1
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Miranda V, Sabeh P, Seiltgens C, Molidperee S, Janelle C, Lemyre E, Campeau PM. Mild phenotypes in patients with different deletions in the 3' enhancer region of SHOX. Eur J Hum Genet 2024:10.1038/s41431-024-01646-3. [PMID: 38914686 DOI: 10.1038/s41431-024-01646-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/06/2024] [Accepted: 06/08/2024] [Indexed: 06/26/2024] Open
Abstract
Haploinsufficiency of the short stature homeobox-containing (SHOX) gene leads to a phenotypic spectrum ranging from Leri-Weill dyschondrosteosis (LWD) to SHOX-deficient short stature. SHOX nullizygosity leads to Langer mesomelic dysplasia. Pathogenic variants can include whole or partial gene deletions or duplications, point mutations within the coding sequence, and deletions of upstream and downstream regulatory elements. Here we report two families: a non-consanguineous family with a deletion downstream of SHOX, in which the homozygous proband presented with isolated Madelung deformity, without LWD or short stature, as well as a 9-year-old girl with Madelung deformities, mesomelia, a dominant family history of Madelung deformity and a heterozygous deletion of the CNE9 region in the 3' downstream region of SHOX. These case reports provide additional information on the effects of 3' downstream deletions of SHOX, by demonstrating the limited phenotype associated with the recurrent 47.5 kb deletion in a homozygous state and the CNE9 deletion in a heterozygous state.
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Affiliation(s)
- Valancy Miranda
- Shriners Hospital for Children, Montreal, QC, Canada
- Sainte Justine University Health Centre, Montreal, QC, Canada
| | - Pascale Sabeh
- Sainte Justine University Health Centre, Montreal, QC, Canada
| | | | | | - Chantal Janelle
- Shriners Hospital for Children, Montreal, QC, Canada
- Sainte Justine University Health Centre, Montreal, QC, Canada
| | | | - Philippe M Campeau
- Shriners Hospital for Children, Montreal, QC, Canada.
- Sainte Justine University Health Centre, Montreal, QC, Canada.
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2
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Cai M, Chen X, Li Y, Lin N, Huang H, Xu L. Genetic analysis, ultrasound phenotype, and pregnancy outcomes of fetuses with Xp22.33 or Yp11.32 microdeletions. J Perinat Med 2024; 52:96-101. [PMID: 37846158 DOI: 10.1515/jpm-2023-0190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/27/2023] [Indexed: 10/18/2023]
Abstract
OBJECTIVES The phenotypes of Xp22.33 or Yp11.32 microdeletions comprising the short-stature homeobox (SHOX) gene have been extensively described in adults and children. Herein, the prenatal ultrasound phenotype and pregnancy outcomes of fetuses with Xp22.33/Yp11.32 microdeletions were analyzed to improve our understanding, diagnosis, and monitoring of this genetic condition in the fetal stage. METHODS A total of 9,100 pregnant women referred to tertiary units for prenatal diagnosis were evaluated by chromosomal microarray analysis(CMA). RESULTS Seven (0.08 %) fetuses had Xp22.33/Yp11.32 microdeletions, ranging from 243 kb to 1.1 Mb, that comprised SHOX. The ultrasonic phenotypes differed among these fetuses, with three fetuses presenting abnormal bone development, one had labial-palatal deformity and strawberry head, two had an abnormal ultrasonic soft marker, and one had no abnormalities. After genetic counseling, only one couple underwent pedigree assessment, which confirmed the paternal origin of the microdeletion. This infant presented delayed speech development, whereas other three infants showed a typical postnatal development. In three cases, the parents chose to terminate the pregnancy. CONCLUSIONS The ultrasonic phenotype of fetuses with Xp22.33/Yp11.32 microdeletions resulting in SHOX heterozygosity loss is variable. Prenatal CMA can quickly and effectively diagnose Xp22.33/Yp11.32 microdeletions and SHOX loss, which may help prenatal counseling.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
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3
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Spurná Z, Čapková P, Punová L, DuchoslavovÁ J, Aleksijevic D, Venháčová P, Srovnal J, Štellmachová J, Curtisová V, Bitnerová V, Petřková J, Kolaříková K, Janíková M, Kratochvílová R, Vrtěl P, Vodička R, Vrtěl R, Zapletalová J. Clinical-genetic analysis of selected genes involved in the development of the human skeleton in 128 Czech patients with suspected congenital skeletal abnormalities. Gene 2024; 892:147881. [PMID: 37806643 DOI: 10.1016/j.gene.2023.147881] [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: 06/01/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Congenital skeletal abnormalities are a heterogeneous group of diseases most commonly associated with small or disproportionate growth, cranial and facial dysmorphisms, delayed bone maturation, etc. Nonetheless, no detailed genotype-phenotype correlation in patients with specific genetic variants is readily available. Ergo, this study focuses on the analysis of patient phenotypes with candidate variants in genes involved in bone growth as detected by molecular genetic analysis. METHODS In this study we used molecular genetic methods to analyse the ACAN, COL2A1, FGFR3, IGFALS, IGF1, IGF1R, GHR, NPR2, STAT5B and SHOX genes in 128 Czech children with suspected congenital skeletal abnormalities. Pathogenic variants and variants of unclear clinical significance were identified and we compared their frequency in this study cohort to the European non-Finnish population. Furthermore, a prediction tool was utilised to determine their possible impact on the final protein. All clinical patient data was obtained during pre-test genetic counselling. RESULTS Pathogenic variants were identified in the FGFR3, GHR, COL2A1 and SHOX genes in a total of six patients. Furthermore, we identified 23 variants with unclear clinical significance and high allelic frequency in this cohort of patients with skeletal abnormalities. Five of them have not yet been reported in the scientific literature. CONCLUSION Congenital skeletal abnormalities may lead to a number of musculoskeletal, neurological, cardiovascular problems. Knowledge of specific pathogenic variants may help us in therapeutic procedures.
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Affiliation(s)
- Z Spurná
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - P Čapková
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic.
| | - L Punová
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - J DuchoslavovÁ
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - D Aleksijevic
- Paediatrics Department, Palacký University and University Hospital, Olomouc, Czech Republic
| | - P Venháčová
- Paediatrics Department, Palacký University and University Hospital, Olomouc, Czech Republic
| | - J Srovnal
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic; Institute of Molecular and Translational Medicine, Czech Advanced Technology and Research Institute, Palacky University in Olomouc, Czech Republic; Cancer Research Czech Republic, Olomouc, Czech Republic
| | - J Štellmachová
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - V Curtisová
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - V Bitnerová
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - J Petřková
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; First Department of Internal Medicine - Cardiology, University Hospital Olomouc, Olomouc, Czech Republic; First Department of Internal Medicine - Cardiology, Palacký University in Olomouc, Olomouc, Czech Republic; Institute of Pathological Physiology, Palacký University in Olomouc, Olomouc, Czech Republic
| | - K Kolaříková
- Department of Neurology, University Hospital Olomouc, Czech Republic; Department of Neurology, Palacky University Olomouc, Czech Republic
| | - M Janíková
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic; Institute of Clinical and Molecular Pathology, Palacký University in Olomouc, Olomouc, Czech Republic
| | - R Kratochvílová
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic
| | - P Vrtěl
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - R Vodička
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - R Vrtěl
- Institute of Medical Genetics, Olomouc University Hospital, Olomouc, Czech Republic; Institute of Medical Genetics, Palacký University in Olomouc, Olomouc, Czech Republic
| | - J Zapletalová
- Paediatrics Department, Palacký University and University Hospital, Olomouc, Czech Republic
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4
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Bunyan DJ, Hobbs JI, Duncan-Flavell PJ, Howarth RJ, Beal S, Baralle D, Thomas NS. SHOX Whole Gene Duplications Are Overrepresented in SHOX Haploinsufficiency Phenotype Cohorts. Cytogenet Genome Res 2023; 162:587-598. [PMID: 36927524 DOI: 10.1159/000530171] [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: 12/19/2022] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Transcription of SHOX is dependent upon the interaction of the gene with a complex array of flanking regulatory elements. Duplications that contain flanking regulatory elements but not the SHOX gene have been reported in individuals with SHOX haploinsufficiency syndromes, suggesting that alterations to the physical organisation or genomic architecture may affect SHOX transcription. Individuals with tall stature and an additional X or Y chromosome have an extra copy of both the SHOX gene and the entire SHOX regulatory region, so all three copies of SHOX can be expressed fully. However, for a duplication of the SHOX gene that does not include all of the flanking regulatory elements, the potential effect on SHOX expression is difficult to predict. We present nine unpublished individuals with a SHOX whole gene duplication in whom the duplication contains variable amounts of the SHOX regulatory region, and we review 29 similar cases from the literature where phenotypic data were clearly stated. While tall stature was present in a proportion of these cases, we present evidence that SHOX whole gene duplications can also result in a phenotype more typically associated with SHOX haploinsufficiency and are significantly overrepresented in Leri-Weill dyschondrosteosis and idiopathic short stature probands compared to population controls. Although similar-looking duplications do not always produce a consistent phenotype, there may be potential genotype-phenotype correlations regarding the duplication size, regulatory element content, and the breakpoint proximity to the SHOX gene. Although ClinGen does not currently consider SHOX whole gene duplications to be clinically significant, the ClinGen triplosensitivity score does not take into account the context of the duplication, and more is now known about SHOX duplications and the role of flanking elements in SHOX regulation. The evidence presented here suggests that these duplications should not be discounted without considering the extent of the duplication and the patient phenotype, and should be included in diagnostic laboratory reports as variants of uncertain significance. Given the uncertain pathogenicity of these duplications, any reports should encourage the exclusion of all other causes of short stature where possible.
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Affiliation(s)
- David J Bunyan
- Wessex Genomics Laboratory Service, Salisbury District Hospital, Salisbury, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - James I Hobbs
- Wessex Genomics Laboratory Service, Salisbury District Hospital, Salisbury, UK
| | | | - Rachel J Howarth
- Wessex Genomics Laboratory Service, Salisbury District Hospital, Salisbury, UK
| | - Sarah Beal
- Wessex Genomics Laboratory Service, Salisbury District Hospital, Salisbury, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Nicholas Simon Thomas
- Wessex Genomics Laboratory Service, Salisbury District Hospital, Salisbury, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
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5
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Fukami M, Shindo J, Ogata T, Kageyama I, Kamimaki T. SHOX far-downstream deletion in a patient with nonsyndromic short stature. Am J Med Genet A 2022; 188:2173-2177. [PMID: 35319168 DOI: 10.1002/ajmg.a.62734] [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: 01/05/2022] [Revised: 02/20/2022] [Accepted: 03/04/2022] [Indexed: 11/08/2022]
Abstract
Haploinsufficiency of SHOX represents one of the major genetic causes of nonsyndromic short stature. To date, eight DNA elements around SHOX exons have been proposed as putative enhancer regions. Although six copy-number variations (CNVs) downstream to the known enhancer regions have recently been identified in patients with short stature, the pathogenicity of these CNVs remains uncertain. Here, we identified a paternally derived SHOX far-downstream deletion in a boy. The deletion involved a ~100 kb genomic interval at a position >60 kb away from the known enhancer regions. The boy exhibited moderate short stature with nonspecific skeletal changes. The height of the father was within the normal range but lower than the mid-parental height. The deletion of the boy and the six previously reported CNVs mostly overlapped; however, all CNVs had unique breakpoints. The deletion of our case encompassed a ~30 kb genomic interval that has previously been associated with a 4C-seq peak, as well as several SHOX-regulatory SNPs/indels. These results indicate that the SHOX far-downstream region contains a novel cis-acting enhancer, whose deletion leads to nonsyndromic short stature of various degree. In addition, our data highlight genomic instability of SHOX-flanking regions that underlies diverse nonrecurrent CNVs.
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Affiliation(s)
- Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Junya Shindo
- Department of Pediatrics, Shizuoka City Shimizu Hospital, Shizuoka, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Hamamatsu Medical Center, Hamamatsu, Japan
| | - Ikuko Kageyama
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Kamimaki
- Department of Pediatrics, Shizuoka City Shimizu Hospital, Shizuoka, Japan
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6
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Bunyan DJ, Gevers E, Hobbs JI, Duncan-Flavell PJ, Howarth RJ, Holder-Espinasse M, Klee P, Van-Heurk R, Lemmens L, Carminho-Rodrigues MT, Mohamed Z, Goturu A, Hughes CR, Ajzensztejn M, Thomas NS. Rare dosage abnormalities flanking the SHOX gene. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00209-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Transcriptional regulation of the SHOX gene is highly complex. Much of our understanding has come from the study of copy number changes of conserved non-coding sequences both upstream and downstream of the gene. Downstream deletions have been frequently reported in patients with Leri–Weill dyschondrosteosis or idiopathic short stature. In contrast, there are only four cases in the literature of upstream deletions that remove regulatory elements. Although duplications flanking the SHOX gene have also been reported, their pathogenicity is more difficult to establish. To further evaluate the role of flanking copy number variants in SHOX-related disorders, we describe nine additional patients from a large SHOX diagnostic cohort.
Results
The nine cases presented here include five with duplications (two upstream of SHOX and three downstream), one with a downstream triplication and three with upstream deletions. Two of the deletions remove a single conserved non-coding element (CNE-3) while the third does not remove any known regulatory element but is just 4 kb upstream of SHOX, and the deleted region may be important in limb bud development. We also describe six families with novel sequence gains flanking SHOX. Three families had increased dosage of a proposed regulatory element approximately 380 kb downstream of SHOX (X:970,000), including one family with the first ever reported triplication of this region. One family had two in cis downstream duplications co-segregating with LWD, and the two others had a duplication of just the upstream SHOX regulatory element CNE-5.
Conclusions
This study further extends our knowledge of the range of variants that may potentially cause SHOX-related phenotypes and may aid in determining the clinical significance of similar variants.
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7
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Fanelli A, Vannelli S, Babu D, Mellone S, Cucci A, Monzani A, Al Essa W, Secco A, Follenzi A, Bellone S, Prodam F, Giordano M. Copy number variations residing outside the SHOX enhancer region are involved in Short Stature and Léri-Weill dyschondrosteosis. Mol Genet Genomic Med 2021; 10:e1793. [PMID: 34811950 PMCID: PMC8801136 DOI: 10.1002/mgg3.1793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 07/19/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background SHOX enhancer CNVs, affecting one or more of the seven recognized evolutionary conserved non‐coding elements (CNEs) represent one of the most frequent cause of SHOX‐haploinsufficiency. During the diagnostic workflow deletions/duplications have been identified downstream SHOX not including any of the these CNEs. Methods Fine tiling aCGH and breakpoint PCR were used to characterize the critical interval and to search for novel alterations in a cohort of selected patients. Results Screening of 252 controls provided evidence that duplications in this area represent likely benign variants whereas none of the deletions were detected. These findings suggested that other alterations relevant for SHOX‐haploinsufficiency might be missed by the standard diagnostic methods. To identify such undisclosed elements, the aCGH was used to reanalyze 52 unresolved cases with clinical features strongly suggestive of SHOX‐haploinsufficiency. This analysis followed by the screening of 210 patients detected two partially overlapping small deletions of ~12 and ~8 kb in four unrelated individuals, approximately 15 kb downstream SHOX, that were absent in 720 normal stature individuals. Conclusion Our results strengthen the hypothesis that alterations of yet unidentified cis‐regulatory elements residing outside those investigated through conventional methods, might explain the phenotype in ISS/LWD patients thus enlarging the spectrum of variants contributing to SHOX‐haploinsufficiency.
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Affiliation(s)
- Antonella Fanelli
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Silvia Vannelli
- Endocrinologia Pediatrica, Dipartimento di Pediatria e Specialità Pediatriche, Ospedale Regina Margherita, Citta della Salute e della Scienza, Torino, Italy
| | - Deepak Babu
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Simona Mellone
- Laboratorio di Genetica, S.C.D.U Biochimica Clinica, Azienda Ospedaliera Universitaria "Maggiore della Carità", Novara, Italy
| | - Alessia Cucci
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Alice Monzani
- Divisione di Pediatria, AOU "Maggiore della Carità", Novara, Italy
| | - Wael Al Essa
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Andrea Secco
- SC Pediatria e DEA Pediatrico, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Antonia Follenzi
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Simonetta Bellone
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy.,Divisione di Pediatria, AOU "Maggiore della Carità", Novara, Italy
| | - Flavia Prodam
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy.,Divisione di Endocrinologia, AOU "Maggiore della Carità", Novara, Italy
| | - Mara Giordano
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy.,Laboratorio di Genetica, S.C.D.U Biochimica Clinica, Azienda Ospedaliera Universitaria "Maggiore della Carità", Novara, Italy
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8
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Sadler B, Haller G, Antunes L, Nikolov M, Amarillo I, Coe B, Dobbs MB, Gurnett CA. Rare and de novo duplications containing SHOX in clubfoot. J Med Genet 2020; 57:851-857. [PMID: 32518174 PMCID: PMC7688552 DOI: 10.1136/jmedgenet-2020-106842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 11/12/2022]
Abstract
Introduction Congenital clubfoot is a common birth defect that affects at least 0.1% of all births. Nearly 25% cases are familial and the remaining are sporadic in inheritance. Copy number variants (CNVs) involving transcriptional regulators of limb development, including PITX1 and TBX4, have previously been shown to cause familial clubfoot, but much of the heritability remains unexplained. Methods Exome sequence data from 816 unrelated clubfoot cases and 2645 in-house controls were analysed using coverage data to identify rare CNVs. The precise size and location of duplications were then determined using high-density Affymetrix Cytoscan chromosomal microarray (CMA). Segregation in families and de novo status were determined using qantitative PCR. Results Chromosome Xp22.33 duplications involving SHOX were identified in 1.1% of cases (9/816) compared with 0.07% of in-house controls (2/2645) (p=7.98×10−5, OR=14.57) and 0.27% (38/13592) of Atherosclerosis Risk in Communities/the Wellcome Trust Case Control Consortium 2 controls (p=0.001, OR=3.97). CMA validation confirmed an overlapping 180.28 kb duplicated region that included SHOX exons as well as downstream non-coding regions. In four of six sporadic cases where DNA was available for unaffected parents, the duplication was de novo. The probability of four de novo mutations in SHOX by chance in a cohort of 450 sporadic clubfoot cases is 5.4×10–10. Conclusions Microduplications of the pseudoautosomal chromosome Xp22.33 region (PAR1) containing SHOX and downstream enhancer elements occur in ~1% of patients with clubfoot. SHOX and regulatory regions have previously been implicated in skeletal dysplasia as well as idiopathic short stature, but have not yet been reported in clubfoot. SHOX duplications likely contribute to clubfoot pathogenesis by altering early limb development.
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Affiliation(s)
- Brooke Sadler
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Gabe Haller
- Department of Orthopedic Surgery, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Lilian Antunes
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Momchil Nikolov
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Ina Amarillo
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Bradley Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew B Dobbs
- Department of Orthopedic Surgery, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Christina A Gurnett
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
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9
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Ogushi K, Muroya K, Shima H, Jinno T, Miyado M, Fukami M. SHOX far-downstream copy-number variations involving cis-regulatory nucleotide variants in two sisters with Leri-Weill dyschondrosteosis. Am J Med Genet A 2019; 179:1778-1782. [PMID: 31228230 DOI: 10.1002/ajmg.a.61275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/27/2019] [Accepted: 06/11/2019] [Indexed: 11/09/2022]
Abstract
SHOX haploinsufficiency leading to Leri-Weill dyschondrosteosis (LWD) and idiopathic short stature typically results from intragenic mutations or copy-number variations (CNVs) involving SHOX and/or its putative enhancer regions that are distributed in the genomic interval between 400 kb and 840 kb from Xpter/Ypter. Here, we report two sisters with LWD, who carried a deletion in the far-downstream region of SHOX. The 0.62 Mb deletion contained 50 single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels), whose genotypes were linked to SHOX expression levels in the Genotype-Tissue Expression portal. Notably, most of these SNPs/indels accumulated within a ~20 kb interval that was positioned ~900 kb away from Xpter/Ypter. These SNPs/indels showed similar minor allele frequencies, indicating that they reside within a haplotype block. The ~20 kb interval was not evolutionarily conserved; however, it was associated with the previously determined peak of chromosome conformation capture profiling (4C)-seq. Importantly, the deletion in the present cases partially overlapped with CNVs of three previous cases with skeletal deformity and/or short stature. The results indicate that far-downstream CNVs constitute rare genetic causes of SHOX haploinsufficiency. These CNVs possibly impair SHOX expression through copy-number changes of a human-specific cis-regulatory haplotype block. This notion awaits further validation.
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Affiliation(s)
- Kenichiro Ogushi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Koji Muroya
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hirohito Shima
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko Jinno
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Mami Miyado
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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10
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Ogushi K, Hattori A, Suzuki E, Shima H, Izawa M, Yagasaki H, Horikawa R, Uetake K, Umezawa A, Ishii T, Muroya K, Namba N, Tanaka T, Hirano Y, Yamamoto H, Soneda S, Matsubara K, Kagami M, Miyado M, Fukami M. DNA Methylation Status of SHOX-Flanking CpG Islands in Healthy Individuals and Short Stature Patients with Pseudoautosomal Copy Number Variations. Cytogenet Genome Res 2019; 158:56-62. [PMID: 31158835 DOI: 10.1159/000500468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2018] [Indexed: 11/19/2022] Open
Abstract
SHOX resides in the short arm pseudoautosomal region (PAR1) of the sex chromosomes and escapes X inactivation. SHOX haploinsufficiency underlies idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD). A substantial percentage of cases with SHOX haploinsufficiency arise from pseudoautosomal copy number variations (CNVs) involving putative enhancer regions of SHOX. Our previous study using peripheral blood samples showed that some CpG dinucleotides adjacent to SHOX exon 1 were hypomethylated in a healthy woman and methylated in a woman with gross X chromosomal rearrangements. However, it remains unknown whether submicroscopic pseudoautosomal CNVs cause aberrant DNA methylation of SHOX-flanking CpG islands. In this study, we examined the DNA methylation status of SHOX-flanking CpG islands in 50 healthy individuals and 10 ISS/LWD patients with pseudoautosomal CNVs. In silico analysis detected 3 CpG islands within the 20-kb region from the translation start site of SHOX. Pyrosequencing and bisulfite sequencing of genomic DNA samples revealed that these CpG islands were barely methylated in peripheral blood cells and cultured chondrocytes of healthy individuals, as well as in peripheral blood cells of ISS/LWD patients with pseudoautosomal CNVs. These results, in conjunction with our previous findings, indicate that the DNA methylation status of SHOX-flanking CpG islands can be affected by gross X-chromosomal abnormalities, but not by submicroscopic CNVs in PAR1. Such CNVs likely disturb SHOX expression through DNA methylation-independent mechanisms, which need to be determined in future studies.
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11
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Skuplik I, Benito-Sanz S, Rosin JM, Bobick BE, Heath KE, Cobb J. Identification of a limb enhancer that is removed by pathogenic deletions downstream of the SHOX gene. Sci Rep 2018; 8:14292. [PMID: 30250174 PMCID: PMC6155277 DOI: 10.1038/s41598-018-32565-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/11/2018] [Indexed: 01/06/2023] Open
Abstract
Haploinsufficiency of the human SHOX gene causes Léri-Weill dyschondrosteosis (LWD), characterized by shortening of the middle segments of the limbs and Madelung deformity of the wrist. As many as 35% of LWD cases are caused by deletions of non-coding sequences downstream of SHOX that presumably remove an enhancer or enhancers necessary for SHOX expression in developing limbs. We searched for these active sequences using a transgenic mouse assay and identified a 563 basepair (bp) enhancer with specific activity in the limb regions where SHOX functions. This enhancer has previously escaped notice because of its poor evolutionary conservation, although it does contain 100 bp that are conserved in non-rodent mammals. A primary cell luciferase assay confirmed the enhancer activity of the conserved core sequence and demonstrated that putative HOX binding sites are required for its activity. This enhancer is removed in most non-coding deletions that cause LWD. However, we did not identify any likely pathogenic variants of the enhancer in a screen of 124 LWD individuals for whom no causative mutation had been found, suggesting that only larger deletions in the region commonly cause LWD. We hypothesize that loss of this enhancer contributes to the pathogenicity of deletions downstream of SHOX.
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Affiliation(s)
- Isabella Skuplik
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada
| | - Sara Benito-Sanz
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ and Skeletal dysplasia multidisciplinary unit (UMDE), Hospital Universitario La Paz, Universidad Autónoma de Madrid, P° Castellana 261, 28046, Madrid, Spain.,CIBERER, ISCIII, Madrid, Spain
| | - Jessica M Rosin
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada
| | - Brent E Bobick
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada
| | - Karen E Heath
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ and Skeletal dysplasia multidisciplinary unit (UMDE), Hospital Universitario La Paz, Universidad Autónoma de Madrid, P° Castellana 261, 28046, Madrid, Spain. .,CIBERER, ISCIII, Madrid, Spain.
| | - John Cobb
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada.
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12
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Hirschfeldova K, Solc R. Comparison of SHOX and associated elements duplications distribution between patients (Lėri-Weill dyschondrosteosis/idiopathic short stature) and population sample. Gene 2017. [PMID: 28629824 DOI: 10.1016/j.gene.2017.06.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of heterozygous duplications of SHOX and associated elements on Lėri-Weill dyschondrosteosis (LWD) and idiopathic short stature (ISS) development is less distinct when compared to reciprocal deletions. The aim of our study was to compare frequency and distribution of duplications within SHOX and associated elements between population sample and LWD (ISS) patients. A preliminary analysis conducted on Czech population sample of 250 individuals compared to our previously reported sample of 352 ISS/LWD Czech patients indicated that rather than the difference in frequency of duplications it is the difference in their distribution. Particularly, there was an increased frequency of duplications residing to the CNE-9 enhancer in our LWD/ISS sample. To see whether the obtained data are consistent across published studies we made a literature survey to get published cases with SHOX or associated elements duplication and formed the merged LWD, the merged ISS, and the merged population samples. Relative frequency of particular region duplication in each of those merged samples were calculated. There was a significant difference in the relative frequency of CNE-9 enhancer duplications (11 vs. 3) and complete SHOX (exon1-6b) duplications (4 vs. 24) (p-value 0.0139 and p-value 0.000014, respectively) between the merged LWD sample and the merged population sample. We thus propose that partial SHOX duplications and small duplications encompassing CNE-9 enhancer could be highly penetrant alleles associated with ISS and LWD development.
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Affiliation(s)
- Katerina Hirschfeldova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00 Prague, Czech Republic.
| | - Roman Solc
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University in Prague, Vinicna 7, 128 43 Prague, Czech Republic.
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13
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Auger J, Baptiste A, Benabbad I, Thierry G, Costa JM, Amouyal M, Kottler ML, Leheup B, Touraine R, Schmitt S, Lebrun M, Cormier Daire V, Bonnefont JP, de Roux N, Elie C, Rosilio M. Genotype-Phenotype Relationship in Patients and Relatives with SHOX Region Anomalies in the French Population. Horm Res Paediatr 2017; 86:309-318. [PMID: 27676402 DOI: 10.1159/000448282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The aim of our study was to describe a large population with anomalies involving the SHOX region, responsible for idiopathic short stature and Léri-Weill dyschondrosteosis (LWD), and to identify a possible genotype/phenotype correlation. METHODS We performed a retrospective multicenter study on French subjects with a SHOX region anomaly diagnosed by multiplex ligation-dependent probe amplification or Sanger sequencing. Phenotypes were collected in each of the 7 genetic laboratories practicing this technique for SHOX analysis. RESULTS Among 205 index cases and 100 related cases, 91.3% had LWD. For index cases, median age at evaluation was 11.7 (9.0; 15.9) years and mean height standard deviation score was -2.3 ± 1.1. A deletion of either SHOX or PAR1 or both was found in 74% of patients. Duplications and point mutations/indels affected 8 and 18% of the population, respectively. Genotype-phenotype correlation showed that deletions were more frequently associated with Madelung deformity and mesomelic shortening in girls, as well as with presence of radiologic anomalies, than duplications. CONCLUSIONS Our results highlight genotype-phenotype relationships in the French population with a SHOX defect and provide new information showing that clinical expression is milder in cases of duplication compared to deletions.
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Affiliation(s)
- Julie Auger
- Department of Pediatrics and Medical Genetics, Brabois Hospital, Vandoeuvre-lès-Nancy, France
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14
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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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15
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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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16
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Shima H, Tanaka T, Kamimaki T, Dateki S, Muroya K, Horikawa R, Kanno J, Adachi M, Naiki Y, Tanaka H, Mabe H, Yagasaki H, Kure S, Matsubara Y, Tajima T, Kashimada K, Ishii T, Asakura Y, Fujiwara I, Soneda S, Nagasaki K, Hamajima T, Kanzaki S, Jinno T, Ogata T, Fukami M. Systematic molecular analyses of SHOX in Japanese patients with idiopathic short stature and Leri-Weill dyschondrosteosis. J Hum Genet 2016; 61:585-91. [PMID: 26984564 DOI: 10.1038/jhg.2016.18] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/09/2016] [Accepted: 02/15/2016] [Indexed: 02/07/2023]
Abstract
The etiology of idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD) in European patients is known to include SHOX mutations and copy-number variations (CNVs) involving SHOX and/or the highly evolutionarily conserved non-coding DNA elements (CNEs) flanking the gene. However, the frequency and types of SHOX abnormalities in non-European patients and the clinical importance of mutations in the CNEs remains to be clarified. Here, we performed systematic molecular analyses of SHOX for 328 Japanese patients with ISS or LWD. SHOX abnormalities accounted for 3.8% of ISS and 50% of LWD cases. CNVs around SHOX were identified in 16 cases, although the ~47 kb deletion frequently reported in European patients was absent in our cases. Probably damaging mutations and benign/silent substitutions were detected in four cases, respectively. Although CNE-linked substitutions were detected in 15 cases, most of them affected poorly conserved nucleotides and were shared by unaffected individuals. These results suggest that the frequency and mutation spectrum of SHOX abnormalities are comparable between Asian and European patients, with the exception of a European-specific downstream deletion. Furthermore, this study highlights the clinical importance and genetic heterogeneity of the SHOX-flanking CNVs, and indicates a limited clinical significance of point mutations in the CNEs.
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Affiliation(s)
- Hirohito Shima
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan
| | | | - Tsutomu Kamimaki
- Department of Pediatrics, Shizuoka City Shimizu Hospital, Shizuoka, Japan
| | - Sumito Dateki
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Koji Muroya
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Reiko Horikawa
- Division of Endocrinology and Metabolism, National Center for Child Health and Development, Tokyo, Japan
| | - Junko Kanno
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Masanori Adachi
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yasuhiro Naiki
- Division of Endocrinology and Metabolism, National Center for Child Health and Development, Tokyo, Japan
| | - Hiroyuki Tanaka
- Department of Pediatrics, Okayama Saiseikai General Hospital, Okayama, Japan
| | - Hiroyo Mabe
- Department of Child Development, Kumamoto University Hospital, Kumamoto, Japan
| | - Hideaki Yagasaki
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Chuo, Japan
| | - Shigeo Kure
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Yoichi Matsubara
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan.,National Research Institute for Child Health and Development, Tokyo, Japan
| | - Toshihiro Tajima
- Department of Pediatrics, Hokkaido University School of Medicine, Sapporo, Japan
| | - Kenichi Kashimada
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomohiro Ishii
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Yumi Asakura
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Ikuma Fujiwara
- Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shun Soneda
- Department of Pediatrics, St Marianna University School of Medicine, Kawasaki, Japan
| | - Keisuke Nagasaki
- Division of Pediatrics, Department of Homeostatic Regulation and Development, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Takashi Hamajima
- Division of Endocrinology and Metabolism, Aichi Children's Health and Medical Center, Obu, Japan
| | - Susumu Kanzaki
- Division of Pediatrics and Perinatology, Tottori University Faculty of Medicine, Yonago, Japan
| | - Tomoko Jinno
- Department of Molecular Endocrinology, National Research Institute 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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17
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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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18
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Bunyan DJ, Baffico M, Capone L, Vannelli S, Iughetti L, Schmitt S, Taylor EJ, Herridge AA, Shears D, Forabosco A, Coviello DA. Duplications upstream and downstream of SHOX identified as novel causes of Leri-Weill dyschondrosteosis or idiopathic short stature. Am J Med Genet A 2015; 170A:949-57. [PMID: 26698168 DOI: 10.1002/ajmg.a.37524] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/04/2015] [Indexed: 11/11/2022]
Abstract
Leri-Weill dyschondrosteosis is a pseudoautosomal dominantly-inherited skeletal dysplasia ascribed to haploinsufficiency of the SHOX gene caused by deletions, point mutations, or partial duplications of the gene, or to heterozygous deletions upstream or downstream of the intact SHOX gene involving conserved non-coding cis-regulatory DNA elements that show enhancer activity. Recently, two SHOX conserved non-coding element duplications, one upstream and one downstream, were reported in patients referred with idiopathic short stature. To further evaluate the role of these duplications in SHOX-related disorders, we describe seven patients (five with Leri-Weill dyschondrosteosis and two with short stature) all of whom have duplications of part of the upstream or downstream conserved non-coding element regions, identified by multiplex ligation-dependent probe amplification. In addition, we show data from 32 patients with an apparently identical downstream duplication that includes a proposed putative regulatory element (identified by multiplex ligation-dependent probe amplification or array comparative genome hybridization), which results in a variable phenotype from normal to mild Leri-Weill dyschondrosteosis. These additional data provide further evidence that duplications of upstream and downstream long range cis-regulatory DNA elements can result in a SHOX-related phenotype.
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Affiliation(s)
- David J Bunyan
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom
| | - Maria Baffico
- Laboratory of Human Genetics, E.O. Ospedali Galliera, Genoa, Italy
| | - Lucia Capone
- Genomic Research Center, Cante di Montevecchio, Fano PU, Italy
| | | | - Lorenzo Iughetti
- Department of Medical and Surgical Sciences of Mothers, Children, and Adults, University of Modena and Reggio Emilia, Modena MO, Italy
| | - Sébastien Schmitt
- Laboratory of Molecular Genetics, Institute of Biology, CHU de Nantes, Nantes, France
| | - Emma-Jane Taylor
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom
| | - Adam A Herridge
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom
| | - Deborah Shears
- Clinical Genetics, Churchill Hospital, Oxford, Oxfordshire, United Kingdom
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19
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Verdin H, Fernández-Miñán A, Benito-Sanz S, Janssens S, Callewaert B, De Waele K, De Schepper J, François I, Menten B, Heath KE, Gómez-Skarmeta JL, De Baere E. Profiling of conserved non-coding elements upstream of SHOX and functional characterisation of the SHOX cis-regulatory landscape. Sci Rep 2015; 5:17667. [PMID: 26631348 PMCID: PMC4668379 DOI: 10.1038/srep17667] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/02/2015] [Indexed: 02/07/2023] Open
Abstract
Genetic defects such as copy number variations (CNVs) in non-coding regions containing conserved non-coding elements (CNEs) outside the transcription unit of their target gene, can underlie genetic disease. An example of this is the short stature homeobox (SHOX) gene, regulated by seven CNEs located downstream and upstream of SHOX, with proven enhancer capacity in chicken limbs. CNVs of the downstream CNEs have been reported in many idiopathic short stature (ISS) cases, however, only recently have a few CNVs of the upstream enhancers been identified. Here, we set out to provide insight into: (i) the cis-regulatory role of these upstream CNEs in human cells, (ii) the prevalence of upstream CNVs in ISS, and (iii) the chromatin architecture of the SHOX cis-regulatory landscape in chicken and human cells. Firstly, luciferase assays in human U2OS cells, and 4C-seq both in chicken limb buds and human U2OS cells, demonstrated cis-regulatory enhancer capacities of the upstream CNEs. Secondly, CNVs of these upstream CNEs were found in three of 501 ISS patients. Finally, our 4C-seq interaction map of the SHOX region reveals a cis-regulatory domain spanning more than 1 Mb and harbouring putative new cis-regulatory elements.
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Affiliation(s)
- Hannah Verdin
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Ana Fernández-Miñán
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Sara Benito-Sanz
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.,Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
| | - Sandra Janssens
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | | | - Jean De Schepper
- Department of Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Inge François
- Department of Pediatric Endocrinology, University Hospitals Leuven, Leuven, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Karen E Heath
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.,Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
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