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Alexandrou A, Papaevripidou I, Tsangaras K, Alexandrou I, Tryfonidis M, Christophidou-Anastasiadou V, Zamba-Papanicolaou E, Koumbaris G, Neocleous V, Phylactou LA, Skordis N, Tanteles GA, Sismani C. Identification of a novel 15.5 kb SHOX deletion associated with marked intrafamilial phenotypic variability and analysis of its molecular origin. J Genet 2017; 95:839-845. [PMID: 27994182 DOI: 10.1007/s12041-016-0698-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Haploinsufficiency of the short stature homeobox contaning SHOX gene has been shown to result in a spectrum of phenotypes ranging from Leri-Weill dyschondrosteosis (LWD) at the more severe end to SHOX-related short stature at the milder end of the spectrum. Most alterations are whole gene deletions, point mutations within the coding region, or microdeletions in its flanking sequences. Here, we present the clinical and molecular data as well as the potential molecular mechanism underlying a novel microdeletion, causing a variable SHOX-related haploinsufficiency disorder in a three-generation family. The phenotype resembles that of LWD in females, in males, however, the phenotypic expression is milder. The 15523-bp SHOX intragenic deletion, encompassing exons 3-6, was initially detected by array-CGH, followed by MLPA analysis. Sequencing of the breakpoints indicated an Alu recombination-mediated deletion (ARMD) as the potential causative mechanism.
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Affiliation(s)
- Angelos Alexandrou
- Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus.
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Identification of 15 novel partial SHOX deletions and 13 partial duplications, and a review of the literature reveals intron 3 to be a hotspot region. J Hum Genet 2016; 62:229-234. [PMID: 27604558 DOI: 10.1038/jhg.2016.113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/29/2016] [Accepted: 08/02/2016] [Indexed: 12/31/2022]
Abstract
Short stature homeobox gene (SHOX) is located in the pseudoautosomal region 1 of the sex chromosomes. It encodes a transcription factor implicated in the skeletal growth. Point mutations, deletions or duplications of SHOX or its transcriptional regulatory elements are associated with two skeletal dysplasias, Léri-Weill dyschondrosteosis (LWD) and Langer mesomelic dysplasia (LMD), as well as in a small proportion of idiopathic short stature (ISS) individuals. We have identified a total of 15 partial SHOX deletions and 13 partial SHOX duplications in LWD, LMD and ISS patients referred for routine SHOX diagnostics during a 10 year period (2004-2014). Subsequently, we characterized these alterations using MLPA (multiplex ligation-dependent probe amplification assay), fine-tiling array CGH (comparative genomic hybridation) and breakpoint PCR. Nearly half of the alterations have a distal or proximal breakpoint in intron 3. Evaluation of our data and that in the literature reveals that although partial deletions and duplications only account for a small fraction of SHOX alterations, intron 3 appears to be a breakpoint hotspot, with alterations arising by non-allelic homologous recombination, non-homologous end joining or other complex mechanisms.
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Marchini A, Ogata T, Rappold GA. A Track Record on SHOX: From Basic Research to Complex Models and Therapy. Endocr Rev 2016; 37:417-48. [PMID: 27355317 PMCID: PMC4971310 DOI: 10.1210/er.2016-1036] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SHOX deficiency is the most frequent genetic growth disorder associated with isolated and syndromic forms of short stature. Caused by mutations in the homeobox gene SHOX, its varied clinical manifestations include isolated short stature, Léri-Weill dyschondrosteosis, and Langer mesomelic dysplasia. In addition, SHOX deficiency contributes to the skeletal features in Turner syndrome. Causative SHOX mutations have allowed downstream pathology to be linked to defined molecular lesions. Expression levels of SHOX are tightly regulated, and almost half of the pathogenic mutations have affected enhancers. Clinical severity of SHOX deficiency varies between genders and ranges from normal stature to profound mesomelic skeletal dysplasia. Treatment options for children with SHOX deficiency are available. Two decades of research support the concept of SHOX as a transcription factor that integrates diverse aspects of bone development, growth plate biology, and apoptosis. Due to its absence in mouse, the animal models of choice have become chicken and zebrafish. These models, therefore, together with micromass cultures and primary cell lines, have been used to address SHOX function. Pathway and network analyses have identified interactors, target genes, and regulators. Here, we summarize recent data and give insight into the critical molecular and cellular functions of SHOX in the etiopathogenesis of short stature and limb development.
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Affiliation(s)
- Antonio Marchini
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Tsutomu Ogata
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Gudrun A Rappold
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
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4
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Tropeano M, Howley D, Gazzellone MJ, Wilson CE, Ahn JW, Stavropoulos DJ, Murphy CM, Eis PS, Hatchwell E, Dobson RJB, Robertson D, Holder M, Irving M, Josifova D, Nehammer A, Ryten M, Spain D, Pitts M, Bramham J, Asherson P, Curran S, Vassos E, Breen G, Flinter F, Ogilvie CM, Collier DA, Scherer SW, McAlonan GM, Murphy DG. Microduplications at the pseudoautosomal SHOX locus in autism spectrum disorders and related neurodevelopmental conditions. J Med Genet 2016; 53:536-47. [PMID: 27073233 DOI: 10.1136/jmedgenet-2015-103621] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/10/2016] [Indexed: 11/04/2022]
Abstract
BACKGROUND The pseudoautosomal short stature homeobox-containing (SHOX) gene encodes a homeodomain transcription factor involved in cell-cycle and growth regulation. SHOX/SHOX enhancers deletions cause short stature and skeletal abnormalities in a female-dominant fashion; duplications appear to be rare. Neurodevelopmental disorders (NDDs), such as autism spectrum disorders (ASDs), are complex disorders with high heritability and skewed sex ratio; several rare (<1% frequency) CNVs have been implicated in risk. METHODS We analysed data from a discovery series of 90 adult ASD cases, who underwent clinical genetic testing by array-comparative genomic hybridisation (CGH). Twenty-seven individuals harboured CNV abnormalities, including two unrelated females with microduplications affecting SHOX. To determine the prevalence of SHOX duplications and delineate their associated phenotypic spectrum, we subsequently examined array-CGH data from a follow-up sample of 26 574 patients, including 18 857 with NDD (3541 with ASD). RESULTS We found a significant enrichment of SHOX microduplications in the NDD cases (p=0.00036; OR 2.21) and, particularly, in those with ASD (p=9.18×10(-7); OR 3.63) compared with 12 594 population-based controls. SHOX duplications affecting the upstream or downstream enhancers were enriched only in females with NDD (p=0.0043; OR 2.69/p=0.00020; OR 7.20), but not in males (p=0.404; OR 1.38/p=0.096; OR 2.21). CONCLUSIONS Microduplications at the SHOX locus are a low penetrance risk factor for ASD/NDD, with increased risk in both sexes. However, a concomitant duplication of SHOX enhancers may be required to trigger a NDD in females. Since specific SHOX isoforms are exclusively expressed in the developing foetal brain, this may reflect the pathogenic effect of altered SHOX protein dosage on neurodevelopment.
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Affiliation(s)
- Maria Tropeano
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, CS, Italy
| | - Deirdre Howley
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Matthew J Gazzellone
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - C Ellie Wilson
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK Individual Differences, Language and Cognition Lab, Department of Developmental and Educational Psychology, University of Seville, Seville, Spain
| | - Joo Wook Ahn
- Department of Cytogenetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Clodagh M Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK
| | - Peggy S Eis
- Population Diagnostics, Inc., Melville, New York, USA
| | - Eli Hatchwell
- Population Diagnostics, Inc., Melville, New York, USA
| | - Richard J B Dobson
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Dene Robertson
- Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK
| | - Muriel Holder
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Melita Irving
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dragana Josifova
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Annelise Nehammer
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Mina Ryten
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Debbie Spain
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Mark Pitts
- Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK
| | - Jessica Bramham
- UCD School of Psychology, University College Dublin, Dublin, Ireland
| | - Philip Asherson
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Sarah Curran
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Evangelos Vassos
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Frances Flinter
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - David A Collier
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Discovery Neuroscience Research, Eli Lilly and Company Ltd, Erl Wood Manor, Windlesham, Surrey, UK
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Grainne M McAlonan
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Declan G Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
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Ratan SK, Sharma A, Kapoor S, Polipalli SK, Dubey D, Mishra TK, Sinha SK, Agarwal SK. Polymorphism of 3' UTR of MAMLD1 gene is also associated with increased risk of isolated hypospadias in Indian children: a preliminary report. Pediatr Surg Int 2016; 32:515-24. [PMID: 26815876 DOI: 10.1007/s00383-016-3856-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/05/2016] [Indexed: 01/30/2023]
Abstract
OBJECTIVE To study MAMLD1 gene polymorphisms, serum LH and testosterone levels amongst Indian children with isolated hypospadias (IH) and controls. MATERIALS AND METHODS Screening of the MAMLD1 gene was performed by PCR sequencing method in 100 Indian children aged 0-12 years presenting with IH and 100 controls. LH and testosterone hormone levels were also assessed (categorized in four age-wise groups). RESULTS IH subjects had significantly higher incidence of MAMLD1 polymorphism as compared to controls (33 vs 15 %, p = 0.01). Of various genomic variants identified in this study, the noteworthy novel ones were missense mutation P299A and single nucleotide polymorphism c.2960C>T in 3' UTR of Exon 7. While p 299A was found to cause protein structural instability consequent to amino acid change, eighty percent subjects with c.2960C>T in 3' UTR of Exon 7 (corresponding to newly discovered currently non-validated exon 11) were found to have lower testosterone levels when compared with their age group mean. IH showed statistically higher incidence of c.2960C>T in comparison to controls (22 vs 10 %, p value 0.046) and about 2.5-folds higher risk of this anomaly. CONCLUSION Occurrence of MAMDL1 gene polymorphisms, specially of c.2960C>T in 3' UTR of its exon 7 is associated with a higher risk of IH in Indian children, probably by lowering androgenic levels.
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Affiliation(s)
- Simmi K Ratan
- Department of Pediatric Surgery, Maulana Azad Medical College and Associated LokNayak Hospital, G-8/6, Second Floor, Malviya Nagar, New Delhi, 110017, India.
| | - Anju Sharma
- Department of Biochemistry, Maulana Azad Medical College and Associated LokNayak Hospital, New Delhi, India
| | - Seema Kapoor
- Department of Pediatrics, Maulana Azad Medical College and Associated LokNayak Hospital, New Delhi, India
| | - Sunil K Polipalli
- Department of Biochemistry, Maulana Azad Medical College and Associated LokNayak Hospital, New Delhi, India
| | - Divya Dubey
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Tarun K Mishra
- Department of Biochemistry, Maulana Azad Medical College and Associated LokNayak Hospital, New Delhi, India
| | - Shandip K Sinha
- Department of Pediatric Surgery, Maulana Azad Medical College and Associated LokNayak Hospital, G-8/6, Second Floor, Malviya Nagar, New Delhi, 110017, India
| | - Satish K Agarwal
- Department of Pediatric Surgery, Maulana Azad Medical College and Associated LokNayak Hospital, G-8/6, Second Floor, Malviya Nagar, New Delhi, 110017, India
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6
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Fukami M, Seki A, Ogata T. SHOX Haploinsufficiency as a Cause of Syndromic and Nonsyndromic Short Stature. Mol Syndromol 2016; 7:3-11. [PMID: 27194967 DOI: 10.1159/000444596] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2016] [Indexed: 12/26/2022] Open
Abstract
SHOX in the short arm pseudoautosomal region (PAR1) of sex chromosomes is one of the major growth genes in humans. SHOX haploinsufficiency results in idiopathic short stature and Léri-Weill dyschondrosteosis and is associated with the short stature of patients with Turner syndrome. The SHOX protein likely controls chondrocyte apoptosis by regulating multiple target genes including BNP,Fgfr3, Agc1, and Ctgf. SHOX haploinsufficiency frequently results from deletions and duplications in PAR1 involving SHOX exons and/or the cis-acting enhancers, while exonic point mutations account for a small percentage of cases. The clinical severity of SHOX haploinsufficiency reflects hormonal conditions rather than mutation types. Growth hormone treatment seems to be beneficial for cases with SHOX haploinsufficiency, although the long-term outcomes of this therapy require confirmation. Future challenges in SHOX research include elucidating its precise function in the developing limbs, identifying additional cis-acting enhancers, and determining optimal therapeutic strategies for patients.
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Affiliation(s)
- Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Hamamatsu, Japan
| | - Atsuhito Seki
- Department of Orthopedic Surgery, National Center for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Hamamatsu, Japan; Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
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7
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Rare pseudoautosomal copy-number variations involving SHOX and/or its flanking regions in individuals with and without short stature. J Hum Genet 2015; 60:553-6. [PMID: 26040210 DOI: 10.1038/jhg.2015.53] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/21/2015] [Accepted: 04/20/2015] [Indexed: 02/07/2023]
Abstract
Pseudoautosomal region 1 (PAR1) contains SHOX, in addition to seven highly conserved non-coding DNA elements (CNEs) with cis-regulatory activity. Microdeletions involving SHOX exons 1-6a and/or the CNEs result in idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD). Here, we report six rare copy-number variations (CNVs) in PAR1 identified through copy-number analyzes of 245 ISS/LWD patients and 15 unaffected individuals. The six CNVs consisted of three microduplications encompassing SHOX and some of the CNEs, two microduplications in the SHOX 3'-region affecting one or four of the downstream CNEs, and a microdeletion involving SHOX exon 6b and its neighboring CNE. The amplified DNA fragments of two SHOX-containing duplications were detected at chromosomal regions adjacent to the original positions. The breakpoints of a SHOX-containing duplication resided within Alu repeats. A microduplication encompassing four downstream CNEs was identified in an unaffected father-daughter pair, whereas the other five CNVs were detected in ISS patients. These results suggest that microduplications involving SHOX cause ISS by disrupting the cis-regulatory machinery of this gene and that at least some of microduplications in PAR1 arise from Alu-mediated non-allelic homologous recombination. The pathogenicity of other rare PAR1-linked CNVs, such as CNE-containing microduplications and exon 6b-flanking microdeletions, merits further investigation.
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Seki A, Jinno T, Suzuki E, Takayama S, Ogata T, Fukami M. Skeletal Deformity Associated with SHOX Deficiency. Clin Pediatr Endocrinol 2014; 23:65-72. [PMID: 25110390 PMCID: PMC4125598 DOI: 10.1297/cpe.23.65] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 04/18/2014] [Indexed: 02/03/2023] Open
Abstract
SHOX haploinsufficiency due to mutations in the coding exons or microdeletions involving the coding exons and/or the enhancer regions accounts for approximately 80% and 2-16% of genetic causes of Leri-Weill dyschondrosteosis and idiopathic short stature, respectively. The most characteristic feature in patients with SHOX deficiency is Madelung deformity, a cluster of anatomical changes in the wrist that can be attributed to premature epiphyseal fusion of the distal radius. Computed tomography of SHOX-deficient patients revealed a thin bone cortex and an enlarged total bone area at the diaphysis of the radius, while histopathological analyses showed a disrupted columnar arrangement of chondrocytes and an expanded hypertrophic layer of the growth plate. Recent studies have suggested that perturbed programmed cell death of hypertrophic chondrocytes may underlie the skeletal changes related to SHOX deficiency. Furthermore, the formation of an aberrant ligament tethering the lunate and radius has been implicated in the development of Madelung deformity. Blood estrogen levels and mutation types have been proposed as phenotypic determinants of SHOX deficiency, although other unknown factors may also affect clinical severity of this entity.
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Affiliation(s)
- Atsuhito Seki
- Department of Orthopedic Surgery, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoko Jinno
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Erina Suzuki
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shinichiro Takayama
- Department of Orthopedic Surgery, National Center for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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Gatta V, Palka C, Chiavaroli V, Franchi S, Cannataro G, Savastano M, Cotroneo AR, Chiarelli F, Mohn A, Stuppia L. Spectrum of phenotypic anomalies in four families with deletion of the SHOX enhancer region. BMC MEDICAL GENETICS 2014; 15:87. [PMID: 25056248 PMCID: PMC4112833 DOI: 10.1186/1471-2350-15-87] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/08/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND SHOX alterations have been reported in 67% of patients affected by Léri-Weill dyschondrosteosis (LWD), with a larger prevalence of gene deletions than point mutations. It has been recently demonstrated that these deletions can involve the SHOX enhancer region, rather that the coding region, with variable phenotype of the affected patients.Here, we report a SHOX gene analysis carried out by MLPA in 14 LWD patients from 4 families with variable phenotype. CASE PRESENTATION All patients presented a SHOX enhancer deletion. In particular, a patient with a severe bilateral Madelung deformity without short stature showed a homozygous alteration identical to the recently described 47.5 kb PAR1 deletion. Moreover, we identified, for the first time, in three related patients with a severe bilateral Madelung deformity, a smaller deletion than the 47.5 kb PAR1 deletion encompassing the same enhancer region (ECR1/CNE7). CONCLUSIONS Data reported in this study provide new information about the spectrum of phenotypic alterations showed by LWD patients with different deletions of the SHOX enhancer region.
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Affiliation(s)
- Valentina Gatta
- Department of Psychological, Humanities and Territory Sciences, School of Medicine and Health Sciences, "G, d'Annunzio" University of Chieti, via dei Vestini 31, 66013 Chieti, Italy.
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10
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Tsuchiya T, Shibata M, Numabe H, Jinno T, Nakabayashi K, Nishimura G, Nagai T, Ogata T, Fukami M. Compound heterozygous deletions in pseudoautosomal region 1 in an infant with mild manifestations of langer mesomelic dysplasia. Am J Med Genet A 2013; 164A:505-10. [PMID: 24311385 DOI: 10.1002/ajmg.a.36284] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 09/13/2013] [Indexed: 11/11/2022]
Abstract
Haploinsufficiency of SHOX on the short arm pseudoautosomal region (PAR1) leads to Leri-Weill dyschondrosteosis (LWD), and nullizygosity of SHOX results in Langer mesomelic dysplasia (LMD). Molecular defects of LWD/LMD include various microdeletions in PAR1 that involve exons and/or the putative upstream or downstream enhancer regions of SHOX, as well as several intragenic mutations. Here, we report on a Japanese male infant with mild manifestations of LMD and hitherto unreported microdeletions in PAR1. Clinical analysis revealed mesomelic short stature with various radiological findings indicative of LMD. Molecular analyses identified compound heterozygous deletions, that is, a maternally inherited ∼46 kb deletion involving the upstream region and exons 1-5 of SHOX, and a paternally inherited ∼500 kb deletion started from a position ∼300 kb downstream from SHOX. In silico analysis revealed that the downstream deletion did not affect the known putative enhancer regions of SHOX, although it encompassed several non-coding elements which were well conserved among various species with SHOX orthologs. These results provide the possibility of the presence of a novel enhancer for SHOX in the genomic region ∼300 to ∼800 kb downstream of the start codon.
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Affiliation(s)
- Takayoshi Tsuchiya
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan; Department of Pediatrics, Dokkyo Medical University Koshigaya Hospital, Koshigaya, Japan
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11
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Sandoval GTV, Jaimes GC, Barrios MC, Cespedes C, Velasco HM. SHOX gene and conserved noncoding element deletions/duplications in Colombian patients with idiopathic short stature. Mol Genet Genomic Med 2013; 2:95-102. [PMID: 24689071 PMCID: PMC3960050 DOI: 10.1002/mgg3.39] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 11/06/2022] Open
Abstract
SHOX gene mutations or haploinsufficiency cause a wide range of phenotypes such as Leri Weill dyschondrosteosis (LWD), Turner syndrome, and disproportionate short stature (DSS). However, this gene has also been found to be mutated in cases of idiopathic short stature (ISS) with a 3–15% frequency. In this study, the multiplex ligation-dependent probe amplification (MLPA) technique was employed to determine the frequency of SHOX gene mutations and their conserved noncoding elements (CNE) in Colombian patients with ISS. Patients were referred from different centers around the county. From a sample of 62 patients, 8.1% deletions and insertions in the intragenic regions and in the CNE were found. This result is similar to others published in other countries. Moreover, an isolated case of CNE 9 duplication and a new intron 6b deletion in another patient, associated with ISS, are described. This is one of the first studies of a Latin American population in which deletions/duplications of the SHOX gene and its CNE are examined in patients with ISS.
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Affiliation(s)
| | | | - Mauricio Coll Barrios
- Department of Pediatrics, Hospital De La Misericordia, Universidad Nacional De Colombia Colombia
| | - Camila Cespedes
- Department of Pediatrics, Hospital San Ignacio, Pontificia Universidad Javeriana Colombia
| | - Harvy Mauricio Velasco
- Institute of Genetics, School of Medicine, Master in Human Genetics, Universidad Nacional de Colombia Colombia
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Stuppia L, Antonucci I, Palka G, Gatta V. Use of the MLPA assay in the molecular diagnosis of gene copy number alterations in human genetic diseases. Int J Mol Sci 2012; 13:3245-3276. [PMID: 22489151 PMCID: PMC3317712 DOI: 10.3390/ijms13033245] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 11/16/2022] Open
Abstract
Multiplex Ligation-dependent Probe Amplification (MLPA) assay is a recently developed technique able to evidence variations in the copy number of several human genes. Due to this ability, MLPA can be used in the molecular diagnosis of several genetic diseases whose pathogenesis is related to the presence of deletions or duplications of specific genes. Moreover, MLPA assay can also be used in the molecular diagnosis of genetic diseases characterized by the presence of abnormal DNA methylation. Due to the large number of genes that can be analyzed by a single technique, MLPA assay represents the gold standard for molecular analysis of all pathologies derived from the presence of gene copy number variation. In this review, the main applications of the MLPA technique for the molecular diagnosis of human diseases are described.
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Affiliation(s)
- Liborio Stuppia
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Ivana Antonucci
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Giandomenico Palka
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Valentina Gatta
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
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Dateki S, Fukami M, Uematsu A, Kaji M, Iso M, Ono M, Mizota M, Yokoya S, Motomura K, Kinoshita E, Moriuchi H, Ogata T. Mutation and gene copy number analyses of six pituitary transcription factor genes in 71 patients with combined pituitary hormone deficiency: identification of a single patient with LHX4 deletion. J Clin Endocrinol Metab 2010; 95:4043-7. [PMID: 20534763 DOI: 10.1210/jc.2010-0150] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT Mutations of multiple transcription factor genes involved in pituitary development have been identified in a minor portion of patients with combined pituitary hormone deficiency (CPHD). However, copy number aberrations involving such genes have been poorly investigated in patients with CPHD. OBJECTIVE We aimed to report the results of mutation and gene copy number analyses in patients with CPHD. SUBJECTS AND METHODS Seventy-one Japanese patients with CPHD were examined for mutations and gene copy number aberrations affecting POU1F1, PROP1, HESX1, LHX3, LHX4, and SOX3 by PCR-direct sequencing and multiplex ligation-dependent probe amplification. When a deletion was indicated, it was further studied by fluorescence in situ hybridization, oligoarray comparative genomic hybridization, and serial sequencing for long PCR products encompassing the deletion junction. RESULTS We identified a de novo heterozygous 522,009-bp deletion involving LHX4 in a patient with CPHD (GH, TSH, PRL, LH, and FSH deficiencies), anterior pituitary hypoplasia, ectopic posterior pituitary, and underdeveloped sella turcica. We also identified five novel heterozygous missense substitutions (p.V201I and p.H387P in LHX4, p.T63M and p.A322T in LHX3, and p.V53L in SOX3) that were assessed as rare variants by sequencing analyses for control subjects and available parents and by functional studies and in silico analyses. CONCLUSIONS The results imply the rarity of abnormalities affecting the six genes in patients with CPHD and the significance of the gene copy number analysis in such patients.
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Affiliation(s)
- Sumito Dateki
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development, 2-10-1 Ohkura, Setagaya, Tokyo 157-8535, Japan
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Funari MFA, Jorge AAL, Souza SCAL, Billerbeck AEC, Arnhold IJP, Mendonca BB, Nishi MY. Usefulness of MLPA in the detection of SHOX deletions. Eur J Med Genet 2010; 53:234-8. [PMID: 20538086 DOI: 10.1016/j.ejmg.2010.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 06/01/2010] [Indexed: 12/18/2022]
Abstract
SHOX haploinsufficiency causes a wide spectrum of short stature phenotypes, such as Leri-Weill dyschondrosteosis (LWD) and disproportionate short stature (DSS). SHOX deletions are responsible for approximately two thirds of isolated haploinsufficiency; therefore, it is important to determine the most appropriate methodology for detection of gene deletion. In this study, three methodologies for the detection of SHOX deletions were compared: the fluorescence in situ hybridization (FISH), microsatellite analysis and multiplex ligation-dependent probe amplification (MLPA). Forty-four patients (8 LWD and 36 DSS) were analyzed. The cosmid LLNOYCO3'M'34F5 was used as a probe for the FISH analysis and microsatellite analysis were performed using three intragenic microsatellite markers. MLPA was performed using commercial kits. Twelve patients (8 LWD and 4 DSS) had deletions in SHOX area detected by MLPA and 2 patients generated discordant results with the other methodologies. In the first case, the deletion was not detected by FISH. In the second case, both FISH and microsatellite analyses were unable to identify the intragenic deletion. In conclusion, MLPA was more sensitive, less expensive and less laborious; therefore, it should be used as the initial molecular method for the detection of SHOX gene deletion.
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Affiliation(s)
- Mariana F A Funari
- Unidade de Endocrinologia do Desenvolvimento, Hospital das Clinicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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Funari MFA, Jorge AAL, Pinto EM, Arnhold IJP, Mendonca BB, Nishi MY. Cryptic intragenic deletion of the SHOX gene in a family with Léri-Weill dyschondrosteosis detected by Multiplex Ligation-Dependent Probe Amplification (MLPA). ACTA ACUST UNITED AC 2009; 52:1382-7. [PMID: 19169498 DOI: 10.1590/s0004-27302008000800029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 10/02/2008] [Indexed: 11/22/2022]
Abstract
LWD is associated to SHOX haploinsufficiency, in most cases, due to gene deletion. Generally FISH and microsatellite analysis are used to identify SHOX deletion. MLPA is a new method of detecting gene copy variation, allowing simultaneous analysis of several regions. Here we describe the presence of a SHOX intragenic deletion in a family with LWD, analyzed through different methodologies. Genomic DNA of 11 subjects from one family were studied by microsatellite analysis, direct sequencing and MLPA. FISH was performed in two affected individuals. Microsatellite analysis showed that all affected members shared the same haplotype suggesting the involvement of SHOX. MLPA detected an intragenic deletion involving exons IV-VIa, which was not detected by FISH and microsatellite analysis. In conclusion, the MLPA technique was proved to be the best solution on detecting this small deletion, it has the advantage of being less laborious also allowing the analysis of several regions simultaneously.
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Thomas NS, Harvey JF, Bunyan DJ, Rankin J, Grigelioniene G, Bruno DL, Tan TY, Tomkins S, Hastings R. Clinical and molecular characterization of duplications encompassing the human SHOX gene reveal a variable effect on stature. Am J Med Genet A 2009; 149A:1407-14. [PMID: 19533800 DOI: 10.1002/ajmg.a.32914] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Deletions of the SHOX gene are well documented and cause disproportionate short stature and variable skeletal abnormalities. In contrast interstitial SHOX duplications limited to PAR1 appear to be very rare and the clinical significance of the only case report in the literature is unclear. Mapping of this duplication has now shown that it includes the entire SHOX gene but little flanking sequence and so will not encompass any of the long-range enhancers required for SHOX transcription. We now describe the clinical and molecular characterization of three additional cases. The duplications all included the SHOX coding sequence but varied in the amount of flanking sequence involved. The probands were ascertained for a variety of reasons: hypotonia and features of Asperger syndrome, Leri-Weill dyschondrosteosis (LWD), and a family history of cleft palate. However, the presence of a duplication did not correlate with any of these features or with evidence of skeletal abnormality. Remarkably, the proband with LWD had inherited both a SHOX deletion and a duplication. The effect of the duplications on stature was variable: height appeared to be elevated in some carriers, particularly in those with the largest duplications, but was still within the normal range. SHOX duplications are likely to be under ascertained and more cases need to be identified and characterized in detail in order to accurately determine their phenotypic consequences.
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Affiliation(s)
- N Simon Thomas
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK.
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