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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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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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3
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Hicks MR, Pyle AD. The emergence of the stem cell niche. Trends Cell Biol 2023; 33:112-123. [PMID: 35934562 PMCID: PMC9868094 DOI: 10.1016/j.tcb.2022.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 02/03/2023]
Abstract
Stem cell niches are composed of dynamic microenvironments that support stem cells over a lifetime. The emerging niche is distinct from the adult because its main role is to support the progenitors that build organ systems in development. Emerging niches mature through distinct stages to form the adult niche and enable proper stem cell support. As a model of emerging niches, this review highlights how differences in the skeletal muscle microenvironment influence emerging versus satellite cell (SC) niche formation in skeletal muscle, which is among the most regenerative tissue systems. We contrast how stem cell niches regulate intrinsic properties between progenitor and stem cells throughout development to adulthood. We describe new applications for generating emerging niches from human pluripotent stem cells (hPSCs) using developmental principles and highlight potential applications for regeneration and therapeutics.
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Affiliation(s)
- Michael R Hicks
- Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - April D Pyle
- Microbiology, Immunology, and Molecular Genetics, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA.
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4
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Gherlan I, Braha E, Manole D, Radomir L, Nedelcu I, Popa O, Schipor S. RARE DOSAGE ABNORMALITIES - COPY NUMBER VARIATIONS FLANKING THE SHOX GENE. ACTA ENDOCRINOLOGICA (BUCHAREST, ROMANIA : 2005) 2023; 19:115-124. [PMID: 37601716 PMCID: PMC10439321 DOI: 10.4183/aeb.2023.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Background Molecular defects in the SHOX gene including deletions, duplications or pathogenic point mutations are responsible for well-known pathologies involving short stature as a clinical manifestation: Léri-Weill dyschondrosteosis, Langer mesomelic dysplasia, Turner syndrome or idiopathic short stature. Duplications flanking the SHOX gene (upstream or downstream of the intact SHOX gene involving conserved non-coding cis-regulatory DNA elements - CNEs) have been described but their clinical involvement is still difficult to understand. Results We describe two cases with short stature and normal GH-IGF1 status. Multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (arrayCGH) identified in both cases heterozygous duplications involving downstream regions of SHOX gene, within CNEs (CNE8, CNE9 and CNE4, CNE5, CNE6, ECR1, CNE8, CNE9 and surrounding areas, respectively). One of the cases showed a maternally inherited duplication. Although every case has several particularities, we consider that duplications in these non-coding regions of SHOX gene may explain the short stature phenotype. Conclusion To our knowledge, these are the first Romanian-reported cases of ISS with a large duplication of downstream SHOX enhancers CNEs region. The spectrum of phenotypic consequences and the exact mechanism of the presumed clinical expression of these genetic alterations still needs to be evaluated and described.
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Affiliation(s)
- I. Gherlan
- Pediatric Endocrinology Department, “C.I. Parhon” National Institute of Endocrinology Bucharest, Romania
- “Carol Davila” University of Medicine and Pharmacy, Faculty of Dentistry, Bucharest, Romania
| | - E. Braha
- Research Department, “C.I. Parhon” National Institute of Endocrinology Bucharest, Romania
| | - D.C. Manole
- Pediatric Endocrinology Department, “C.I. Parhon” National Institute of Endocrinology Bucharest, Romania
| | - L. Radomir
- Pediatric Endocrinology Department, “C.I. Parhon” National Institute of Endocrinology Bucharest, Romania
| | - I. Nedelcu
- Research Department, “C.I. Parhon” National Institute of Endocrinology Bucharest, Romania
| | - O. Popa
- Research Department, “C.I. Parhon” National Institute of Endocrinology Bucharest, Romania
| | - S. Schipor
- Research Department, “C.I. Parhon” National Institute of Endocrinology Bucharest, Romania
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Soriano-Sexto A, Gallego D, Leal F, Castejón-Fernández N, Navarrete R, Alcaide P, Couce ML, Martín-Hernández E, Quijada-Fraile P, Peña-Quintana L, Yahyaoui R, Correcher P, Ugarte M, Rodríguez-Pombo P, Pérez B. Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism. Int J Mol Sci 2022; 23:ijms232112850. [PMID: 36361642 PMCID: PMC9654865 DOI: 10.3390/ijms232112850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/24/2022] Open
Abstract
Inborn errors of metabolism (IEM) constitute a huge group of rare diseases affecting 1 in every 1000 newborns. Next-generation sequencing has transformed the diagnosis of IEM, leading to its proposed use as a second-tier technology for confirming cases detected by clinical/biochemical studies or newborn screening. The diagnosis rate is, however, still not 100%. This paper reports the use of a personalized multi-omics (metabolomic, genomic and transcriptomic) pipeline plus functional genomics to aid in the genetic diagnosis of six unsolved cases, with a clinical and/or biochemical diagnosis of galactosemia, mucopolysaccharidosis type I (MPS I), maple syrup urine disease (MSUD), hyperphenylalaninemia (HPA), citrullinemia, or urea cycle deficiency. Eight novel variants in six genes were identified: six (four of them deep intronic) located in GALE, IDUA, PTS, ASS1 and OTC, all affecting the splicing process, and two located in the promoters of IDUA and PTS, thus affecting these genes’ expression. All the new variants were subjected to functional analysis to verify their pathogenic effects. This work underscores how the combination of different omics technologies and functional analysis can solve elusive cases in clinical practice.
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Affiliation(s)
- Alejandro Soriano-Sexto
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Diana Gallego
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Fátima Leal
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Natalia Castejón-Fernández
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Patricia Alcaide
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - María L. Couce
- Unit for the Diagnosis and Treatment of Congenital Metabolic Diseases, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, University of Santiago de Compostela, CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
| | - Elena Martín-Hernández
- Unidad de Enfermedades Mitocondriales-Metabólicas Hereditarias, Servicio de Pediatría, Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) para Enfermedades Metabólicas Hereditarias, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Pilar Quijada-Fraile
- Unidad de Enfermedades Mitocondriales-Metabólicas Hereditarias, Servicio de Pediatría, Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) para Enfermedades Metabólicas Hereditarias, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Luis Peña-Quintana
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, Complejo Hospitalario Universitario Insular Materno-Infantil (CHUIMI), Universidad de Las Palmas de Gran Canaria, Asociación Canaria para La Investigación Pediátrica, Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBEROBN) ISCIII, 35016 Gran Canaria, Spain
| | - Raquel Yahyaoui
- Laboratory of Metabolic Disorders and Newborn Screening, Institute of Biomedical Research in Málaga (IBIMA-Plafatorma BIONAND), IBIMA-RARE, Málaga Regional University Hospital, 29010 Málaga, Spain
| | - Patricia Correcher
- Nutrition and Metabolophaties Unit, Hospital Universitario La Fe, 46026 Valencia, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
- Correspondence:
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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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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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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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Identification of limb-specific Lmx1b auto-regulatory modules with Nail-patella syndrome pathogenicity. Nat Commun 2021; 12:5533. [PMID: 34545091 PMCID: PMC8452625 DOI: 10.1038/s41467-021-25844-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/31/2021] [Indexed: 01/18/2023] Open
Abstract
LMX1B haploinsufficiency causes Nail-patella syndrome (NPS; MIM 161200), characterized by nail dysplasia, absent/hypoplastic patellae, chronic kidney disease, and glaucoma. Accordingly in mice, Lmx1b has been shown to play crucial roles in the development of the limb, kidney and eye. Although one functional allele of Lmx1b appears adequate for development, Lmx1b null mice display ventral-ventral distal limbs with abnormal kidney, eye and cerebellar development, more disruptive, but fully concordant with NPS. In Lmx1b functional knockouts (KOs), Lmx1b transcription in the limb is decreased nearly 6-fold, indicating autoregulation. Herein, we report on two conserved Lmx1b-associated cis-regulatory modules (LARM1 and LARM2) that are bound by Lmx1b, amplify Lmx1b expression with unique spatial modularity in the limb, and are necessary for Lmx1b-mediated limb dorsalization. These enhancers, being conserved across vertebrates (including coelacanth, but not other fish species), and required for normal locomotion, provide a unique opportunity to study the role of dorsalization in the fin to limb transition. We also report on two NPS patient families with normal LMX1B coding sequence, but with loss-of-function variations in the LARM1/2 region, stressing the role of regulatory modules in disease pathogenesis. Nail-patella syndrome (NPS) is characterized by nail dysplasia, absent/hypoplastic patellae, chronic kidney disease, and glaucoma and can be caused by haploinsufficiency of LMX1B; however, not all patients harbor pathogenic LMX1B mutations. Here the authors show that loss-of-function variations in upstream enhancer sequences are responsible for a limb specific form of human NPS.
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Eid OM, Eid MM, Abdelrahman AH, Abdel kader RMA, Farid M, Mahrous R, Mekkawy MK, Kamel AK, Mazen I, El-Bassyouni HT. Screening of the SHOX/PAR1 region using MLPA and miRNA expression profiling in a group of Egyptian children with non-syndromic short stature. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00090-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Short stature is defined as a body height below the third percentile, based on chronological age, or 2 standard deviations (SD) below the national height standard. The prevalence of short stature is around 2% of children worldwide. Several gene deficiencies have been associated with the etiology of short stature. The SHOX is an important candidate gene for short stature, as its haploinsufficiency underlies syndromic and non-syndromic short stature. Partial and complete duplications of SHOX have been reported in patients with short stature. Proper genetic diagnosis of these children allows for appropriate therapeutic approaches to be administered. Since copy number variation (CNV) is a possible mechanism of interhuman variability and pathogenic disease, the multiplex ligation-dependent probe amplification technique (MLPA) can be used as an initial screening technique. Cartilage tissue expresses specific microRNAs (miRNAs), which play an essential role in the regulation of chondrocyte proliferation and differentiation during growth plate development. We aimed to assess the SHOX/PAR1 region using CNV profiling for non-syndromic short stature in Egyptian children with and without growth hormone deficiency using the MLPA technique and expression profiling of miR-1, miR-15a, and miR-140 using quantitative real-time polymerase chain reaction (qRT-PCR) in a group of Egyptian children with non-syndromic short stature.
Results
Of the fifty cases included in this study, different CNVs were detected in ten children (20%), in/outside the SHOX region. Moreover, in children with short stature, the expression level of miRNA-140 was significantly different from that of healthy controls.
Conclusions
This is one of the first studies that have assessed CNVs in the SHOX/PAR1 region in a group of Egyptian children with short stature. MLPA analysis of SHOX/PAR1 identified different CNVs in children with non-syndromic short stature, suggesting that the MLPA should be used as an initial screening technique in short children, as proper genetic diagnosis of these children leads to implementation of the appropriate therapeutic approach. Alterations in the levels of miRNA-140 in children with short stature suggest that changes in the expression levels of this miRNA are associated with the pathogenesis of short stature.
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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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Sun Y, Luo Y, Qian Y, Chen M, Wang L, Li H, Zou Y, Dong M. Heterozygous Deletion of the SHOX Gene Enhancer in two Females With Clinical Heterogeneity Associating With Skewed XCI and Escaping XCI. Front Genet 2019; 10:1086. [PMID: 31781162 PMCID: PMC6852097 DOI: 10.3389/fgene.2019.01086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022] Open
Abstract
Skewed X-chromosome inactivation (XCI) plays an important role in the phenotypic heterogeneity of X-linked disorders. However, the role of skewed XCI in XCI-escaping gene SHOX regulation is unclear. Here, we focused on a heterozygous deletion of SHOX gene enhancer with clinical heterogeneity. Using SNP array, we detected that the female proband with Leri-Weill dyschondrosteosis (LWD) carried an 857 kb deletion on Xp22.3 (encompassing SHOX enhancer) and a 5,707 kb large-fragment deletion on Xq25q26. XCI analysis revealed that the X-chromosome with the Xq25q26 large-fragment deletion was completely inactivated, which forced the complete activation of the other X-chromosome carrying SHOX enhancer deletion. While the Xp22.3 deletion locates on the escaping XCI region, under the combined action of skewed XCI and escaping XCI, transcription of SHOX gene was mainly from the activated X-chromosome with SHOX enhancer defect, involving in the formation of LWD phenotype. Interestingly, this SHOX enhancer deletion was inherited from her healthy mother, who also demonstrated completely skewed XCI. However, the X-chromosome with SHOX enhancer deletion was inactivated, and the normal X-chromosome was activated. Combing with escaping XCI, her phenotype was almost normal. In summary, this study was a rare report of SHOX gene enhancer deletion in a family with clinical heterogeneity due to skewed inactivation of different X-chromosomes, which can help in the genetic counseling and prenatal diagnosis of disorders in females with SHOX defect.
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Affiliation(s)
- Yixi Sun
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Yuqin Luo
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Yeqing Qian
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Min Chen
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Liya Wang
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Hongge Li
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Yu Zou
- Department of Diagnostic Radiology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Minyue Dong
- Department of Reproductive Genetics, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China.,Key Laboratory of Women's Reproductive Health of Zhejiang Province, Zhejiang University, Hangzhou, China
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Identification of rs11615992 as a novel regulatory SNP for human P2RX7 by allele-specific expression. Mol Genet Genomics 2019; 295:23-30. [PMID: 31410611 DOI: 10.1007/s00438-019-01598-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 07/26/2019] [Indexed: 12/12/2022]
Abstract
P2RX7 (purinergic receptor P2X 7) is an important membrane ion channel and involved in multiple physiological processes. One non-synonymous SNP on P2RX7, rs3751143, had been proven to reduce ion channel function and further associated with multiple diseases. However, it was still unclear whether there were other cis-regulatory elements for P2RX7, which might further contribute to related diseases. Allele-specific expression (ASE) is a robust and sensitive approach to identify the potential functional region in human genome. In the current study, we measured ASE on rs3751143 in lung tissues and observed a consistent excess of A allele over C (P = 0.001), which indicated that SNP(s) in linkage disequilibrium (LD) could regulate P2RX7 expression. By analyzing the 1000 genomes project data for Chinese, one SNP locating ~ 5 kb away and downstream of P2RX7, rs11615992, was disclosed to be in strong LD with rs3751143. The dual-luciferase assay confirmed that rs11615992 could alter target gene expression in lung cell line. Through chromosome conformation capture, it was verified that the region surrounding rs11615992 could interact with P2RX7 promoter and effect as an enhancer. By chromatin immunoprecipitation, the related transcription factor POU2F1 (POU class 2 homeobox 1) was recognized to bind the region spanning rs11615992. Our work identified a novel long-distance cis-regulatory SNP for P2RX7, which might contribute to multiple diseases.
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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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