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Münch J, Engesser M, Schönauer R, Hamm JA, Hartig C, Hantmann E, Akay G, Pehlivan D, Mitani T, Coban Akdemir Z, Tüysüz B, Shirakawa T, Dateki S, Claus LR, van Eerde AM, Smol T, Devisme L, Franquet H, Attié-Bitach T, Wagner T, Bergmann C, Höhn AK, Shril S, Pollack A, Wenger T, Scott AA, Paolucci S, Buchan J, Gabriel GC, Posey JE, Lupski JR, Petit F, McCarthy AA, Pazour GJ, Lo CW, Popp B, Halbritter J. Biallelic pathogenic variants in roundabout guidance receptor 1 associate with syndromic congenital anomalies of the kidney and urinary tract. Kidney Int 2022; 101:1039-1053. [PMID: 35227688 PMCID: PMC10010616 DOI: 10.1016/j.kint.2022.01.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) represent the most common cause of chronic kidney failure in children. Despite growing knowledge of the genetic causes of CAKUT, the majority of cases remain etiologically unsolved. Genetic alterations in roundabout guidance receptor 1 (ROBO1) have been associated with neuronal and cardiac developmental defects in living individuals. Although Slit-Robo signaling is pivotal for kidney development, diagnostic ROBO1 variants have not been reported in viable CAKUT to date. By next-generation-sequencing methods, we identified six unrelated individuals and two non-viable fetuses with biallelic truncating or combined missense and truncating variants in ROBO1. Kidney and genitourinary manifestation included unilateral or bilateral kidney agenesis, vesicoureteral junction obstruction, vesicoureteral reflux, posterior urethral valve, genital malformation, and increased kidney echogenicity. Further clinical characteristics were remarkably heterogeneous, including neurodevelopmental defects, intellectual impairment, cerebral malformations, eye anomalies, and cardiac defects. By in silico analysis, we determined the functional significance of identified missense variants and observed absence of kidney ROBO1 expression in both human and murine mutant tissues. While its expression in multiple tissues may explain heterogeneous organ involvement, variability of the kidney disease suggests gene dosage effects due to a combination of null alleles with mild hypomorphic alleles. Thus, comprehensive genetic analysis in CAKUT should include ROBO1 as a new cause of recessively inherited disease. Hence, in patients with already established ROBO1-associated cardiac or neuronal disorders, screening for kidney involvement is indicated.
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Affiliation(s)
- Johannes Münch
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Marie Engesser
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Ria Schönauer
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - J Austin Hamm
- East Tennessee Children's Hospital, Genetic Center, Knoxville, Tennessee, USA
| | - Christin Hartig
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Elena Hantmann
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Department of Pediatrics, University of Utah, Salt Lake, Utah, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA; Texas Children's Hospital, Houston, Texas, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Beyhan Tüysüz
- Department of Pediatric Genetics, Istanbul University Cerrahpasa Medical Faculty, Istanbul, Turkey
| | | | - Sumito Dateki
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Laura R Claus
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Thomas Smol
- Centre Hospitalier Universitaire de Lille, Institut de Génétique Médicale, Lille, France
| | - Louise Devisme
- Centre Hospitalier Universitaire de Lille, Institut de Pathologie, Lille, France
| | - Hélène Franquet
- Centre Hospitalier Universitaire de Lille, Institut de Pathologie, Lille, France
| | - Tania Attié-Bitach
- Laboratoire de biologie médicale multisites SeqOIA, Paris, France; Service de Médecine Génomique des Maladies Rares, APHP.Centre, Université de Paris, Paris, France
| | - Timo Wagner
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany
| | - Carsten Bergmann
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany; Department of Medicine, Nephrology, University Hospital Freiburg, Freiburg, Germany
| | - Anne Kathrin Höhn
- Division of Pathology, University of Leipzig Medical Center, Leipzig, Germany
| | - Shirlee Shril
- Division of Nephrology, Boston Children's Hospital, Boston, USA
| | - Ari Pollack
- Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
| | - Tara Wenger
- Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
| | - Abbey A Scott
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, Washington, USA
| | - Sarah Paolucci
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Jillian Buchan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Texas Children's Hospital, Houston, Texas, USA; Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Florence Petit
- Centre Hospitalier Universitaire de Lille, Clinique de Génétique Guy Fontaine, Lille, France
| | | | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Worcester, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
| | - Bernt Popp
- Institute for Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
| | - Jan Halbritter
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany.
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Riedhammer KM, Siegel C, Alhaddad B, Montoya C, Kovacs-Nagy R, Wagner M, Meitinger T, Hoefele J. Identification of a Novel Heterozygous De Novo 7-bp Frameshift Deletion in PBX1 by Whole-Exome Sequencing Causing a Multi-Organ Syndrome Including Bilateral Dysplastic Kidneys and Hypoplastic Clavicles. Front Pediatr 2017; 5:251. [PMID: 29226118 PMCID: PMC5705563 DOI: 10.3389/fped.2017.00251] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 08/18/2017] [Accepted: 11/07/2017] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Congenital anomalies of the kidney and urinary tract (CAKUT) represent the primary cause of chronic kidney disease in children. Many genes have been attributed to the genesis of this disorder. Recently, haploinsufficiency of PBX1 caused by microdeletions has been shown to result in bilateral renal hypoplasia and other organ malformations. MATERIALS AND METHODS Here, we report on a 14-year-old male patient with congenital bilateral dysplastic kidneys, cryptorchidism, hypoplastic clavicles, developmental delay, impaired intelligence, and minor dysmorphic features. Presuming a syndromic origin, we performed SNP array analysis to scan for large copy number variations (CNVs) followed by whole-exome sequencing (WES). Sanger sequencing was done to confirm the variant's de novo status. RESULTS SNP array analysis did not reveal any microdeletions or -duplications larger than 50 or 100 kb, respectively. WES identified a novel heterozygous 7-bp frameshift deletion in PBX1 (c.413_419del, p.Gly138Valfs*40) resulting in a loss-of-function. The de novo status could be confirmed by Sanger sequencing. DISCUSSION By WES, we identified a novel heterozygous de novo 7-bp frameshift deletion in PBX1. Our findings expand the spectrum of causative variants in PBX1-related CAKUT. In this case, WES proved to be the apt technique to detect the variant responsible for the patient's phenotype, as single gene testing is not feasible given the multitude of genes involved in CAKUT and SNP array analysis misses rare single-nucleotide variants and small Indels.
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Affiliation(s)
- Korbinian Maria Riedhammer
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Corinna Siegel
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Bader Alhaddad
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Carmen Montoya
- KfH Center of Pediatric Nephrology, Children's Hospital Munich Schwabing, Munich, Germany
| | - Reka Kovacs-Nagy
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany.,Institute of Neurogenomics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
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