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van der Ven AT, Connaughton DM, Ityel H, Mann N, Nakayama M, Chen J, Vivante A, Hwang DY, Schulz J, Braun DA, Schmidt JM, Schapiro D, Schneider R, Warejko JK, Daga A, Majmundar AJ, Tan W, Jobst-Schwan T, Hermle T, Widmeier E, Ashraf S, Amar A, Hoogstraaten CA, Hugo H, Kitzler TM, Kause F, Kolvenbach CM, Dai R, Spaneas L, Amann K, Stein DR, Baum MA, Somers MJG, Rodig NM, Ferguson MA, Traum AZ, Daouk GH, Bogdanović R, Stajić N, Soliman NA, Kari JA, El Desoky S, Fathy HM, Milosevic D, Al-Saffar M, Awad HS, Eid LA, Selvin A, Senguttuvan P, Sanna-Cherchi S, Rehm HL, MacArthur DG, Lek M, Laricchia KM, Wilson MW, Mane SM, Lifton RP, Lee RS, Bauer SB, Lu W, Reutter HM, Tasic V, Shril S, Hildebrandt F. Whole-Exome Sequencing Identifies Causative Mutations in Families with Congenital Anomalies of the Kidney and Urinary Tract. J Am Soc Nephrol 2018; 29:2348-2361. [PMID: 30143558 PMCID: PMC6115658 DOI: 10.1681/asn.2017121265] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 06/11/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Congenital anomalies of the kidney and urinary tract (CAKUT) are the most prevalent cause of kidney disease in the first three decades of life. Previous gene panel studies showed monogenic causation in up to 12% of patients with CAKUT. METHODS We applied whole-exome sequencing to analyze the genotypes of individuals from 232 families with CAKUT, evaluating for mutations in single genes known to cause human CAKUT and genes known to cause CAKUT in mice. In consanguineous or multiplex families, we additionally performed a search for novel monogenic causes of CAKUT. RESULTS In 29 families (13%), we detected a causative mutation in a known gene for isolated or syndromic CAKUT that sufficiently explained the patient's CAKUT phenotype. In three families (1%), we detected a mutation in a gene reported to cause a phenocopy of CAKUT. In 15 of 155 families with isolated CAKUT, we detected deleterious mutations in syndromic CAKUT genes. Our additional search for novel monogenic causes of CAKUT in consanguineous and multiplex families revealed a potential single, novel monogenic CAKUT gene in 19 of 232 families (8%). CONCLUSIONS We identified monogenic mutations in a known human CAKUT gene or CAKUT phenocopy gene as the cause of disease in 14% of the CAKUT families in this study. Whole-exome sequencing provides an etiologic diagnosis in a high fraction of patients with CAKUT and will provide a new basis for the mechanistic understanding of CAKUT.
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Affiliation(s)
- Amelie T van der Ven
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dervla M Connaughton
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Hadas Ityel
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nina Mann
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Makiko Nakayama
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jing Chen
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daw-Yang Hwang
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Julian Schulz
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - David Schapiro
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ronen Schneider
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jillian K Warejko
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ankana Daga
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amar J Majmundar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weizhen Tan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tobias Hermle
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eugen Widmeier
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shazia Ashraf
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ali Amar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charlotte A Hoogstraaten
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Hannah Hugo
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Thomas M Kitzler
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Franziska Kause
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Caroline M Kolvenbach
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rufeng Dai
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Leslie Spaneas
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kassaundra Amann
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Deborah R Stein
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michelle A Baum
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael J G Somers
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nancy M Rodig
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael A Ferguson
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Avram Z Traum
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ghaleb H Daouk
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Radovan Bogdanović
- Department of Pediatric Nephrology, Institute for Mother and Child Health Care, Belgrade, Serbia
| | - Natasa Stajić
- Department of Pediatric Nephrology, Institute for Mother and Child Health Care, Belgrade, Serbia
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Cairo University, Egypt
- Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Jameela A Kari
- Department of Pediatrics and
- Pediatric Nephrology Center of Excellence, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Sherif El Desoky
- Department of Pediatrics and
- Pediatric Nephrology Center of Excellence, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hanan M Fathy
- Pediatric Nephrology Unit, University of Alexandria, Alexandria, Egypt
| | - Danko Milosevic
- University of Zagreb School of Medicine, University Hospital Center Zagreb, Zagreb, Croatia
| | - Muna Al-Saffar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Hazem S Awad
- Pediatric Nephrology Department, Dubai Kidney Center Of Excellence, Dubai Hospital, Dubai, United Arab Emirates
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Kidney Center Of Excellence, Dubai Hospital, Dubai, United Arab Emirates
| | - Aravind Selvin
- Department of Pediatric Nephrology, Institute of Child Health and Hospital for Children, The Tamil Nadu Dr. M.G.R. Medical University, Chennai, Tamil Nadu, India
| | - Prabha Senguttuvan
- Department of Pediatric Nephrology, Dr. Mehta's Multi-Specialty Hospital, Chennai, Tamil Nadu, India
| | | | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Michael W Wilson
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Rockefeller University, New York, New York
| | - Richard S Lee
- Department of Urology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Weining Lu
- Renal Section, Department of Medicine and Pathology, Boston University Medical Center, Boston, Massachusetts
| | - Heiko M Reutter
- Institute of Human Genetics and
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; and
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts;
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Naert T, Vleminckx K. CRISPR/Cas9 disease models in zebrafish and Xenopus: The genetic renaissance of fish and frogs. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 28:41-52. [PMID: 30205880 DOI: 10.1016/j.ddtec.2018.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/29/2018] [Accepted: 07/13/2018] [Indexed: 12/11/2022]
Abstract
The speed by which clinical genomics is currently identifying novel potentially pathogenic variants is outperforming the speed by which these can be functionally (genotype-phenotype) annotated in animal disease models. However, over the past few years the emergence of CRISPR/Cas9 as a straight-forward genome editing technology has revolutionized disease modeling in vertebrate non-mammalian model organisms such as zebrafish, medaka and Xenopus. It is now finally possible, by CRISPR/Cas9, to rapidly establish clinically relevant disease models in these organisms. Interestingly, these can provide both cost-effective genotype-phenotype correlations for gene-(variants) and genomic rearrangements obtained from clinical practice, as well as be exploited to perform translational research to improve prospects of disease afflicted patients. In this review, we show an extensive overview of these new CRISPR/Cas9-mediated disease models and provide future prospects that will allow increasingly accurate modeling of human disease in zebrafish, medaka and Xenopus.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Belgium; Cancer Research Institute Ghent, Belgium
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Belgium; Center for Medical Genetics, Ghent University, Belgium; Cancer Research Institute Ghent, Belgium.
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53
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Schrauwen I, Kari E, Mattox J, Llaci L, Smeeton J, Naymik M, Raible DW, Knowles JA, Crump JG, Huentelman MJ, Friedman RA. De novo variants in GREB1L are associated with non-syndromic inner ear malformations and deafness. Hum Genet 2018; 137:459-470. [PMID: 29955957 PMCID: PMC6082420 DOI: 10.1007/s00439-018-1898-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/19/2018] [Indexed: 11/24/2022]
Abstract
Congenital inner ear malformations affecting both the osseous and membranous labyrinth can have a devastating impact on hearing and language development. With the exception of an enlarged vestibular aqueduct, non-syndromic inner ear malformations are rare, and their underlying molecular biology has thus far remained understudied. To identify molecular factors that might be important in the developing inner ear, we adopted a family-based trio exome sequencing approach in young unrelated subjects with severe inner ear malformations. We identified two previously unreported de novo loss-of-function variants in GREB1L [c.4368G>T;p.(Glu1410fs) and c.982C>T;p.(Arg328*)] in two affected subjects with absent cochleae and eighth cranial nerve malformations. The cochlear aplasia in these affected subjects suggests that a developmental arrest or problem at a very early stage of inner ear development exists, e.g., during the otic pit formation. Craniofacial Greb1l RNA expression peaks in mice during this time frame (E8.5). It also peaks in the developing inner ear during E13-E16, after which it decreases in adulthood. The crucial function of Greb1l in craniofacial development is also evidenced in knockout mice, which develop severe craniofacial abnormalities. In addition, we show that Greb1l-/- zebrafish exhibit a loss of abnormal sensory epithelia innervation. An important role for Greb1l in sensory epithelia innervation development is supported by the eighth cranial nerve deficiencies seen in both affected subjects. In conclusion, we demonstrate that GREB1L is a key player in early inner ear and eighth cranial nerve development. Abnormalities in cochleovestibular anatomy can provide challenges for cochlear implantation. Combining a molecular diagnosis with imaging techniques might aid the development of individually tailored therapeutic interventions in the future.
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Affiliation(s)
- Isabelle Schrauwen
- Molecular and Human Genetics Department, Center for Statistical Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA.
| | - Elina Kari
- Division of Otolaryngology, Head and Neck Surgery, Department of Surgery, University of California, San Diego, ECOB-East Campus Office Building Room 3-013, 9444 Medical Center Drive, Mail Code 7220, La Jolla, CA, 92037, USA
| | - Jacob Mattox
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery, Keck University of Southern California School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Lorida Llaci
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - Joanna Smeeton
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Marcus Naymik
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - David W Raible
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA
| | - James A Knowles
- Department of Cell Biology-MSC 5, SUNY Downstate Medical Center, 450 Clarkson Avenue, BSB 2-5, Brooklyn, NY, 11203, USA
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, 1975 Zonal Ave., Los Angeles, CA, 90033, USA
| | - Matthew J Huentelman
- Neurogenomics Division and Center for Rare Childhood Disorders, Translational Genomics Research Institute, 445 N 5th str, Phoenix, AZ, 85004, USA
| | - Rick A Friedman
- Division of Otolaryngology, Head and Neck Surgery, Department of Surgery, University of California, San Diego, ECOB-East Campus Office Building Room 3-013, 9444 Medical Center Drive, Mail Code 7220, La Jolla, CA, 92037, USA
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54
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Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Hrabě de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, Nutter LMJ, Reilly PT, Seavitt JR, Seong JK, Simon M, Wardle-Jones H, Mallon AM, Smedley D, Parkinson HE. The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation. CONSERV GENET 2018; 19:995-1005. [PMID: 30100824 PMCID: PMC6061128 DOI: 10.1007/s10592-018-1072-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/03/2018] [Indexed: 01/08/2023]
Abstract
The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.
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Affiliation(s)
- Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Pilar Cacheiro
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Terrence F. Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Juan Antonio Aguilar-Pimentel
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Steve D. M. Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | - Ann M. Flenniken
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - K. C. Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA 95618 USA
| | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
| | - Hugh Morgan
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | | | - Lauryl M. J. Nutter
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
| | - Patrick T. Reilly
- PHENOMIN-iCS, 1 Rue Laurent Fries, 67404 Illkirch Cedex, Alsace France
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Interdisciplinary Program for Bioinformatics and Program for Cancer Biology, Seoul National University, Seoul, Republic of Korea
| | - Michelle Simon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | | | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - the IMPC consortium
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA UK
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
- Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
- Mouse Biology Program, University of California, Davis, CA 95618 USA
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
- PHENOMIN-iCS, 1 Rue Laurent Fries, 67404 Illkirch Cedex, Alsace France
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Interdisciplinary Program for Bioinformatics and Program for Cancer Biology, Seoul National University, Seoul, Republic of Korea
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Rasmussen M, Sunde L, Nielsen ML, Ramsing M, Petersen A, Hjortshøj TD, Olsen TE, Tabor A, Hertz JM, Johnsen I, Sperling L, Petersen OB, Jensen UB, Møller FG, Petersen MB, Lildballe DL. Targeted gene sequencing and whole-exome sequencing in autopsied fetuses with prenatally diagnosed kidney anomalies. Clin Genet 2018; 93:860-869. [PMID: 29194579 DOI: 10.1111/cge.13185] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 01/16/2023]
Abstract
Identification of fetal kidney anomalies invites questions about underlying causes and recurrence risk in future pregnancies. We therefore investigated the diagnostic yield of next-generation sequencing in fetuses with bilateral kidney anomalies and the correlation between disrupted genes and fetal phenotypes. Fetuses with bilateral kidney anomalies were screened using an in-house-designed kidney-gene panel. In families where candidate variants were not identified, whole-exome sequencing was performed. Genes uncovered by this analysis were added to our kidney panel. We identified likely deleterious variants in 11 of 56 (20%) families. The kidney-gene analysis revealed likely deleterious variants in known kidney developmental genes in 6 fetuses and TMEM67 variants in 2 unrelated fetuses. Kidney histology was similar in the latter 2 fetuses-presenting a distinct prenatal form of nephronophthisis. Exome sequencing identified ROBO1 variants in one family and a GREB1L variant in another family. GREB1L and ROBO1 were added to our kidney-gene panel and additional variants were identified. Next-generation sequencing substantially contributes to identifying causes of fetal kidney anomalies. Genetic causes may be supported by histological examination of the kidneys. This is the first time that SLIT-ROBO signaling is implicated in human bilateral kidney agenesis.
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Affiliation(s)
- M Rasmussen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - L Sunde
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - M L Nielsen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - M Ramsing
- Department of Pathology, Randers Regional Hospital, Randers, Denmark
| | - A Petersen
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | - T D Hjortshøj
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - T E Olsen
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | - A Tabor
- Department of Obstetrics, Center of Fetal Medicine, Rigshospitalet, Copenhagen, Denmark
| | - J M Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - I Johnsen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - L Sperling
- Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - O B Petersen
- Department of Gynecology and Obstetrics, Aarhus University Hospital, Aarhus, Denmark
| | - U B Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - F G Møller
- Department of Pediatrics, Herning Regional Hospital, Herning, Denmark
| | - M B Petersen
- Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - D L Lildballe
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
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56
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Sanna-Cherchi S, Westland R, Ghiggeri GM, Gharavi AG. Genetic basis of human congenital anomalies of the kidney and urinary tract. J Clin Invest 2018; 128:4-15. [PMID: 29293093 DOI: 10.1172/jci95300] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The clinical spectrum of congenital anomalies of the kidney and urinary tract (CAKUT) encompasses a common birth defect in humans that has significant impact on long-term patient survival. Overall, data indicate that approximately 20% of patients may have a genetic disorder that is usually not detected based on standard clinical evaluation, implicating many different mutational mechanisms and pathogenic pathways. In particular, 10% to 15% of CAKUT patients harbor an unsuspected genomic disorder that increases risk of neurocognitive impairment and whose early recognition can impact clinical care. The emergence of high-throughput genomic technologies is expected to provide insight into the common and rare genetic determinants of diseases and offer opportunities for early diagnosis with genetic testing.
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Affiliation(s)
- Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA.,Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, Netherlands
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis and Transplantation, Istituto Giannina Gaslini, Genoa, Italy
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
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De Tomasi L, David P, Humbert C, Silbermann F, Arrondel C, Tores F, Fouquet S, Desgrange A, Niel O, Bole-Feysot C, Nitschké P, Roume J, Cordier MP, Pietrement C, Isidor B, Khau Van Kien P, Gonzales M, Saint-Frison MH, Martinovic J, Novo R, Piard J, Cabrol C, Verma IC, Puri R, Journel H, Aziza J, Gavard L, Said-Menthon MH, Heidet L, Saunier S, Jeanpierre C. Mutations in GREB1L Cause Bilateral Kidney Agenesis in Humans and Mice. Am J Hum Genet 2017; 101:803-814. [PMID: 29100091 DOI: 10.1016/j.ajhg.2017.09.026] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/28/2017] [Indexed: 12/25/2022] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) constitute a major cause of chronic kidney disease in children and 20% of prenatally detected anomalies. CAKUT encompass a spectrum of developmental kidney defects, including renal agenesis, hypoplasia, and cystic and non-cystic dysplasia. More than 50 genes have been reported as mutated in CAKUT-affected case subjects. However, the pathophysiological mechanisms leading to bilateral kidney agenesis (BKA) remain largely elusive. Whole-exome or targeted exome sequencing of 183 unrelated familial and/or severe CAKUT-affected case subjects, including 54 fetuses with BKA, led to the identification of 16 heterozygous variants in GREB1L (growth regulation by estrogen in breast cancer 1-like), a gene reported as a target of retinoic acid signaling. Four loss-of-function and 12 damaging missense variants, 14 being absent from GnomAD, were identified. Twelve of them were present in familial or simplex BKA-affected case subjects. Female BKA-affected fetuses also displayed uterus agenesis. We demonstrated a significant association between GREB1L variants and BKA. By in situ hybridization, we showed expression of Greb1l in the nephrogenic zone in developing mouse kidney. We generated a Greb1l knock-out mouse model by CRISPR-Cas9. Analysis at E13.5 revealed lack of kidneys and genital tract anomalies in male and female Greb1l-/- embryos and a slight decrease in ureteric bud branching in Greb1l+/- embryos. We showed that Greb1l invalidation in mIMCD3 cells affected tubulomorphogenesis in 3D-collagen culture, a phenotype rescued by expression of the wild-type human protein. This demonstrates that GREB1L plays a major role in early metanephros and genital development in mice and humans.
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Sanna-Cherchi S, Khan K, Westland R, Krithivasan P, Fievet L, Rasouly HM, Ionita-Laza I, Capone VP, Fasel DA, Kiryluk K, Kamalakaran S, Bodria M, Otto EA, Sampson MG, Gillies CE, Vega-Warner V, Vukojevic K, Pediaditakis I, Makar GS, Mitrotti A, Verbitsky M, Martino J, Liu Q, Na YJ, Goj V, Ardissino G, Gigante M, Gesualdo L, Janezcko M, Zaniew M, Mendelsohn CL, Shril S, Hildebrandt F, van Wijk JAE, Arapovic A, Saraga M, Allegri L, Izzi C, Scolari F, Tasic V, Ghiggeri GM, Latos-Bielenska A, Materna-Kiryluk A, Mane S, Goldstein DB, Lifton RP, Katsanis N, Davis EE, Gharavi AG. Exome-wide Association Study Identifies GREB1L Mutations in Congenital Kidney Malformations. Am J Hum Genet 2017; 101:789-802. [PMID: 29100090 DOI: 10.1016/j.ajhg.2017.09.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/22/2017] [Indexed: 01/02/2023] Open
Abstract
Renal agenesis and hypodysplasia (RHD) are major causes of pediatric chronic kidney disease and are highly genetically heterogeneous. We conducted whole-exome sequencing in 202 case subjects with RHD and identified diagnostic mutations in genes known to be associated with RHD in 7/202 case subjects. In an additional affected individual with RHD and a congenital heart defect, we found a homozygous loss-of-function (LOF) variant in SLIT3, recapitulating phenotypes reported with Slit3 inactivation in the mouse. To identify genes associated with RHD, we performed an exome-wide association study with 195 unresolved case subjects and 6,905 control subjects. The top signal resided in GREB1L, a gene implicated previously in Hoxb1 and Shha signaling in zebrafish. The significance of the association, which was p = 2.0 × 10-5 for novel LOF, increased to p = 4.1 × 10-6 for LOF and deleterious missense variants combined, and augmented further after accounting for segregation and de novo inheritance of rare variants (joint p = 2.3 × 10-7). Finally, CRISPR/Cas9 disruption or knockdown of greb1l in zebrafish caused specific pronephric defects, which were rescued by wild-type human GREB1L mRNA, but not mRNA containing alleles identified in case subjects. Together, our study provides insight into the genetic landscape of kidney malformations in humans, presents multiple candidates, and identifies SLIT3 and GREB1L as genes implicated in the pathogenesis of RHD.
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Affiliation(s)
| | - Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Rik Westland
- Division of Nephrology, Columbia University, New York, NY 10032, USA; Department of Pediatric Nephrology, VU University Medical Center, Amsterdam 1007 MB, the Netherlands
| | - Priya Krithivasan
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Lorraine Fievet
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Hila Milo Rasouly
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | | | | | - David A Fasel
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Sitharthan Kamalakaran
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa 16147, Italy
| | - Edgar A Otto
- University of Michigan School of Medicine, Department of Internal Medicine-Nephrology, Ann Arbor, MI 48109, USA
| | - Matthew G Sampson
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI 48109, USA
| | - Christopher E Gillies
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI 48109, USA
| | - Virginia Vega-Warner
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI 48109, USA
| | - Katarina Vukojevic
- Department of Anatomy, Histology, and Embryology, School of Medicine, University of Split, Split 21000, Croatia
| | - Igor Pediaditakis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Gabriel S Makar
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Adele Mitrotti
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Miguel Verbitsky
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Jeremiah Martino
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Qingxue Liu
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Young-Ji Na
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Vinicio Goj
- Pediatric Unit, Fatebenefratelli Hospital, Milan 20121, Italy
| | - Gianluigi Ardissino
- Pediatric Nephrology and Dialysis Unit, Fondazione Ca' Granda IRCCS Ospedale Maggiore Policlinico Milano, 20122 Milan, Italy
| | - Maddalena Gigante
- Department of Medical and Surgical Sciences, University of Foggia, Foggia 71121, Italy
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari 70121, Italy
| | - Magdalena Janezcko
- Department of Medical Genetics, Chair of Pediatrics, Jagiellonian University, Collegium Medicum, Krakow 31-008, Poland
| | | | - Cathy Lee Mendelsohn
- Department of Urology, Pathology and Cell Biology, Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam 1007 MB, the Netherlands
| | - Adela Arapovic
- Department of Pediatrics, University Hospital of Split, Split 21000, Croatia
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split 21000, Croatia; School of Medicine, University of Split, Split 21000, Croatia
| | - Landino Allegri
- Department of Medicine and Surgery, University of Parma, Parma 43100, Italy
| | - Claudia Izzi
- Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari, Brescia 25018, Italy; Dipartimento Ostetrico Ginecologico, Azienda Ospedaliera Spedali Civili di Brescia, Brescia 25018, Italy
| | - Francesco Scolari
- Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari, Brescia 25018, Italy
| | - Velibor Tasic
- Department of Pediatric Nephrology, University Children's Hospital, Medical Faculty of Skopje, Skopje 1000, Macedonia
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa 16147, Italy
| | - Anna Latos-Bielenska
- Department of Medical Genetics, Poznan University of Medical Sciences, and Center for Medical Genetics GENESIS, Poznan 61-701, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and Center for Medical Genetics GENESIS, Poznan 61-701, Poland
| | - Shrikant Mane
- Department of Human Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Richard P Lifton
- Department of Human Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, New York, NY 10032, USA
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