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Schumann A, Schultheiss UT, Ferreira CR, Blau N. Clinical and biochemical footprints of inherited metabolic diseases. XIV. Metabolic kidney diseases. Mol Genet Metab 2023; 140:107683. [PMID: 37597335 DOI: 10.1016/j.ymgme.2023.107683] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023]
Abstract
Kidney disease is a global health burden with high morbidity and mortality. Causes of kidney disease are numerous, extending from common disease groups like diabetes and arterial hypertension to rare conditions including inherited metabolic diseases (IMDs). Given its unique anatomy and function, the kidney is a target organ in about 10% of known IMDs, emphasizing the relevant contribution of IMDs to kidney disease. The pattern of injury affects all segments of the nephron including glomerular disease, proximal and distal tubular damage, kidney cyst formation, built-up of nephrocalcinosis and stones as well as severe malformations. We revised and updated the list of known metabolic etiologies associated with kidney involvement and found 190 relevant IMDs. This represents the 14th of a series of educational articles providing a comprehensive and revised list of metabolic differential diagnoses according to system involvement.
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Affiliation(s)
- Anke Schumann
- Department of General Paediatrics, Adolescent Medicine and Neonatology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany.
| | - Ulla T Schultheiss
- Department of Medicine IV, Nephrology and Primary Care, Faculty of Medicine, and Medical Center, University of Freiburg, Institute of Genetic Epidemiology, Freiburg, Germany.
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA.
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital, Zürich, Switzerland.
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2
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Ramadesikan S, Lee J, Aguilar RC. The Future of Genetic Disease Studies: Assembling an Updated Multidisciplinary Toolbox. Front Cell Dev Biol 2022; 10:886448. [PMID: 35573700 PMCID: PMC9096115 DOI: 10.3389/fcell.2022.886448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
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Sadler B, Wilborn J, Antunes L, Kuensting T, Hale AT, Gannon SR, McCall K, Cruchaga C, Harms M, Voisin N, Reymond A, Cappuccio G, Brunetti-Pierri N, Tartaglia M, Niceta M, Leoni C, Zampino G, Ashley-Koch A, Urbizu A, Garrett ME, Soldano K, Macaya A, Conrad D, Strahle J, Dobbs MB, Turner TN, Shannon CN, Brockmeyer D, Limbrick DD, Gurnett CA, Haller G. Rare and de novo coding variants in chromodomain genes in Chiari I malformation. Am J Hum Genet 2021; 108:100-114. [PMID: 33352116 DOI: 10.1016/j.ajhg.2020.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Chiari I malformation (CM1), the displacement of the cerebellum through the foramen magnum into the spinal canal, is one of the most common pediatric neurological conditions. Individuals with CM1 can present with neurological symptoms, including severe headaches and sensory or motor deficits, often as a consequence of brainstem compression or syringomyelia (SM). We conducted whole-exome sequencing (WES) on 668 CM1 probands and 232 family members and performed gene-burden and de novo enrichment analyses. A significant enrichment of rare and de novo non-synonymous variants in chromodomain (CHD) genes was observed among individuals with CM1 (combined p = 2.4 × 10-10), including 3 de novo loss-of-function variants in CHD8 (LOF enrichment p = 1.9 × 10-10) and a significant burden of rare transmitted variants in CHD3 (p = 1.8 × 10-6). Overall, individuals with CM1 were found to have significantly increased head circumference (p = 2.6 × 10-9), with many harboring CHD rare variants having macrocephaly. Finally, haploinsufficiency for chd8 in zebrafish led to macrocephaly and posterior hindbrain displacement reminiscent of CM1. These results implicate chromodomain genes and excessive brain growth in CM1 pathogenesis.
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Iancu D, Ashton E. Inherited Renal Tubulopathies-Challenges and Controversies. Genes (Basel) 2020; 11:genes11030277. [PMID: 32150856 PMCID: PMC7140864 DOI: 10.3390/genes11030277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/29/2020] [Accepted: 02/29/2020] [Indexed: 12/23/2022] Open
Abstract
Electrolyte homeostasis is maintained by the kidney through a complex transport function mostly performed by specialized proteins distributed along the renal tubules. Pathogenic variants in the genes encoding these proteins impair this function and have consequences on the whole organism. Establishing a genetic diagnosis in patients with renal tubular dysfunction is a challenging task given the genetic and phenotypic heterogeneity, functional characteristics of the genes involved and the number of yet unknown causes. Part of these difficulties can be overcome by gathering large patient cohorts and applying high-throughput sequencing techniques combined with experimental work to prove functional impact. This approach has led to the identification of a number of genes but also generated controversies about proper interpretation of variants. In this article, we will highlight these challenges and controversies.
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Affiliation(s)
- Daniela Iancu
- UCL-Centre for Nephrology, Royal Free Campus, University College London, Rowland Hill Street, London NW3 2PF, UK
- Correspondence: ; Tel.: +44-2381204172; Fax: +44-020-74726476
| | - Emma Ashton
- Rare & Inherited Disease Laboratory, London North Genomic Laboratory Hub, Great Ormond Street Hospital for Children National Health Service Foundation Trust, Levels 4-6 Barclay House 37, Queen Square, London WC1N 3BH, UK;
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Fomchenko EI, Erson-Omay EZ, Kundishora AJ, Hong CS, Daniel AA, Allocco A, Duy PQ, Darbinyan A, Marks AM, DiLuna ML, Kahle KT, Huttner A. Genomic alterations underlying spinal metastases in pediatric H3K27M-mutant pineal parenchymal tumor of intermediate differentiation: case report. J Neurosurg Pediatr 2019; 25:121-130. [PMID: 31653819 DOI: 10.3171/2019.8.peds18664] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 08/21/2019] [Indexed: 11/06/2022]
Abstract
Pediatric midline tumors are devastating high-grade lesions with a dismal prognosis and no curative surgical options. Here, the authors report the clinical presentation, surgical management, whole-exome sequencing (WES), and clonality analysis of a patient with a radically resected H3K27M-mutant pineal parenchymal tumor (PPT) and spine metastases consistent with PPT of intermediate differentiation (PPTID). They identified somatic mutations in H3F3A (H3K27M), FGFR1, and NF1 both in the original PPT and in the PPTID metastases. They also found 12q amplification containing CDK4/MDM2 and chromosome 17 loss of heterozygosity overlapping with NF1 that resulted in biallelic NF1 loss. They noted a hypermutated phenotype with increased C>T transitions within the PPTID metastases and 2p amplification overlapping with the MYCN locus. Clonality analysis detected three founder clones maintained during progression and metastasis. Tumor clones present within the PPTID metastases but not the pineal midline tumor harbored mutations in APC and TIMP2.While the majority of H3K27M mutations are found in pediatric midline gliomas, it is increasingly recognized that this mutation is present in a wider range of lesions with a varied morphological appearance. The present case appears to be the first description of H3K27M mutation in PPTID. Somatic mutations in H3F3A, FGFR1, and NF1 have been suggested to be driver mutations in pediatric midline gliomas. Their clonality and presence in over 80% of tumor cells in our patient's PPTID are consistent with similarly crucial roles in early tumorigenesis, with progression mediated by copy number variations and chromosomal aberrations involving known oncogenes and tumor suppressors. The roles of APC and TIMP2 mutations in progression and metastasis remain to be investigated.
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Affiliation(s)
| | | | | | | | - Ava A Daniel
- 8Yale College, Yale University, New Haven, Connecticut
| | | | | | | | | | | | - Kristopher T Kahle
- Departments of1Neurosurgery
- 4Centers for Mendelian Genomics and Yale Program on Neurogenetics, Yale School of Medicine; and
- 5Pediatrics
- 6Cellular & Molecular Physiology, and
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Fomchenko EI, Duran D, Jin SC, Dong W, Erson-Omay EZ, Antwi P, Allocco A, Gaillard JR, Huttner A, Gunel M, DiLuna ML, Kahle KT. De novo MYH9 mutation in congenital scalp hemangioma. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002998. [PMID: 29903892 PMCID: PMC6071566 DOI: 10.1101/mcs.a002998] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/30/2018] [Indexed: 12/19/2022] Open
Abstract
Congenital hemangiomas are tumor-like vascular malformations with poorly understood pathogenesis. We report the case of a neonate with a massive congenital scalp hemangioma that required urgent neurosurgical removal on the second day of life because of concern for high-flow arteriovenous shunting. Exome sequencing identified a rare damaging de novo germline mutation in MYH9 (c.5308C>T, p.[Arg1770Cys]), encoding the MYH9 nonmuscle myosin IIA. MYH9 has a probability of loss-of-function intolerance (pLI) score of >0.99 and is highly intolerant to missense variation (z score = 5.59). The p.(Arg1770Cys) mutation substitutes an evolutionarily conserved amino acid in the protein's critical myosin tail domain and is predicted to be highly deleterious by SIFT, PolyPhen-2, MetaSVM, and CADD. MYH9 is a known regulator of cytokinesis, VEGF-regulated angiogenesis, and p53-dependent tumorigenesis. These findings reveal a novel association of germline de novo MYH9 mutation with congenital hemangioma.
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Affiliation(s)
- Elena I Fomchenko
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Daniel Duran
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - E Zeynep Erson-Omay
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Prince Antwi
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - August Allocco
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Jonathan R Gaillard
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Anita Huttner
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Murat Gunel
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA.,Centers for Mendelian Genomics and Yale Program on Neurogenetics, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Michael L DiLuna
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA.,Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA.,Centers for Mendelian Genomics and Yale Program on Neurogenetics, Yale School of Medicine, New Haven, Connecticut 06519, USA.,Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut 06519, USA.,Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut 06519, USA
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Antwi P, Hong CS, Duran D, Jin SC, Dong W, DiLuna M, Kahle KT. A novel association of campomelic dysplasia and hydrocephalus with an unbalanced chromosomal translocation upstream of SOX9. Cold Spring Harb Mol Case Stud 2018; 4:a002766. [PMID: 29695406 PMCID: PMC5983176 DOI: 10.1101/mcs.a002766] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/26/2018] [Indexed: 11/29/2022] Open
Abstract
Campomelic dysplasia is a rare skeletal dysplasia characterized by Pierre Robin sequence, craniofacial dysmorphism, shortening and angulation of long bones, tracheobronchomalacia, and occasionally sex reversal. The disease is due to mutations in SOX9 or chromosomal rearrangements involving the long arm of Chromosome 17 harboring the SOX9 locus. SOX9, a transcription factor, is indispensible in establishing and maintaining neural stem cells in the central nervous system. We present a patient with angulation of long bones and external female genitalia on prenatal ultrasound who was subsequently found to harbor the chromosomal abnormality 46, XY, t(6;17) (p21.1;q24.3) on prenatal genetic testing. Comparative genomic hybridization revealed deletions at 6p21.1 and 17q24.3, the latter being 2.3 Mb upstream of SOX9 Whole-exome sequencing did not identify pathogenic variants in SOX9, suggesting that the 17q24.3 deletion represents a translocation breakpoint farther upstream of SOX9 than previously identified. At 2 mo of age the patient developed progressive communicating ventriculomegaly and thinning of the cortical mantle without clinical signs of increased intracranial pressure. This case suggests ventriculomegaly in some cases represents not a primary impairment of cerebrospinal fluid dynamics, but an epiphenomenon driven by a genetic dysregulation of neural progenitor cell fate.
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Affiliation(s)
- Prince Antwi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Christopher S Hong
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Daniel Duran
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Weilai Dong
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, Connecticut 06520, USA
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Development of ultra-deep targeted RNA sequencing for analyzing X-chromosome inactivation in female Dent disease. J Hum Genet 2018; 63:589-595. [DOI: 10.1038/s10038-018-0415-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/09/2018] [Accepted: 01/17/2018] [Indexed: 11/08/2022]
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