5' to 3' degradation; the scavenger decapping enzyme, DcpS, hydrolyzes the cap structure generated by the 3' to 5' decay pathway. Consistent with the important role of decapping in gene expression, cap hydrolysis is exquisitely controlled by multiple regulators that influence association with the cap and the catalytic step. In this review, we will discuss the functions of the two different decapping enzymes, their regulation by cis-elements and trans-factors, and the potential role of the decapping enzymes in human neurological disorders.
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Affiliation(s)
- You Li
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854-8082, USA
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Li F, Shen Y, Köhler U, Sharkey FH, Menon D, Coulleaux L, Malan V, Rio M, McMullan DJ, Cox H, Fagan KA, Gaunt L, Metcalfe K, Heinrich U, Hislop G, Maye U, Sutcliffe M, Wu BL, Thiel BD, Mulchandani S, Conlin LK, Spinner NB, Murphy KM, Batista DAS. Interstitial microduplication of Xp22.31: Causative of intellectual disability or benign copy number variant? Eur J Med Genet 2010; 53:93-9. [PMID: 20132918 DOI: 10.1016/j.ejmg.2010.01.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 01/23/2010] [Indexed: 12/16/2022]
Abstract
The use of comparative genomic hybridization (CGH) and single nucleotide polymorphism (SNP) arrays has dramatically altered the approach to identification of genetic alterations that can explain intellectual disability and /or congenital anomalies. However, the discovery of numerous copy number changes with benign or unknown clinical significance has made interpretation problematic. Submicroscopic duplication of Xp22.31 has been reported as either a possible cause of intellectual disability and/or developmental delay or a benign variant. Here we report 29 individuals with the microduplication found as part of microarray analysis of 7793 samples submitted to an international group of 13 clinical laboratories. The referral reasons varied and included developmental delay, intellectual disability, autism, dysmorphic features and/or multiple congenital anomalies. The size of the Xp22.31 duplication varied between 149 kb and 1.74 Mb and included the steroid sulfatase (STS) gene with the male to female ratio of 0.7. Duplication within this segment is seen at a frequency of 0.15% in a healthy control population, whereas a frequency of 0.37% was observed in our cohort of individuals with abnormal phenotypes. We present a detailed comparison of the breakpoints, inheritance, X-inactivation and clinical phenotype in our cohort and a review of the literature for a total of 41 patients. To date, this report is the largest compilation of clinical and array data regarding the microduplication of Xp22.31 and will serve to broaden the knowledge of regions involving copy number variation (CNV).
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Affiliation(s)
- Feng Li
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
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Langlois S, Armstrong L, Gall K, Hulait G, Livingston J, Nelson T, Power P, Pugash D, Siciliano D, Steinraths M, Mattman A. Steroid sulfatase deficiency and contiguous gene deletion syndrome amongst pregnant patients with low serum unconjugated estriols. Prenat Diagn 2009; 29:966-74. [PMID: 19609942 DOI: 10.1002/pd.2326] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
OBJECTIVE To ascertain all prenatally diagnosed cases of Steroid Sulfatase (STS) deficiency in British Columbia between August 2002 and July 2007 to determine the incidence of this condition, the clinical and laboratory findings, and the risk of a contiguous gene deletion syndrome. METHODS We reviewed the medical records of these patients to obtain detailed information about the maternal serum screening results, family history, investigations performed, and outcome of the pregnancy. RESULTS Thirty pregnant patients were found to have a male fetus/infant with STS deficiency, giving a minimal estimated incidence of this condition of approximately 1 in 1513 males. In twenty nine cases, this condition was isolated. One patient was found to have a contiguous gene deletion syndrome. In cases of sporadic STS deficiency diagnosed prenatally, the frequency of contiguous gene deletion syndrome in this study was 1 out of 12 (8.3%). CONCLUSION The clinical, cytogenetic and molecular data on this series of prenatally diagnosed cases of STS deficiency indicates that this is a common condition and in cases with no family history, the risk of contiguous gene deletion syndrome is significant, and warrants additional molecular genetic investigations of the mother and/or fetus.
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Affiliation(s)
- Sylvie Langlois
- Medical Genetics, University of British Columbia, Vancouver, Canada.
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Abstract
Posttranscriptional regulation is an important control mechanism governing gene expression in neurons. We recently demonstrated that VCX-A, a protein implicated in X-linked mental retardation, is an RNA-binding protein that specifically binds the 5' end of capped mRNAs to prevent their decapping and decay. Previously, expression of VCX-A was reported to be testes restricted. Consistent with a role in cognitive function, we demonstrate that VCX-A is ubiquitously expressed in human tissues including the brain. Moreover, retinoic acid-induced differentiation of human SH-SY5Y neuroblastoma cells promoted the accumulation of VCX-A in distinct cytoplasmic foci within neurites that colocalize with staufen1-containing RNA granules, suggesting a role in translational suppression and/or mRNA transport. Exogenous expression of VCX-A in rat primary hippocampal neurons, which normally do not express the primate-restricted VCX proteins, promoted neurite arborization, and shRNA-directed knockdown of the VCX genes in SH-SY5Y cells resulted in a reduction of both primary and secondary neurite projections upon differentiation. We propose that the cap-binding property of VCX-A reflects a role of this protein in mRNA translational regulation. In support of this hypothesized role, we demonstrate that VCX-A can specifically bind a subset of mRNAs involved in neuritogenesis and is also capable of promoting translational silencing. Thus, VCX-A contains the capacity to modulate the stability and translation of a subset of target mRNAs involved in neuronal differentiation and arborization. It is plausible that defects of these functions in the absence of the VCX genes could contribute to a mental retardation phenotype.
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Cuevas-Covarrubias SA, González-Huerta LM. Analysis of the VCX3A, VCX2 and VCX3B genes shows that VCX3A gene deletion is not sufficient to result in mental retardation in X-linked ichthyosis. Br J Dermatol 2007; 158:483-6. [PMID: 18076704 DOI: 10.1111/j.1365-2133.2007.08373.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND X-linked ichthyosis (XLI), an inborn error of metabolism, is due to steroid sulphatase (STS) deficiency. Most patients with XLI harbour complete deletion of the STS gene and flanking sequences. The presence of low copy number repeats on either side of the STS gene seems to have a major role in the high frequency of these deletions. Some patients with XLI with terminal deletions of Xp22.3 involving marker DXS1139 and the STS gene show mental retardation (MR); VCX3A is the only gene located on this critical region. OBJECTIVES To analyse the VCX3A, VCX, VCX2 and VCX3B genes in 80 unrelated Mexican patients with XLI with normal intelligence. METHODS STS activity was measured in the leucocytes using 7-[3H]-dehydroepiandrosterone sulphate as a substrate. Amplification of the regions from telomeric DXS89 to centromeric DXS1134 including both extremes of the STS and the VCX3A, VCX, VCX2 and VCX3B genes was performed using polymerase chain reaction. RESULTS No STS activity was detected in the patients with XLI (0.00 pmol mg(-1) protein h(-1)). We observed two different deletion patterns: the first group included 62 patients with deletion of VCX3A and VCX genes. The second group included 18 patients with breakpoints at several regions on either side of the STS gene not including the VCX3A gene. CONCLUSIONS These data indicate that more complex mechanisms, apart from possible VCX3A gene participation, are occurring in the genesis of MR in XLI, at least in the sample of Mexican patients analysed.
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Affiliation(s)
- S A Cuevas-Covarrubias
- Servicio de Genética, Hospital General de México, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr Balmis 148, Col. Doctores C.P. 06726, México D.F., Mexico.
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