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Weiss B, Ott T, Vick P, Lui JC, Roeth R, Vogel S, Waldmüller S, Hoffmann S, Baron J, Wit JM, Rappold GA. Identification of novel genes including NAV2 associated with isolated tall stature. Front Endocrinol (Lausanne) 2023; 14:1258313. [PMID: 38152138 PMCID: PMC10752378 DOI: 10.3389/fendo.2023.1258313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/07/2023] [Indexed: 12/29/2023] Open
Abstract
Very tall people attract much attention and represent a clinically and genetically heterogenous group of individuals. Identifying the genetic etiology can provide important insights into the molecular mechanisms regulating linear growth. We studied a three-generation pedigree with five isolated (non-syndromic) tall members and one individual with normal stature by whole exome sequencing; the tallest man had a height of 211 cm. Six heterozygous gene variants predicted as damaging were shared among the four genetically related tall individuals and not present in a family member with normal height. To gain insight into the putative role of these candidate genes in bone growth, we assessed the transcriptome of murine growth plate by microarray and RNA Seq. Two (Ift140, Nav2) of the six genes were well-expressed in the growth plate. Nav2 (p-value 1.91E-62) as well as Ift140 (p-value of 2.98E-06) showed significant downregulation of gene expression between the proliferative and hypertrophic zone, suggesting that these genes may be involved in the regulation of chondrocyte proliferation and/or hypertrophic differentiation. IFT140, NAV2 and SCAF11 have also significantly associated with height in GWAS studies. Pathway and network analysis indicated functional connections between IFT140, NAV2 and SCAF11 and previously associated (tall) stature genes. Knockout of the all-trans retinoic acid responsive gene, neuron navigator 2 NAV2, in Xenopus supports its functional role as a growth promotor. Collectively, our data expand the spectrum of genes with a putative role in tall stature phenotypes and, among other genes, highlight NAV2 as an interesting gene to this phenotype.
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Affiliation(s)
- Birgit Weiss
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Tim Ott
- Department of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Philipp Vick
- Department of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Julian C. Lui
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Ralph Roeth
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Sebastian Vogel
- Department of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Stephan Waldmüller
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Sandra Hoffmann
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Jeffrey Baron
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Jan M. Wit
- Division of Pediatric Endocrinology, Department of Pediatrics, Willem-Alexander Children’s Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Gudrun A. Rappold
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
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Vick P, Eberle B, Choukair D, Weiss B, Roeth R, Schneider I, Paramasivam N, Bettendorf M, Rappold GA. Identification of ZBTB26 as a Novel Risk Factor for Congenital Hypothyroidism. Genes (Basel) 2021; 12:genes12121862. [PMID: 34946811 PMCID: PMC8701029 DOI: 10.3390/genes12121862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
Congenital primary hypothyroidism (CH; OMIM 218700) is characterized by an impaired thyroid development, or dyshormonogenesis, and can lead to intellectual disability and growth retardation if untreated. Most of the children with congenital hypothyroidism present thyroid dysgenesis, a developmental anomaly of the thyroid. Various genes have been associated with thyroid dysgenesis, but all known genes together can only explain a small number of cases. To identify novel genetic causes for congenital hypothyroidism, we performed trio whole-exome sequencing in an affected newborn and his unaffected parents. A predicted damaging de novo missense mutation was identified in the ZBTB26 gene (Zinc Finger A and BTB Domain containing 26). An additional cohort screening of 156 individuals with congenital thyroid dysgenesis identified two additional ZBTB26 gene variants of unknown significance. To study the underlying disease mechanism, morpholino knock-down of zbtb26 in Xenopus laevis was carried out, which demonstrated significantly smaller thyroid anlagen in knock-down animals at tadpole stage. Marker genes expressed in thyroid tissue precursors also indicated a specific reduction in the Xenopus ortholog of human Paired-Box-Protein PAX8, a transcription factor required for thyroid development, which could be rescued by adding zbtb26. Pathway and network analysis indicated network links of ZBTB26 to PAX8 and other genes involved in thyroid genesis and function. GWAS associations of ZBTB26 were found with height. Together, our study added a novel genetic risk factor to the list of genes underlying congenital primary hypothyroidism and provides additional support that de novo mutations, together with inherited variants, might contribute to the genetic susceptibility to CH.
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Affiliation(s)
- Philipp Vick
- Department of Zoology, University of Hohenheim, 70599 Stuttgart, Germany; (P.V.); (I.S.)
| | - Birgit Eberle
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany; (B.E.); (B.W.); (R.R.)
| | - Daniela Choukair
- Division of Paediatric Endocrinology, Children’s Hospital, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany; (D.C.); (M.B.)
| | - Birgit Weiss
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany; (B.E.); (B.W.); (R.R.)
| | - Ralph Roeth
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany; (B.E.); (B.W.); (R.R.)
| | - Isabelle Schneider
- Department of Zoology, University of Hohenheim, 70599 Stuttgart, Germany; (P.V.); (I.S.)
| | - Nagarajan Paramasivam
- Computational Oncology Group, Molecular Diagnostics Program at the National Center for Tumor Diseases (NCT) and DKFZ (German Cancer Research Center), 69120 Heidelberg, Germany;
| | - Markus Bettendorf
- Division of Paediatric Endocrinology, Children’s Hospital, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany; (D.C.); (M.B.)
| | - Gudrun A. Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany; (B.E.); (B.W.); (R.R.)
- Correspondence: ; Tel.: +49-6221-56-5153
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Hoffmann S, Roeth R, Diebold S, Gogel J, Hassel D, Just S, Rappold GA. Identification and Tissue-Specific Characterization of Novel SHOX-Regulated Genes in Zebrafish Highlights SOX Family Members Among Other Genes. Front Genet 2021; 12:688808. [PMID: 34122528 PMCID: PMC8191631 DOI: 10.3389/fgene.2021.688808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/27/2021] [Indexed: 02/01/2023] Open
Abstract
SHOX deficiency causes a spectrum of clinical phenotypes related to skeletal dysplasia and short stature, including Léri-Weill dyschondrosteosis, Langer mesomelic dysplasia, Turner syndrome, and idiopathic short stature. SHOX controls chondrocyte proliferation and differentiation, bone maturation, and cellular growth arrest and apoptosis via transcriptional regulation of its direct target genes NPPB, FGFR3, and CTGF. However, our understanding of SHOX-related pathways is still incomplete. To elucidate the underlying molecular mechanisms and to better understand the broad phenotypic spectrum of SHOX deficiency, we aimed to identify novel SHOX targets. We analyzed differentially expressed genes in SHOX-overexpressing human fibroblasts (NHDF), and confirmed the known SHOX target genes NPPB and FGFR among the most strongly regulated genes, together with 143 novel candidates. Altogether, 23 genes were selected for further validation, first by whole-body characterization in developing shox-deficient zebrafish embryos, followed by tissue-specific expression analysis in three shox-expressing zebrafish tissues: head (including brain, pharyngeal arches, eye, and olfactory epithelium), heart, and pectoral fins. Most genes were physiologically relevant in the pectoral fins, while only few genes were also significantly regulated in head and heart tissue. Interestingly, multiple sox family members (sox5, sox6, sox8, and sox18) were significantly dysregulated in shox-deficient pectoral fins together with other genes (nppa, nppc, cdkn1a, cdkn1ca, cyp26b1, and cy26c1), highlighting an important role for these genes in shox-related growth disorders. Network-based analysis integrating data from the Ingenuity pathways revealed that most of these genes act in a common network. Our results provide novel insights into the genetic pathways and molecular events leading to the clinical manifestation of SHOX deficiency.
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Affiliation(s)
- Sandra Hoffmann
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Ralph Roeth
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany.,nCounter Core Facility, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Sabrina Diebold
- Clinic for Internal Medicine II - Molecular Cardiology, University Hospital Ulm, Ulm, Germany
| | - Jasmin Gogel
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - David Hassel
- Department of Internal Medicine III - Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Steffen Just
- Clinic for Internal Medicine II - Molecular Cardiology, University Hospital Ulm, Ulm, Germany
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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Choukair D, Eberle B, Vick P, Hermanns P, Weiss B, Paramasivam N, Schlesner M, Lornsen K, Roeth R, Klutmann C, Kreis J, Hoffmann GF, Pohlenz J, Rappold GA, Bettendorf M. Identification of Transient Receptor Potential Channel 4-Associated Protein as a Novel Candidate Gene Causing Congenital Primary Hypothyroidism. Horm Res Paediatr 2021; 93:16-29. [PMID: 32428920 DOI: 10.1159/000507114] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/10/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Congenital primary hypothyroidism (CH) is the most common endocrine disorder in neonates. METHODS To identify novel genes, we performed whole exome sequencing (WES) in 6 patients with CH due to thyroid dysgenesis (TD). The potential effects of the most relevant variants were analyzed using in silico prediction tools. The most promising candidate gene, transient receptor potential channel 4-associated protein (TRPC4AP), was sequenced in 179 further patients with TD. Expression of TRPC4AP in human thyroid was investigated using RT-PCR. Trpc4ap- functional analysis was performed in Xenopus laevis using Morpholino (MO) antisense oligomers. RESULTS WES identified a likely damaging mutation in TRPC4AP leading to a de novo stop codon p.Q552*. Targeted sequencing of TRPC4AP demonstrated gene variants with predicted damaging potential in 5 patients resulting each in an amino acid exchange (p.P706S, p.F729L, p.S777C, and p.N229S). We demonstrated that TRPC4AP is expressed in human thyroid gland tissue. Using Xenopus laevis, we showed that the volume of the tadpole thyroid anlage was reduced by 20% in Trpc4ap MO knockdowns compared to controls and by 41% in "Clustered Regularly Interspaced Short Palindromic Repeats"/Cas9-mediated gene knockout experiments. DISCUSSION A recognized interaction of TRPC4AP and the NF-kappa-B-essential-modulator encoded by IKBKG gene was identified by IPA analysis. IKBKG plays a role in activation of the NF-κB-signaling pathway and regulates genes involved in proliferation and survival of thyrocytes and expression of key enzymes of thyroid hormone synthesis. CONCLUSION TRPC4AP was identified as a novel candidate gene in TD, but further studies are needed to validate its role in thyroid function.
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Affiliation(s)
- Daniela Choukair
- Division of Paediatric Endocrinology, Children's Hospital, University of Heidelberg, Heidelberg, Germany,
| | - Birgit Eberle
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Philipp Vick
- Department of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Pia Hermanns
- Division of Paediatric Endocrinology, Children's Hospital, University of Mainz, Mainz, Germany
| | - Birgit Weiss
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Nagarajan Paramasivam
- Theoretical Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katharina Lornsen
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralph Roeth
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Carina Klutmann
- Division of Paediatric Endocrinology, Children's Hospital, University of Mainz, Mainz, Germany
| | - Jennifer Kreis
- Department of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Georg F Hoffmann
- Division of Paediatric Endocrinology, Children's Hospital, University of Heidelberg, Heidelberg, Germany
| | - Joachim Pohlenz
- Division of Paediatric Endocrinology, Children's Hospital, University of Mainz, Mainz, Germany
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Markus Bettendorf
- Division of Paediatric Endocrinology, Children's Hospital, University of Heidelberg, Heidelberg, Germany
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Weiss B, Eberle B, Roeth R, de Bruin C, Lui JC, Paramasivam N, Hinderhofer K, van Duyvenvoorde HA, Baron J, Wit JM, Rappold GA. Evidence That Non-Syndromic Familial Tall Stature Has an Oligogenic Origin Including Ciliary Genes. Front Endocrinol (Lausanne) 2021; 12:660731. [PMID: 34194391 PMCID: PMC8237855 DOI: 10.3389/fendo.2021.660731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Human growth is a complex trait. A considerable number of gene defects have been shown to cause short stature, but there are only few examples of genetic causes of non-syndromic tall stature. Besides rare variants with large effects and common risk alleles with small effect size, oligogenic effects may contribute to this phenotype. Exome sequencing was carried out in a tall male (height 3.5 SDS) and his parents. Filtered damaging variants with high CADD scores were validated by Sanger sequencing in the trio and three other affected and one unaffected family members. Network analysis was carried out to assess links between the candidate genes, and the transcriptome of murine growth plate was analyzed by microarray as well as RNA Seq. Heterozygous gene variants in CEP104, CROCC, NEK1, TOM1L2, and TSTD2 predicted as damaging were found to be shared between the four tall family members. Three of the five genes (CEP104, CROCC, and NEK1) belong to the ciliary gene family. All genes are expressed in mouse growth plate. Pathway and network analyses indicated close functional connections. Together, these data expand the spectrum of genes with a role in linear growth and tall stature phenotypes.
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Affiliation(s)
- Birgit Weiss
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht Karls University Heidelberg, Heidelberg, Germany
| | - Birgit Eberle
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht Karls University Heidelberg, Heidelberg, Germany
| | - Ralph Roeth
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht Karls University Heidelberg, Heidelberg, Germany
| | - Christiaan de Bruin
- Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Julian C. Lui
- Section on Growth and Development, National Institute of Health, Bethesda, MD, United States
| | - Nagarajan Paramasivam
- Computational Oncology Group, Molecular Diagnostics Program at the National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katrin Hinderhofer
- Institute of Human Genetics, Ruprecht Karls University Heidelberg, Heidelberg, Germany
| | | | - Jeffrey Baron
- Section on Growth and Development, National Institute of Health, Bethesda, MD, United States
| | - Jan M. Wit
- Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Gudrun A. Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht Karls University Heidelberg, Heidelberg, Germany
- *Correspondence: Gudrun A. Rappold,
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Hoffmann S, Paone C, Sumer SA, Diebold S, Weiss B, Roeth R, Clauss S, Klier I, Kääb S, Schulz A, Wild PS, Ghrib A, Zeller T, Schnabel RB, Just S, Rappold GA. Functional Characterization of Rare Variants in the SHOX2 Gene Identified in Sinus Node Dysfunction and Atrial Fibrillation. Front Genet 2019; 10:648. [PMID: 31354791 PMCID: PMC6637028 DOI: 10.3389/fgene.2019.00648] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/19/2019] [Indexed: 12/21/2022] Open
Abstract
Sinus node dysfunction (SND) and atrial fibrillation (AF) often coexist; however, the molecular mechanisms linking both conditions remain elusive. Mutations in the homeobox-containing SHOX2 gene have been recently associated with early-onset and familial AF. Shox2 is a key regulator of sinus node development, and its deficiency leads to bradycardia, as demonstrated in animal models. To provide an extended SHOX2 gene analysis in patients with distinct arrhythmias, we investigated SHOX2 as a susceptibility gene for SND and AF by screening 98 SND patients and 450 individuals with AF. The functional relevance of the novel mutations was investigated in vivo and in vitro, together with the previously reported p.H283Q variant. A heterozygous missense mutation (p.P33R) was identified in the SND cohort and four heterozygous variants (p.G77D, p.L129=, p.L130F, p.A293=) in the AF cohort. Overexpression of the pathogenic predicted mutations in zebrafish revealed pericardial edema for p.G77D and the positive control p.H283Q, whereas the p.P33R and p.A293= variants showed no effect. In addition, a dominant-negative effect with reduced heart rates was detected for p.G77D and p.H283Q. In vitro reporter assays demonstrated for both missense variants p.P33R and p.G77D significantly impaired transactivation activity, similar to the described p.H283Q variant. Also, a reduced Bmp4 target gene expression was revealed in zebrafish hearts upon overexpression of the p.P33R mutant. This study associates additional rare variants in the SHOX2 gene implicated in the susceptibility to distinct arrhythmias and allows frequency estimations in the AF cohort (3/990). We also demonstrate for the first time a genetic link between SND and AF involving SHOX2. Moreover, our data highlight the importance of functional investigations of rare variants.
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Affiliation(s)
- Sandra Hoffmann
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Paone
- Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Simon A Sumer
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Sabrina Diebold
- Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Birgit Weiss
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Ralph Roeth
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Sebastian Clauss
- Department of Medicine I, Klinikum Grosshadern, University of Munich (LMU), Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Munich, Munich, Germany
| | - Ina Klier
- Department of Medicine I, Klinikum Grosshadern, University of Munich (LMU), Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Munich, Munich, Germany
| | - Stefan Kääb
- Department of Medicine I, Klinikum Grosshadern, University of Munich (LMU), Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Munich, Munich, Germany
| | - Andreas Schulz
- Preventive Cardiology and Preventive Medicine, Center for Cardiology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Philipp S Wild
- Preventive Cardiology and Preventive Medicine, Center for Cardiology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Adil Ghrib
- Department of General and Interventional Cardiology, University Heart Center Hamburg (UHZ), University Hospital Hamburg/Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Hamburg/Kiel/Luebeck, Hamburg, Germany
| | - Tanja Zeller
- Department of General and Interventional Cardiology, University Heart Center Hamburg (UHZ), University Hospital Hamburg/Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Hamburg/Kiel/Luebeck, Hamburg, Germany
| | - Renate B Schnabel
- Department of General and Interventional Cardiology, University Heart Center Hamburg (UHZ), University Hospital Hamburg/Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Hamburg/Kiel/Luebeck, Hamburg, Germany
| | - Steffen Just
- Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, Heidelberg, Germany
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Montalbano A, Juergensen L, Fukami M, Thiel CT, Hauer NH, Roeth R, Weiss B, Naiki Y, Ogata T, Hassel D, Rappold GA. Functional missense and splicing variants in the retinoic acid catabolizing enzyme CYP26C1 in idiopathic short stature. Eur J Hum Genet 2018; 26:1113-1120. [PMID: 29706635 DOI: 10.1038/s41431-018-0148-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 03/19/2018] [Accepted: 03/27/2018] [Indexed: 11/09/2022] Open
Abstract
Height is a complex quantitative trait with a high heritability. Short stature is diagnosed when height is significantly below the average of the general population for that person's age and sex. We have recently found that the retinoic acid degrading enzyme CYP26C1 modifies SHOX deficiency phenotypes toward more severe clinical manifestations. Here, we asked whether damaging variants in CYP26C1 alone could lead to short stature. We performed exome and Sanger sequencing to analyze 856 individuals with short stature where SHOX deficiency was previously excluded. Three different damaging missense variants and one splicing variant were identified in six independent individuals; the functional significance of the identified variants was tested in vitro or in vivo using zebrafish as a model. The genetic and functional data reported here indicate that CYP26C1 represents a novel gene underlying growth disorders and that damaging variants in the absence of SHOX variants can lead to short stature.
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Affiliation(s)
- Antonino Montalbano
- Department of Human Molecular Genetics, Heidelberg University, 69120, Heidelberg, Germany
| | - Lonny Juergensen
- Department of Internal Medicine III - Cardiology, Heidelberg University, 69120, Heidelberg, Germany
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Christian T Thiel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Nadine H Hauer
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Ralph Roeth
- Department of Human Molecular Genetics, Heidelberg University, 69120, Heidelberg, Germany
| | - Birgit Weiss
- Department of Human Molecular Genetics, Heidelberg University, 69120, Heidelberg, Germany
| | - Yasuhiro Naiki
- Division of Endocrinology and Metabolism, National Center for Child Health and Development, Tokyo, 157-8535, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - David Hassel
- Department of Internal Medicine III - Cardiology, Heidelberg University, 69120, Heidelberg, Germany
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Heidelberg University, 69120, Heidelberg, Germany.
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8
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Martínez C, Rodiño-Janeiro BK, Lobo B, Stanifer ML, Klaus B, Granzow M, González-Castro AM, Salvo-Romero E, Alonso-Cotoner C, Pigrau M, Roeth R, Rappold G, Huber W, González-Silos R, Lorenzo J, de Torres I, Azpiroz F, Boulant S, Vicario M, Niesler B, Santos J. miR-16 and miR-125b are involved in barrier function dysregulation through the modulation of claudin-2 and cingulin expression in the jejunum in IBS with diarrhoea. Gut 2017; 66:1537-1538. [PMID: 28082316 PMCID: PMC5561373 DOI: 10.1136/gutjnl-2016-311477] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Micro-RNAs (miRNAs) play a crucial role in controlling intestinal epithelial barrier function partly by modulating the expression of tight junction (TJ) proteins. We have previously shown differential messenger RNA (mRNA) expression correlated with ultrastructural abnormalities of the epithelial barrier in patients with diarrhoea-predominant IBS (IBS-D). However, the participation of miRNAs in these differential mRNA-associated findings remains to be established. Our aims were (1) to identify miRNAs differentially expressed in the small bowel mucosa of patients with IBS-D and (2) to explore putative target genes specifically involved in epithelial barrier function that are controlled by specific dysregulated IBS-D miRNAs. DESIGN Healthy controls and patients meeting Rome III IBS-D criteria were studied. Intestinal tissue samples were analysed to identify potential candidates by: (a) miRNA-mRNA profiling; (b) miRNA-mRNA pairing analysis to assess the co-expression profile of miRNA-mRNA pairs; (c) pathway analysis and upstream regulator identification; (d) miRNA and target mRNA validation. Candidate miRNA-mRNA pairs were functionally assessed in intestinal epithelial cells. RESULTS IBS-D samples showed distinct miRNA and mRNA profiles compared with healthy controls. TJ signalling was associated with the IBS-D transcriptional profile. Further validation of selected genes showed consistent upregulation in 75% of genes involved in epithelial barrier function. Bioinformatic analysis of putative miRNA binding sites identified hsa-miR-125b-5p and hsa-miR-16 as regulating expression of the TJ genes CGN (cingulin) and CLDN2 (claudin-2), respectively. Consistently, protein expression of CGN and CLDN2 was upregulated in IBS-D, while the respective targeting miRNAs were downregulated. In addition, bowel dysfunction, perceived stress and depression and number of mast cells correlated with the expression of hsa-miR-125b-5p and hsa-miR-16 and their respective target proteins. CONCLUSIONS Modulation of the intestinal epithelial barrier function in IBS-D involves both transcriptional and post-transcriptional mechanisms. These molecular mechanisms include miRNAs as master regulators in controlling the expression of TJ proteins and are associated with major clinical symptoms.
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Affiliation(s)
- Cristina Martínez
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany,Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Barcelona, Spain,Facultat de Medicina, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Bruno K Rodiño-Janeiro
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Barcelona, Spain,Facultat de Medicina, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Beatriz Lobo
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Barcelona, Spain,Facultat de Medicina, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Megan L Stanifer
- Schaller Research Group at CellNetworks, Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Bernd Klaus
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Granzow
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | | | - Eloisa Salvo-Romero
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Barcelona, Spain
| | - Carmen Alonso-Cotoner
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Barcelona, Spain,Facultat de Medicina, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain,Centro deInvestigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain,COST Action BM1106 Genes in Irritable Bowel Syndrome (GENIEUR) European Research Network
| | - Marc Pigrau
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Barcelona, Spain,Facultat de Medicina, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ralph Roeth
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany,nCounter Core Facility, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Gudrun Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Rosa González-Silos
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Justo Lorenzo
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Inés de Torres
- Department of Pathology, Facultat de Medicina, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Fernando Azpiroz
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Barcelona, Spain,Facultat de Medicina, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain,Centro deInvestigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain,COST Action BM1106 Genes in Irritable Bowel Syndrome (GENIEUR) European Research Network
| | - Steeve Boulant
- Schaller Research Group at CellNetworks, Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany,Research Group ‘Cellular Polarity and Viral Infection’ (F140), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - María Vicario
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Barcelona, Spain,Facultat de Medicina, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain,Centro deInvestigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain,COST Action BM1106 Genes in Irritable Bowel Syndrome (GENIEUR) European Research Network
| | - Beate Niesler
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany,COST Action BM1106 Genes in Irritable Bowel Syndrome (GENIEUR) European Research Network,nCounter Core Facility, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Javier Santos
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Barcelona, Spain,Facultat de Medicina, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain,Centro deInvestigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain,COST Action BM1106 Genes in Irritable Bowel Syndrome (GENIEUR) European Research Network
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9
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de Sena Cortabitarte A, Degenhardt F, Strohmaier J, Lang M, Weiss B, Roeth R, Giegling I, Heilmann-Heimbach S, Hofmann A, Rujescu D, Fischer C, Rietschel M, Nöthen MM, Rappold GA, Berkel S. Investigation of SHANK3 in schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2017; 174:390-398. [PMID: 28371232 DOI: 10.1002/ajmg.b.32528] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/03/2017] [Indexed: 12/21/2022]
Abstract
The postsynaptic scaffolding protein SHANK3 is essential for the normal function of glutamatergic synapses in the brain. Emerging evidence suggests that impaired plasticity of glutamatergic synapses contributes to the pathology of schizophrenia (SCZ). To investigate whether variants in the SHANK3 gene contribute to the etiology of SCZ, we sequenced SHANK3 in 500 affected individuals (cohort C1). In total, we identified 48 variants and compared them to European controls from the 1000 Genomes Project and the Exome Variant Server. Five variants showed significant differences in frequencies between patients and controls. We were able to follow three of them up in an independent cohort (C2) comprising 993 SCZ patients and 932 German controls. We could not confirm an association for three of these variants (rs140201628, rs1557620, and rs61729471). Two rare variants with predicted functional relevance were identified in further SCZ individuals of cohort C1: c.3032G>T (p.G1011V) and c.*27C>T. The latter variant was found in one additional SCZ individual and the p.G1011V variant was identified in two additional SCZ individuals from cohort C2. The p.G1011V variant was the most interesting variant in our study; together with previous studies this variant has been identified in 4 out of 1,524 SCZ patients and in 4 out of 2,147 individuals with autism spectrum disorder (ASD), but not in 2468 European Sanger-sequenced controls. Therefore, we consider this variant a promising candidate variant for follow-up studies in larger samples and functional investigations. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Ana de Sena Cortabitarte
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Franziska Degenhardt
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health Mannheim, Faculty of Medicine Mannheim, University of Heidelberg, Mannheim, Germany
| | - Maren Lang
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health Mannheim, Faculty of Medicine Mannheim, University of Heidelberg, Mannheim, Germany
| | - Birgit Weiss
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Ralph Roeth
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Ina Giegling
- Department of Psychiatry, University Hospital Halle (Saale), Halle, Germany
| | | | - Andrea Hofmann
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Dan Rujescu
- Department of Psychiatry, University Hospital Halle (Saale), Halle, Germany
| | - Christine Fischer
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health Mannheim, Faculty of Medicine Mannheim, University of Heidelberg, Mannheim, Germany.,Department of Psychiatry, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.,Interdisciplinary Center for Neurosciences (IZN), University of Heidelberg, Heidelberg, Germany
| | - Simone Berkel
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
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10
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Montalbano A, Juergensen L, Roeth R, Weiss B, Fukami M, Fricke-Otto S, Binder G, Ogata T, Decker E, Nuernberg G, Hassel D, Rappold GA. Retinoic acid catabolizing enzyme CYP26C1 is a genetic modifier in SHOX deficiency. EMBO Mol Med 2016; 8:1455-1469. [PMID: 27861128 PMCID: PMC5167135 DOI: 10.15252/emmm.201606623] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 09/28/2016] [Accepted: 10/10/2016] [Indexed: 12/17/2022] Open
Abstract
Mutations in the homeobox gene SHOX cause SHOX deficiency, a condition with clinical manifestations ranging from short stature without dysmorphic signs to severe mesomelic skeletal dysplasia. In rare cases, individuals with SHOX deficiency are asymptomatic. To elucidate the factors that modify disease severity/penetrance, we studied a three-generation family with SHOX deficiency. The variant p.Phe508Cys of the retinoic acid catabolizing enzyme CYP26C1 co-segregated with the SHOX variant p.Val161Ala in the affected individuals, while the SHOX mutant alone was present in asymptomatic individuals. Two further cases with SHOX deficiency and damaging CYP26C1 variants were identified in a cohort of 68 individuals with LWD The identified CYP26C1 variants affected its catabolic activity, leading to an increased level of retinoic acid. High levels of retinoic acid significantly decrease SHOX expression in human primary chondrocytes and zebrafish embryos. Individual morpholino knockdown of either gene shortens the pectoral fins, whereas depletion of both genes leads to a more severe phenotype. Together, our findings describe CYP26C1 as the first genetic modifier for SHOX deficiency.
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Affiliation(s)
- Antonino Montalbano
- Department of Human Molecular Genetics, Heidelberg University, Heidelberg, Germany
| | - Lonny Juergensen
- Department of Internal Medicine III - Cardiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ralph Roeth
- Department of Human Molecular Genetics, Heidelberg University, Heidelberg, Germany
| | - Birgit Weiss
- Department of Human Molecular Genetics, Heidelberg University, Heidelberg, Germany
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | | | - Gerhard Binder
- Children's Hospital, University of Tübingen, Tübingen, Germany
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Eva Decker
- Bioscientia Center for Human Genetics, Ingelheim, Germany
| | - Gudrun Nuernberg
- Center for Molecular Medicine, Cologne, Germany
- Cologne Center for Genomics, Cologne, Germany
| | - David Hassel
- Department of Internal Medicine III - Cardiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Heidelberg University, Heidelberg, Germany
- Interdisciplinary Centre for Neurosciences (IZN), University of Heidelberg, Heidelberg, Germany
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11
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Durand C, Decker E, Roeth R, Schneider KU, Rappold G. The homeobox transcription factor HOXA9 is a regulator of SHOX in U2OS cells and chicken micromass cultures. PLoS One 2012; 7:e45369. [PMID: 23028966 PMCID: PMC3447975 DOI: 10.1371/journal.pone.0045369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 08/21/2012] [Indexed: 11/18/2022] Open
Abstract
The homeobox gene SHOX encodes for a transcription factor that plays an important role during limb development. Mutations or deletions of SHOX in humans cause short stature in Turner, Langer and Leri-Weill syndrome as well as idiopathic short stature. During embryonic development, SHOX is expressed in a complex spatio-temporal pattern that requires the presence of specific regulatory mechanisms. Up to now, it was known that SHOX is regulated by two upstream promoters and several enhancers on either side of the gene, but no regulators have been identified that can activate or repress the transcription of SHOX by binding to these regulatory elements. We have now identified the homeodomain protein HOXA9 as a positive regulator of SHOX expression in U2OS cells. Using luciferase assays, chromatin immunoprecipitation and electrophoretic mobility shift assays, we could narrow down the HOXA9 binding site to two AT-rich sequences of 31 bp within the SHOX promoter 2. Virus-induced Hoxa9 overexpression in a chicken micromass model validated the regulation of Shox by Hoxa9 (negative regulation). As Hoxa9 and Shox are both expressed in overlapping regions of the developing limb buds, a regulatory relationship of Hoxa9 and Shox during the process of limb development can be assumed.
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Affiliation(s)
- Claudia Durand
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Eva Decker
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Ralph Roeth
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Katja U. Schneider
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
| | - Gudrun Rappold
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
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12
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Sato D, Lionel AC, Leblond CS, Prasad A, Pinto D, Walker S, O'Connor I, Russell C, Drmic IE, Hamdan FF, Michaud JL, Endris V, Roeth R, Delorme R, Huguet G, Leboyer M, Rastam M, Gillberg C, Lathrop M, Stavropoulos DJ, Anagnostou E, Weksberg R, Fombonne E, Zwaigenbaum L, Fernandez BA, Roberts W, Rappold GA, Marshall CR, Bourgeron T, Szatmari P, Scherer SW. SHANK1 Deletions in Males with Autism Spectrum Disorder. Am J Hum Genet 2012; 90:879-87. [PMID: 22503632 DOI: 10.1016/j.ajhg.2012.03.017] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 03/09/2012] [Accepted: 03/19/2012] [Indexed: 12/11/2022] Open
Abstract
Recent studies have highlighted the involvement of rare (<1% frequency) copy-number variations and point mutations in the genetic etiology of autism spectrum disorder (ASD); these variants particularly affect genes involved in the neuronal synaptic complex. The SHANK gene family consists of three members (SHANK1, SHANK2, and SHANK3), which encode scaffolding proteins required for the proper formation and function of neuronal synapses. Although SHANK2 and SHANK3 mutations have been implicated in ASD and intellectual disability, the involvement of SHANK1 is unknown. Here, we assess microarray data from 1,158 Canadian and 456 European individuals with ASD to discover microdeletions at the SHANK1 locus on chromosome 19. We identify a hemizygous SHANK1 deletion that segregates in a four-generation family in which male carriers--but not female carriers--have ASD with higher functioning. A de novo SHANK1 deletion was also detected in an unrelated male individual with ASD with higher functioning, and no equivalent SHANK1 mutations were found in >15,000 controls (p = 0.009). The discovery of apparent reduced penetrance of ASD in females bearing inherited autosomal SHANK1 deletions provides a possible contributory model for the male gender bias in autism. The data are also informative for clinical-genetics interpretations of both inherited and sporadic forms of ASD involving SHANK1.
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Affiliation(s)
- Daisuke Sato
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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13
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Durand C, Roeth R, Dweep H, Vlatkovic I, Decker E, Schneider KU, Rappold G. Alternative splicing and nonsense-mediated RNA decay contribute to the regulation of SHOX expression. PLoS One 2011; 6:e18115. [PMID: 21448463 PMCID: PMC3063249 DOI: 10.1371/journal.pone.0018115] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 02/24/2011] [Indexed: 11/18/2022] Open
Abstract
The human SHOX gene is composed of seven exons and encodes a paired-related homeodomain transcription factor. SHOX mutations or deletions have been associated with different short stature syndromes implying a role in growth and bone formation. During development, SHOX is expressed in a highly specific spatiotemporal expression pattern, the underlying regulatory mechanisms of which remain largely unknown. We have analysed SHOX expression in diverse embryonic, fetal and adult human tissues and detected expression in many tissues that were not known to express SHOX before, e.g. distinct brain regions. By using RT-PCR and comparing the results with RNA-Seq data, we have identified four novel exons (exon 2a, 7-1, 7-2 and 7-3) contributing to different SHOX isoforms, and also established an expression profile for the emerging new SHOX isoforms. Interestingly, we found the exon 7 variants to be exclusively expressed in fetal neural tissues, which could argue for a specific role of these variants during brain development. A bioinformatical analysis of the three novel 3′UTR exons yielded insights into the putative role of the different 3′UTRs as targets for miRNA binding. Functional analysis revealed that inclusion of exon 2a leads to nonsense-mediated RNA decay altering SHOX expression in a tissue and time specific manner. In conclusion, SHOX expression is regulated by different mechanisms and alternative splicing coupled with nonsense-mediated RNA decay constitutes a further component that can be used to fine tune the SHOX expression level.
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Affiliation(s)
- Claudia Durand
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
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14
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Berkel S, Marshall CR, Weiss B, Howe J, Roeth R, Moog U, Endris V, Roberts W, Szatmari P, Pinto D, Bonin M, Riess A, Engels H, Sprengel R, Scherer SW, Rappold GA. Mutations in the SHANK2 synaptic scaffolding gene in autism spectrum disorder and mental retardation. Nat Genet 2010; 42:489-91. [PMID: 20473310 DOI: 10.1038/ng.589] [Citation(s) in RCA: 383] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 04/15/2010] [Indexed: 12/15/2022]
Abstract
Using microarrays, we identified de novo copy number variations in the SHANK2 synaptic scaffolding gene in two unrelated individuals with autism-spectrum disorder (ASD) and mental retardation. DNA sequencing of SHANK2 in 396 individuals with ASD, 184 individuals with mental retardation and 659 unaffected individuals (controls) revealed additional variants that were specific to ASD and mental retardation cases, including a de novo nonsense mutation and seven rare inherited changes. Our findings further link common genes between ASD and intellectual disability.
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Affiliation(s)
- Simone Berkel
- Department of Molecular Human Genetics, Ruprecht-Karls-University, Heidelberg, Germany
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15
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Tyson C, Dawson A, Bal S, Tomiuk M, Anderson T, Tucker D, Riordan D, Chudoba I, Morash B, Mhanni A, Chudley A, McGillivray B, Parslow M, Rappold G, Roeth R, Fawcett C, Qiao Y, Harvard C, Rajcan-Separovic E. Molecular cytogenetic investigation of two patients with Y chromosome rearrangements and intellectual disability. Am J Med Genet A 2009; 149A:490-5. [DOI: 10.1002/ajmg.a.32535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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16
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Rappold G, Blum WF, Shavrikova EP, Crowe BJ, Roeth R, Quigley CA, Ross JL, Niesler B. Genotypes and phenotypes in children with short stature: clinical indicators of SHOX haploinsufficiency. J Med Genet 2006; 44:306-13. [PMID: 17182655 PMCID: PMC2597980 DOI: 10.1136/jmg.2006.046581] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Short stature affects approximately 2% of children, representing one of the more frequent disorders for which clinical attention is sought during childhood. Despite assumed genetic heterogeneity, mutations or deletions of the short stature homeobox-containing gene (SHOX) are found quite frequently in subjects with short stature. Haploinsufficiency of the SHOX gene causes short stature with highly variable clinical severity, ranging from isolated short stature without dysmorphic features to Léri-Weill syndrome, and with no functional copy of the SHOX gene, Langer syndrome. METHODS To characterise the clinical and molecular spectrum of SHOX deficiency in childhood we assessed the association between genotype and phenotype in a large cohort of children of short stature from 14 countries. RESULTS Screening of 1608 unrelated individuals with sporadic or familial short stature revealed SHOX mutations or deletions in 68 individuals (4.2%): complete deletions in 48 (70.6%), partial deletions in 4 (5.9%) and point mutations in 16 individuals (23.5%). Although mean height standard deviation score (SDS) was not different between participants of short stature with or without identified SHOX gene defects (-2.6 vs -2.6), detailed examination revealed that certain bone deformities and dysmorphic signs, such as short forearm and lower leg, cubitus valgus, Madelung deformity, high-arched palate and muscular hypertrophy, differed markedly between participants with or without SHOX gene defects (p<0.001). Phenotypic data were also compared for 33 children with Turner syndrome in whom haploinsufficiency of SHOX is thought to be responsible for the height deficit. CONCLUSION A phenotype scoring system was developed that could assist in identifying the most appropriate subjects for SHOX testing. This study offers a detailed genotype-phenotype analysis in a large cohort of children of short stature, and provides quantitative clinical guidelines for testing of the SHOX gene.
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Affiliation(s)
- Gudrun Rappold
- Department of Molecular Human Genetics, University of Heidelberg, Heidelberg, Germany.
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17
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Muncke N, Niesler B, Roeth R, Schön K, Rüdiger HJ, Goldmuntz E, Goodship J, Rappold G. Mutational analysis of the PITX2 coding region revealed no common cause for transposition of the great arteries (dTGA). BMC Med Genet 2005; 6:20. [PMID: 15890066 PMCID: PMC1142516 DOI: 10.1186/1471-2350-6-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Accepted: 05/12/2005] [Indexed: 11/25/2022]
Abstract
BACKGROUND PITX2 is a bicoid-related homeodomain transcription factor that plays an important role in asymmetric cardiogenesis. Loss of function experiments in mice cause severe heart malformations, including transposition of the great arteries (TGA). TGA accounts for 5-7% of all congenital heart diseases affecting 0.2 per 1000 live births, thereby representing the most frequent cyanotic heart defect diagnosed in the neonatal period. METHODS To address whether altered PITX2 function could also contribute to the formation of dTGA in humans, we screened 96 patients with dTGA by means of dHPLC and direct sequencing for mutations within the PITX2 gene. RESULTS Several SNPs could be detected, but no stop or frame shift mutation. In particular, we found seven intronic and UTR variants, two silent mutations and two polymorphisms within the coding region. CONCLUSION As most sequence variants were also found in controls we conclude that mutations in PITX2 are not a common cause of dTGA.
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Affiliation(s)
- Nadja Muncke
- Institut für Humangenetik, Universität Heidelberg, INF 366, 69120 Heidelberg, Germany
| | - Beate Niesler
- Institut für Humangenetik, Universität Heidelberg, INF 366, 69120 Heidelberg, Germany
| | - Ralph Roeth
- Institut für Humangenetik, Universität Heidelberg, INF 366, 69120 Heidelberg, Germany
| | - Karin Schön
- Institut für Humangenetik, Universität Heidelberg, INF 366, 69120 Heidelberg, Germany
| | - Heinz-Juergen Rüdiger
- Abteilung für Kardiologie, Kinderklinik Heidelberg, INF 153, 69120 Heidelberg, Germany
| | - Elizabeth Goldmuntz
- Division of Cardiology, Department of Pediatrics, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Judith Goodship
- Institute of Human Genetics, International Center for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Gudrun Rappold
- Institut für Humangenetik, Universität Heidelberg, INF 366, 69120 Heidelberg, Germany
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18
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Muncke N, Jung C, Rüdiger H, Ulmer H, Roeth R, Hubert A, Goldmuntz E, Driscoll D, Goodship J, Schön K, Rappold G. Missense mutations and gene interruption in PROSIT240, a novel TRAP240-like gene, in patients with congenital heart defect (transposition of the great arteries). Circulation 2003; 108:2843-50. [PMID: 14638541 DOI: 10.1161/01.cir.0000103684.77636.cd] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Congenital heart disease represents the most common severe birth defect, affecting 0.7% to 1% of all neonates, among whom 5% to 7% display transposition of the great arteries (TGA). TGA represents a septation defect of the common outflow tract of the heart, manifesting around the fifth week during embryonic development. Despite its high prevalence, very little is known about the pathogenesis of this disease. METHODS AND RESULTS Using a positional cloning approach, we isolated a novel gene, PROSIT240 (also termed THRAP2), that is interrupted in a patient with a chromosomal translocation and who displays TGA and mental retardation. High expression of PROSIT240 within the heart (aorta) and brain (cerebellum) was well correlated with the malformations observed in the patient and prompted further analyses. PROSIT240 shows significant homology to the nuclear receptor coactivator TRAP240, suggesting it to be a new component of the thyroid hormone receptor-associated protein (TRAP) complex. Interestingly, several TRAP components have been previously shown to be important in early embryonic development in various organisms, making PROSIT240 an excellent candidate gene to be correlated to the patient's phenotype. Subsequent mutational screening of 97 patients with isolated dextro-looped TGA revealed 3 missense mutations in PROSIT240, which were not detected in 400 control chromosomes. CONCLUSIONS Together, these genetic data suggest that PROSIT240 is involved in early heart and brain development.
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MESH Headings
- Abnormalities, Multiple/genetics
- Adaptor Proteins, Signal Transducing
- Amino Acid Sequence
- Aorta/metabolism
- Carrier Proteins/genetics
- Carrier Proteins/physiology
- Cerebellar Ataxia/genetics
- Cerebellum/abnormalities
- Cerebellum/metabolism
- Child
- Chromosome Deletion
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 12/ultrastructure
- Chromosomes, Human, Pair 17/genetics
- Chromosomes, Human, Pair 17/ultrastructure
- Chromosomes, Human, Pair 22/genetics
- Cohort Studies
- Female
- Heart Defects, Congenital/genetics
- Humans
- Intellectual Disability/genetics
- Mediator Complex
- Microcephaly/genetics
- Molecular Sequence Data
- Multigene Family
- Mutation, Missense
- Organ Specificity
- Sequence Alignment
- Sequence Homology, Amino Acid
- Translocation, Genetic
- Transposition of Great Vessels/genetics
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Affiliation(s)
- Nadja Muncke
- Institut für Humangenetik, Universität Heidelberg, Heidelberg, Germany
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