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Ebach F, Wagner P, Stein R, Dolscheid‐Pommerich R, Reutter H, Hilger AC. Familial congenital lower urinary tract obstruction (LUTO) suggested by screening for lower urinary tract dysfunction in parents of patients: A descriptive study. Health Sci Rep 2024; 7:e1935. [PMID: 38524771 PMCID: PMC10957716 DOI: 10.1002/hsr2.1935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/12/2024] [Accepted: 02/02/2024] [Indexed: 03/26/2024] Open
Abstract
Background Congenital lower urinary tract obstruction (LUTO) describes a heterogeneous group of congenital malformations. Posterior urethral valves (PUV) represent the most common entity. Familial occurrence has been described, suggestive of underlying genetic factors. LUTO can occur in various degrees of severity. In severe forms, oligohydramnios, pulmonary hypoplasia, and renal damage can occur resulting in high pre- and postnatal mortality. On the contrary, mild forms may become apparent through recurrent urinary tract infections. Such high phenotypic variability has been described even within the same family. Here, we systematically screened parents of affected children for symptoms of LUTO. Methods The study population consisted of parents of LUTO patients. Fathers over 50 years of age were excluded, to avoid inclusion of male phenocopies due to early prostatic hypertrophy. Uroflowmetry, ultrasonography for residual urine and hydronephrosis, and laboratory examination of standard renal retention parameters were assessed, and a detailed patient history was taken, including the assessment of the International Prostate Symptom Score. Results Twenty-nine of 42 LUTO families enrolled were found eligible for the present study. Of these, we identified five families in which the father had already been diagnosed with infravesical obstruction (17%). Of the remaining families, nine agreed to participate in our study. Of these nine families, eight families had a child affected with PUV and one family had a child with urethral stenosis. Here, we found two fathers and one mother with symptoms of LUTO suggestive of mild LUTO and one family, in which the unborn male fetal brother of the affected index patient was also diagnosed prenatally with LUTO. Conclusion Our observations suggest that LUTOs have a higher heritability than previously thought and that first-degree relatives of the affected should be clinically assessed for symptoms of LUTO.
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Affiliation(s)
- Fabian Ebach
- Department of Neonatology and Pediatric Intensive CareUniversity Hospital BonnBonnGermany
| | - Pauline Wagner
- Department of Neonatology and Pediatric Intensive CareUniversity Hospital BonnBonnGermany
| | - Raimund Stein
- Center for Pediatric, Adolescent and Reconstructive Urology, University Medical Center Mannheim, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | | | - Heiko Reutter
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology and Pediatric Intensive CareUniversity Hospital ErlangenErlangenGermany
| | - Alina C. Hilger
- Department of Pediatrics and Adolescent MedicineUniversity Hospital ErlangenErlangenGermany
- Research Center on Rare Kidney Diseases (RECORD)University Hospital ErlangenErlangenGermany
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2
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Brar BK, Blakemore K, Hertenstein C, Miller JL, Miller KA, Shamseldin H, Maddirevula S, Hays T, Lianoglou B, Dukhovny S, Baker LA, Sparks TN, Wapner R, Alkuraya FS, Norton ME, Jelin AC. The utility of gene sequencing in identifying an underlying genetic disorder in prenatally suspected lower urinary tract obstruction. Prenat Diagn 2024; 44:196-204. [PMID: 37594370 DOI: 10.1002/pd.6425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 08/19/2023]
Abstract
OBJECTIVE Fetal megacystis generally presents as suspected lower urinary tract obstruction (LUTO), which is associated with severe perinatal morbidity. Genetic etiologies underlying LUTO or a LUTO-like initial presentation are poorly understood. Our objectives are to describe single gene etiologies in fetuses initially ascertained to have suspected LUTO and to elucidate genotype-phenotype correlations. METHODS A retrospective case series of suspected fetal LUTO positive for a molecular diagnosis was collected from five centers in the Fetal Sequencing Consortium. Demographics, sonograms, genetic testing including variant classification, and delivery outcomes were abstracted. RESULTS Seven cases of initially prenatally suspected LUTO-positive for a molecular diagnosis were identified. In no case was the final diagnosis established as urethral obstruction that is, LUTO. All variants were classified as likely pathogenic or pathogenic. Smooth muscle deficiencies involving the bladder wall and interfering with bladder emptying were identified in five cases: MYOCD (2), ACTG2 (2), and MYH11 (1). Other genitourinary and/or non-genitourinary malformations were seen in two cases involving KMT2D (1) and BBS10 (1). CONCLUSION Our series illustrates the value of molecular diagnostics in the workup of fetuses who present with prenatally suspected LUTO but who may have a non-LUTO explanation for their prenatal ultrasound findings.
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Affiliation(s)
- Bobby K Brar
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Karin Blakemore
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Christine Hertenstein
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jena L Miller
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Kristen A Miller
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Hanan Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Thomas Hays
- Department of Pediatrics, Division of Neonatology, Columbia University Irving Medical Center, New York, New York, USA
| | - Billie Lianoglou
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California, USA
| | - Stephanie Dukhovny
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - Linda A Baker
- Department of Urology, Division of Pediatric Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Teresa N Sparks
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mary E Norton
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California, USA
| | - Angie C Jelin
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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3
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Orang A, Dredge BK, Liu CY, Bracken JM, Chen CH, Sourdin L, Whitfield HJ, Lumb R, Boyle ST, Davis MJ, Samuel MS, Gregory PA, Khew-Goodall Y, Goodall GJ, Pillman KA, Bracken CP. Basonuclin-2 regulates extracellular matrix production and degradation. Life Sci Alliance 2023; 6:e202301984. [PMID: 37536977 PMCID: PMC10400885 DOI: 10.26508/lsa.202301984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
Epithelial-mesenchymal transition is essential for tissue patterning and organization. It involves both regulation of cell motility and alterations in the composition and organization of the ECM-a complex environment of proteoglycans and fibrous proteins essential for tissue homeostasis, signaling in response to chemical and biomechanical stimuli, and is often dysregulated under conditions such as cancer, fibrosis, and chronic wounds. Here, we demonstrate that basonuclin-2 (BNC2), a mesenchymal-expressed gene, that is, strongly associated with cancer and developmental defects across genome-wide association studies, is a novel regulator of ECM composition and degradation. We find that at endogenous levels, BNC2 controls the expression of specific collagens, matrix metalloproteases, and other matrisomal components in breast cancer cells, and in fibroblasts that are primarily responsible for the production and processing of the ECM within the tumour microenvironment. In so doing, BNC2 modulates the motile and invasive properties of cancers, which likely explains the association of high BNC2 expression with increasing cancer grade and poor patient prognosis.
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Affiliation(s)
- Ayla Orang
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - B Kate Dredge
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Chi Yau Liu
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Julie M Bracken
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Chun-Hsien Chen
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Laura Sourdin
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Holly J Whitfield
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Rachael Lumb
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Sarah T Boyle
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
| | - Melissa J Davis
- South Australian ImmunogGENomics Cancer Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
- Division of Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
- Fraser Institute, University of Queensland, Wooloongabba, Australia
| | - Michael S Samuel
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine and School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Yeesim Khew-Goodall
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine and School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine and School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine and School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, Australia
- Department of Medicine and School of Biological Sciences, University of Adelaide, Adelaide, Australia
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Flores-Torres J, Sanchez-Valle A, Duncan JR, Panzarino V, Rodriguez JM, Kirby RS. Lower Urinary Tract Obstruction in Newborns. Adv Pediatr 2023; 70:131-144. [PMID: 37422291 DOI: 10.1016/j.yapd.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2023]
Abstract
Lower urinary tract obstruction (LUTO) is a rare birth defect with a prevalence between 1 in 5,000 and 1 in 25,000 pregnancies. LUTO is one of the most common causes of congenital abnormalities of the renal tract. Several genetic conditions have been associated with LUTO. Most common causes of LUTO are posterior urethral valves and urethral atresia. Despite available prenatal and postnatal treatments, LUTO is a significant cause of morbidity and mortality in newborns causing significant end stage renal disease and pulmonary hypoplasia.
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Affiliation(s)
- Jaime Flores-Torres
- Division of Neonatology, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa General Hospital, 5 Tampa General Circle HMT 4th Floor, Suite 450, Tampa, FL 33606, USA.
| | - Amarilis Sanchez-Valle
- Division of Genetics and Metabolism, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa General Hospital, 2 Tampa General Circle, Tampa, FL 33606, USA
| | - Jose R Duncan
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Morsani College of Medicine, University of South Florida, Tampa General Hospital, 2 Tampa General Circle, Tampa, FL 33606, USA
| | - Valerie Panzarino
- Division of Pediatric Nephrology, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa General Hospital, 2 Tampa General Circle, Tampa, FL 33606, USA
| | - Jessica Marie Rodriguez
- Division of Pediatric Nephrology, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa General Hospital, Tampa, FL, USA; Johns Hopkins All Children's Hospital, St. Joseph's Hospital, 601 5th Street South, Suite 304,Street, Petersburg, FL 33701, USA
| | - Russell S Kirby
- Chiles Center, College of Public Health, University of South Florida, 13201 Bruce B Downs Boulevard, MDC56, Tampa, FL 33612, USA
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Hey S, Whyte D, Hoang MC, Le N, Natvig J, Wingfield C, Onyeama C, Howrylak J, Toby IT. Analysis of CDR3 Sequences from T-Cell Receptor β in Acute Respiratory Distress Syndrome. Biomolecules 2023; 13:biom13050825. [PMID: 37238695 DOI: 10.3390/biom13050825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Acute Respiratory Distress Syndrome (ARDS) is an illness that typically develops in people who are significantly ill or have serious injuries. ARDS is characterized by fluid build-up that occurs in the alveoli. T-cells are implicated as playing a role in the modulation of the aberrant response leading to excessive tissue damage and, eventually, ARDS. Complementarity Determining Region 3 (CDR3) sequences derived from T-cells are key players in the adaptive immune response. This response is governed by an elaborate specificity for distinct molecules and the ability to recognize and vigorously respond to repeated exposures to the same molecules. Most of the diversity in T-cell receptors (TCRs) is contained in the CDR3 regions of the heterodimeric cell-surface receptors. For this study, we employed the novel technology of immune sequencing to assess lung edema fluid. Our goal was to explore the landscape of CDR3 clonal sequences found within these samples. We obtained more than 3615 CDR3 sequences across samples in the study. Our data demonstrate that: (1) CDR3 sequences from lung edema fluid exhibit distinct clonal populations, and (2) CDR3 sequences can be further characterized based on biochemical features. Analysis of these CDR3 sequences offers insight into the CDR3-driven T-cell repertoire of ARDS. These findings represent the first step towards applications of this technology with these types of biological samples in the context of ARDS.
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Affiliation(s)
- Sara Hey
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | - Dayjah Whyte
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | - Minh-Chau Hoang
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | - Nick Le
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | - Joseph Natvig
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | - Claire Wingfield
- Department of Biology, University of Dallas, Irving, TX 75062, USA
| | | | - Judie Howrylak
- Pulmonary, Allergy and Critical Care Division, Penn State Milton S. Hershey Medical Center, Hershey, PA 17033, USA
| | - Inimary T Toby
- Department of Biology, University of Dallas, Irving, TX 75062, USA
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6
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Kolvenbach CM, Dworschak GC, Rieke JM, Woolf AS, Reutter H, Odermatt B, Hilger AC. Modelling human lower urinary tract malformations in zebrafish. Mol Cell Pediatr 2023; 10:2. [PMID: 36977792 PMCID: PMC10050536 DOI: 10.1186/s40348-023-00156-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Advances in molecular biology are improving our understanding of the genetic causes underlying human congenital lower urinary tract (i.e., bladder and urethral) malformations. This has recently led to the identification of the first disease-causing variants in the gene BNC2 for isolated lower urinary tract anatomical obstruction (LUTO), and of WNT3 and SLC20A1 as genes implicated in the pathogenesis of the group of conditions called bladder-exstrophy-epispadias complex (BEEC). Implicating candidate genes from human genetic data requires evidence of their influence on lower urinary tract development and evidence of the found genetic variants' pathogenicity. The zebrafish (Danio rerio) has many advantages for use as a vertebrate model organism for the lower urinary tract. Rapid reproduction with numerous offspring, comparable anatomical kidney and lower urinary tract homology, and easy genetic manipulability by Morpholino®-based knockdown or CRISPR/Cas editing are among its advantages. In addition, established marker staining for well-known molecules involved in urinary tract development using whole-mount in situ hybridization (WISH) and the usage of transgenic lines expressing fluorescent protein under a tissue-specific promoter allow easy visualization of phenotypic abnormalities of genetically modified zebrafish. Assays to examine the functionality of the excretory organs can also be modeled in vivo with the zebrafish. The approach of using these multiple techniques in zebrafish not only enables rapid and efficient investigation of candidate genes for lower urinary tract malformations derived from human data, but also cautiously allows transferability of causality from a non-mammalian vertebrate to humans.
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Affiliation(s)
- Caroline M Kolvenbach
- Institute of Anatomy, Medical Faculty, University of Bonn, Bonn, Germany.
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Gabriel C Dworschak
- Institute of Anatomy, Medical Faculty, University of Bonn, Bonn, Germany
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Department of Neuropediatrics, University Hospital Bonn, Bonn, Germany
| | - Johanna M Rieke
- Department of Pediatrics, Children's Hospital Medical Center, University Hospital Bonn, Bonn, Germany
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Heiko Reutter
- Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Benjamin Odermatt
- Institute of Anatomy, Medical Faculty, University of Bonn, Bonn, Germany
| | - Alina C Hilger
- Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
- Research Center On Rare Kidney Diseases (RECORD), University Hospital Erlangen, Erlangen, Germany
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7
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Kolvenbach CM, Felger T, Schierbaum L, Thiffault I, Pastinen T, Szczepańska M, Zaniew M, Adamczyk P, Bayat A, Yilmaz Ö, Lindenberg TT, Thiele H, Hildebrandt F, Hinderhofer K, Moog U, Hilger AC, Sullivan B, Bartik L, Gnyś P, Grote P, Odermatt B, Reutter HM, Dworschak GC. X-linked variations in SHROOM4are implicated in congenital anomalies of the urinary tract and the anorectal, cardiovascular and central nervous systems. J Med Genet 2022; 60:587-596. [PMID: 36379543 DOI: 10.1136/jmg-2022-108738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/01/2022] [Indexed: 11/16/2022]
Abstract
BackgroundSHROOM4is thought to play an important role in cytoskeletal modification and development of the early nervous system. Previously, single-nucleotide variants (SNVs) or copy number variations (CNVs) inSHROOM4have been associated with the neurodevelopmental disorder Stocco dos Santos syndrome, but not with congenital anomalies of the urinary tract and the visceral or the cardiovascular system.MethodsHere, exome sequencing and CNV analyses besides expression studies in zebrafish and mouse andknockdown(KD) experiments using a splice blocking morpholino in zebrafish were performed to study the role ofSHROOM4during embryonic development.ResultsIn this study, we identified putative disease-causing SNVs and CNVs inSHROOM4in six individuals from four families with congenital anomalies of the urinary tract and the anorectal, cardiovascular and central nervous systems (CNS). Embryonic mouse and zebrafish expression studies showedShroom4expression in the upper and lower urinary tract, the developing cloaca, the heart and the cerebral CNS. KD studies in zebrafish larvae revealed pronephric cysts, anomalies of the cloaca and the heart, decreased eye-to-head ratio and higher mortality compared with controls. These phenotypes could be rescued by co-injection of human wild-typeSHROOM4mRNA and morpholino.ConclusionThe identified SNVs and CNVs in affected individuals with congenital anomalies of the urinary tract, the anorectal, the cardiovascular and the central nervous systems, and subsequent embryonic mouse and zebrafish studies suggestSHROOM4as a developmental gene for different organ systems.
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8
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Clinical variant interpretation and biologically relevant reference transcripts. NPJ Genom Med 2022; 7:59. [PMID: 36257961 PMCID: PMC9579139 DOI: 10.1038/s41525-022-00329-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/29/2022] [Indexed: 12/03/2022] Open
Abstract
Clinical variant interpretation is highly dependent on the choice of reference transcript. Although the longest transcript has traditionally been chosen as the reference, APPRIS principal and MANE Select transcripts, biologically supported reference sequences, are now available. In this study, we show that MANE Select and APPRIS principal transcripts are the best reference transcripts for clinical variation. APPRIS principal and MANE Select transcripts capture almost all ClinVar pathogenic variants, and they are particularly powerful over the 94% of coding genes in which they agree. We find that a vanishingly small number of ClinVar pathogenic variants affect alternative protein products. Alternative isoforms that are likely to be clinically relevant can be predicted using TRIFID scores, the highest scoring alternative transcripts are almost 700 times more likely to house pathogenic variants. We believe that APPRIS, MANE and TRIFID are essential tools for clinical variant interpretation.
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9
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Kagan M, Pleniceanu O, Vivante A. The genetic basis of congenital anomalies of the kidney and urinary tract. Pediatr Nephrol 2022; 37:2231-2243. [PMID: 35122119 DOI: 10.1007/s00467-021-05420-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022]
Abstract
During the past decades, remarkable progress has been made in our understanding of the molecular basis of kidney diseases, as well as in the ability to pinpoint disease-causing genetic changes. Congenital anomalies of the kidney and urinary tract (CAKUT) are remarkably diverse, and may be either isolated to the kidney or involve other systems, and are notorious in their variable genotype-phenotype correlations. Genetic conditions underlying CAKUT are individually rare, but collectively contribute to disease etiology in ~ 16% of children with CAKUT. In this review, we will discuss basic concepts of kidney development and genetics, common causes of monogenic CAKUT, and the approach to diagnosing and managing a patient with suspected monogenic CAKUT. Altogether, the concepts presented herein represent an introduction to the emergence of nephrogenetics, a fast-growing multi-disciplinary field that is focused on deciphering the causes and manifestations of genetic kidney diseases as well as providing the framework for managing patients with genetic forms of CAKUT.
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Affiliation(s)
- Maayan Kagan
- Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Oren Pleniceanu
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Kidney Research Lab, The Institute of Nephrology and Hypertension, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Asaf Vivante
- Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601, Ramat Gan, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. .,Talpiot Medical Leadership Program, Tel HaShomer, Ramat Gan, Israel.
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10
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Chan MMY, Sadeghi-Alavijeh O, Lopes FM, Hilger AC, Stanescu HC, Voinescu CD, Beaman GM, Newman WG, Zaniew M, Weber S, Ho YM, Connolly JO, Wood D, Maj C, Stuckey A, Kousathanas A, Kleta R, Woolf AS, Bockenhauer D, Levine AP, Gale DP. Diverse ancestry whole-genome sequencing association study identifies TBX5 and PTK7 as susceptibility genes for posterior urethral valves. eLife 2022; 11:e74777. [PMID: 36124557 PMCID: PMC9512401 DOI: 10.7554/elife.74777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 08/15/2022] [Indexed: 12/12/2022] Open
Abstract
Posterior urethral valves (PUV) are the commonest cause of end-stage renal disease in children, but the genetic architecture of this rare disorder remains unknown. We performed a sequencing-based genome-wide association study (seqGWAS) in 132 unrelated male PUV cases and 23,727 controls of diverse ancestry, identifying statistically significant associations with common variants at 12q24.21 (p=7.8 × 10-12; OR 0.4) and rare variants at 6p21.1 (p=2.0 × 10-8; OR 7.2), that were replicated in an independent European cohort of 395 cases and 4151 controls. Fine mapping and functional genomic data mapped these loci to the transcription factor TBX5 and planar cell polarity gene PTK7, respectively, the encoded proteins of which were detected in the developing urinary tract of human embryos. We also observed enrichment of rare structural variation intersecting with candidate cis-regulatory elements, particularly inversions predicted to affect chromatin looping (p=3.1 × 10-5). These findings represent the first robust genetic associations of PUV, providing novel insights into the underlying biology of this poorly understood disorder and demonstrate how a diverse ancestry seqGWAS can be used for disease locus discovery in a rare disease.
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Affiliation(s)
- Melanie MY Chan
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
| | | | - Filipa M Lopes
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Alina C Hilger
- Children's Hospital, University of BonnBonnGermany
- Institute of Human Genetics, University of BonnBonnGermany
| | - Horia C Stanescu
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
| | - Catalin D Voinescu
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
| | - Glenda M Beaman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation TrustManchesterUnited Kingdom
- Evolution and Genomic Sciences, School of Biological Sciences, University of ManchesterManchesterUnited Kingdom
| | - William G Newman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation TrustManchesterUnited Kingdom
- Evolution and Genomic Sciences, School of Biological Sciences, University of ManchesterManchesterUnited Kingdom
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona GóraZielona GoraPoland
| | - Stefanie Weber
- Department of Pediatric Nephrology, University of MarburgMarburgGermany
| | - Yee Mang Ho
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - John O Connolly
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Department of Adolescent Urology, University College London Hospitals NHS Foundation TrustLondonUnited Kingdom
| | - Dan Wood
- Department of Adolescent Urology, University College London Hospitals NHS Foundation TrustLondonUnited Kingdom
| | - Carlo Maj
- Center for Human Genetics, University of MarburgMarburgGermany
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of BonnBonnGermany
| | - Alexander Stuckey
- Genomics England, Queen Mary University of LondonLondonUnited Kingdom
| | | | - Robert Kleta
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Nephrology Department, Great Ormond Street Hospital for Children NHS Foundation TrustLondonUnited Kingdom
| | - Adrian S Woolf
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
- Royal Manchester Children’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Detlef Bockenhauer
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Nephrology Department, Great Ormond Street Hospital for Children NHS Foundation TrustLondonUnited Kingdom
| | - Adam P Levine
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Research Department of Pathology, University College LondonLondonUnited Kingdom
| | - Daniel P Gale
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
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11
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Functional genomics uncovers the transcription factor BNC2 as required for myofibroblastic activation in fibrosis. Nat Commun 2022; 13:5324. [PMID: 36088459 PMCID: PMC9464213 DOI: 10.1038/s41467-022-33063-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 08/31/2022] [Indexed: 11/21/2022] Open
Abstract
Tissue injury triggers activation of mesenchymal lineage cells into wound-repairing myofibroblasts, whose unrestrained activity leads to fibrosis. Although this process is largely controlled at the transcriptional level, whether the main transcription factors involved have all been identified has remained elusive. Here, we report multi-omics analyses unraveling Basonuclin 2 (BNC2) as a myofibroblast identity transcription factor. Using liver fibrosis as a model for in-depth investigations, we first show that BNC2 expression is induced in both mouse and human fibrotic livers from different etiologies and decreases upon human liver fibrosis regression. Importantly, we found that BNC2 transcriptional induction is a specific feature of myofibroblastic activation in fibrotic tissues. Mechanistically, BNC2 expression and activities allow to integrate pro-fibrotic stimuli, including TGFβ and Hippo/YAP1 signaling, towards induction of matrisome genes such as those encoding type I collagen. As a consequence, Bnc2 deficiency blunts collagen deposition in livers of mice fed a fibrogenic diet. Additionally, our work establishes BNC2 as potentially druggable since we identified the thalidomide derivative CC-885 as a BNC2 inhibitor. Altogether, we propose that BNC2 is a transcription factor involved in canonical pathways driving myofibroblastic activation in fibrosis. Myofibroblasts contribute to the development of liver fibrosis. Here, the authors report that the transcription factor Basonuclin 2 (BNC2) integrates fibrogenic signals and drives myofibroblastic transcriptional activation in liver fibrosis.
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12
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Klaus R, Lange-Sperandio B. Chronic Kidney Disease in Boys with Posterior Urethral Valves-Pathogenesis, Prognosis and Management. Biomedicines 2022; 10:biomedicines10081894. [PMID: 36009441 PMCID: PMC9405968 DOI: 10.3390/biomedicines10081894] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 02/08/2023] Open
Abstract
Posterior urethral valves (PUV) are the most common form of lower urinary tract obstructions (LUTO). The valves can be surgically corrected postnatally; however, the impairment of kidney and bladder development is irreversible and has lifelong implications. Chronic kidney disease (CKD) and bladder dysfunction are frequent problems. Approximately 20% of PUV patients will reach end-stage kidney disease (ESKD). The subvesical obstruction in PUV leads to muscular hypertrophy and fibrotic remodelling in the bladder, which both impair its function. Kidney development is disturbed and results in dysplasia, hypoplasia, inflammation and renal fibrosis, which are hallmarks of CKD. The prognoses of PUV patients are based on prenatal and postnatal parameters. Prenatal parameters include signs of renal hypodysplasia in the analysis of fetal urine. Postnatally, the most robust predictor of PUV is the nadir serum creatinine after valve ablation. A value that is below 0.4 mg/dl implies a very low risk for ESKD, whereas a value above 0.85 mg/dl indicates a high risk for ESKD. In addition, bladder dysfunction and renal dysplasia point towards an unbeneficial kidney outcome. Experimental urinary markers such as MCP-1 and TGF-β, as well as microalbuminuria, indicate progression to CKD. Until now, prenatal intervention may improve survival but yields no renal benefit. The management of PUV patients includes control of bladder dysfunction and CKD treatment to slow down progression by controlling hypertension, proteinuria and infections. In kidney transplantation, aggressive bladder management is essential to ensure optimal graft survival.
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13
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Khan K, Ahram DF, Liu YP, Westland R, Sampogna RV, Katsanis N, Davis EE, Sanna-Cherchi S. Multidisciplinary approaches for elucidating genetics and molecular pathogenesis of urinary tract malformations. Kidney Int 2022; 101:473-484. [PMID: 34780871 PMCID: PMC8934530 DOI: 10.1016/j.kint.2021.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Advances in clinical diagnostics and molecular tools have improved our understanding of the genetically heterogeneous causes underlying congenital anomalies of kidney and urinary tract (CAKUT). However, despite a sharp incline of CAKUT reports in the literature within the past 2 decades, there remains a plateau in the genetic diagnostic yield that is disproportionate to the accelerated ability to generate robust genome-wide data. Explanations for this observation include (i) diverse inheritance patterns with incomplete penetrance and variable expressivity, (ii) rarity of single-gene drivers such that large sample sizes are required to meet the burden of proof, and (iii) multigene interactions that might produce either intra- (e.g., copy number variants) or inter- (e.g., effects in trans) locus effects. These challenges present an opportunity for the community to implement innovative genetic and molecular avenues to explain the missing heritability and to better elucidate the mechanisms that underscore CAKUT. Here, we review recent multidisciplinary approaches at the intersection of genetics, genomics, in vivo modeling, and in vitro systems toward refining a blueprint for overcoming the diagnostic hurdles that are pervasive in urinary tract malformation cohorts. These approaches will not only benefit clinical management by reducing age at molecular diagnosis and prompting early evaluation for comorbid features but will also serve as a springboard for therapeutic development.
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Affiliation(s)
- Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address)
| | - Dina F. Ahram
- Division of Nephrology, Columbia University, New York, USA
| | - Yangfan P. Liu
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA
| | - Rik Westland
- Division of Nephrology, Columbia University, New York, USA.,Department of Pediatric Nephrology, Amsterdam UMC- Emma Children’s Hospital, Amsterdam, NL
| | | | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA; Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA (current address); Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
| | - Erica E. Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address).,Department of Pediatrics and Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,To whom correspondence should be addressed: ADDRESS CORRESPONDENCE TO: Simone Sanna-Cherchi, MD, Division of Nephrology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA; Phone: 212-851-4925; Fax: 212-851-5461; . Erica E. Davis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7662; Fax: 312-503-7343; , Nicholas Katsanis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7339; Fax: 312-503-7343;
| | - Simone Sanna-Cherchi
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, New York, USA.
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14
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van der Zanden LFM, Maj C, Borisov O, van Rooij IALM, Quaedackers JSLT, Steffens M, Schierbaum L, Schneider S, Waffenschmidt L, Kiemeney LALM, de Wall LLL, Heilmann S, Hofmann A, Gehlen J, Schumacher J, Szczepanska M, Taranta-Janusz K, Kroll P, Krzemien G, Szmigielska A, Schreuder MF, Weber S, Zaniew M, Roeleveld N, Reutter H, Feitz WFJ, Hilger AC. Genome-wide association study in patients with posterior urethral valves. Front Pediatr 2022; 10:988374. [PMID: 36238604 PMCID: PMC9552614 DOI: 10.3389/fped.2022.988374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Congenital lower urinary tract obstructions (LUTO) are most often caused by posterior urethral valves (PUV), a male limited anatomical obstruction of the urethra affecting 1 in 4,000 male live births. Little is known about the genetic background of PUV. Here, we report the largest genome-wide association study (GWAS) for PUV in 4 cohorts of patients and controls. The final meta-analysis included 756 patients and 4,823 ethnicity matched controls and comprised 5,754,208 variants that were genotyped or imputed and passed quality control in all 4 cohorts. No genome-wide significant locus was identified, but 33 variants showed suggestive significance (P < 1 × 10-5). When considering only loci with multiple variants residing within < 10 kB of each other showing suggestive significance and with the same effect direction in all 4 cohorts, 3 loci comprising a total of 9 variants remained. These loci resided on chromosomes 13, 16, and 20. The present GWAS and meta-analysis is the largest genetic study on PUV performed to date. The fact that no genome-wide significant locus was identified, can be explained by lack of power or may indicate that common variants do not play a major role in the etiology of PUV. Nevertheless, future studies are warranted to replicate and validate the 3 loci that yielded suggestive associations.
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Affiliation(s)
- Loes F M van der Zanden
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Iris A L M van Rooij
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | - Luca Schierbaum
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Sophia Schneider
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Lea Waffenschmidt
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Lambertus A L M Kiemeney
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Liesbeth L L de Wall
- Division of Pediatric Urology, Department of Urology, Radboud Institute for Molecular Life Sciences, Radboudumc Amalia Children's Hospital, Nijmegen, Netherlands
| | - Stefanie Heilmann
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Aybike Hofmann
- Department of Pediatric Urology, Clinic St. Hedwig, University Medical Center Regensburg, Regensburg, Germany
| | - Jan Gehlen
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | | | - Maria Szczepanska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Zabrze, Poland
| | | | - Pawel Kroll
- Neurourology Unit, Pediatric Surgery and Urology Clinic, Poznań, Poland
| | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Michiel F Schreuder
- Department of Pediatric Nephrology, Radboud Institute for Molecular Life Sciences, Radboudumc Amalia Children's Hospital, Nijmegen, Netherlands
| | - Stefanie Weber
- University Children Hospital Marburg, Philipps University Marburg, Marburg, Germany
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Nel Roeleveld
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Heiko Reutter
- Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Wout F J Feitz
- Division of Pediatric Urology, Department of Urology, Radboud Institute for Molecular Life Sciences, Radboudumc Amalia Children's Hospital, Nijmegen, Netherlands
| | - Alina C Hilger
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.,Research Center on Rare Kidney Diseases, University Hospital Erlangen, Erlangen, Germany
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15
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Lopes FM, Woolf AS, Roberts NA. Envisioning treating genetically-defined urinary tract malformations with viral vector-mediated gene therapy. J Pediatr Urol 2021; 17:610-620. [PMID: 34312114 DOI: 10.1016/j.jpurol.2021.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/16/2022]
Abstract
Human urinary tract malformations can cause dysfunctional voiding, urosepsis and kidney failure. Other affected individuals, with severe phenotypes on fetal ultrasound screening, undergo elective termination. Currently, there exist no specific treatments that target the primary biological disease mechanisms that generate these urinary tract malformations. Historically, the pathogenesis of human urinary tract malformations has been obscure. It is now established that some such individuals have defined monogenic causes for their disease. In health, the implicated genes are expressed in either differentiating urinary tract smooth muscle cells, urothelial cells or peripheral nerve cells supplying the bladder. The phenotypes arising from mutations of these genes include megabladder, congenital functional bladder outflow obstruction, and vesicoureteric reflux. We contend that these genetic and molecular insights can now inform the design of novel therapies involving viral vector-mediated gene transfer. Indeed, this technology is being used to treat individuals with early onset monogenic disease outside the urinary tract, such as spinal muscular atrophy. Moreover, it has been contended that human fetal gene therapy, which may be necessary to ameliorate developmental defects, could become a reality in the coming decades. We suggest that viral vector-mediated gene therapies should first be tested in existing mouse models with similar monogenic and anatomical aberrations as found in people with urinary tract malformations. Indeed, gene transfer protocols have been successfully pioneered in newborn and fetal mice to treat non-urinary tract diseases. If similar strategies were successful in animals with urinary tract malformations, this would pave the way for personalized and potentially curative treatments for people with urinary tract malformations.
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Affiliation(s)
- Filipa M Lopes
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, UK
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, UK; Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
| | - Neil A Roberts
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, UK.
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16
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Schierbaum LM, Schneider S, Herms S, Sivalingam S, Fabian J, Reutter H, Weber S, Merz WM, Tkaczyk M, Miklaszewska M, Sikora P, Szmigielska A, Krzemien G, Zachwieja K, Szczepanska M, Taranta-Janusz K, Kroll P, Polok M, Zaniew M, Hilger AC. Genome-Wide Survey for Microdeletions or -Duplications in 155 Patients with Lower Urinary Tract Obstructions (LUTO). Genes (Basel) 2021; 12:genes12091449. [PMID: 34573432 PMCID: PMC8468665 DOI: 10.3390/genes12091449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 01/28/2023] Open
Abstract
Lower urinary tract obstruction (LUTO) is, in most cases, caused by anatomical blockage of the bladder outlet. The most common form are posterior urethral valves (PUVs), a male-limited phenotype. Here, we surveyed the genome of 155 LUTO patients to identify disease-causing CNVs. Raw intensity data were collected for CNVs detected in LUTO patients and 4.392 healthy controls using CNVPartition, QuantiSNP and PennCNV. Overlapping CNVs between patients and controls were discarded. Additional filtering implicated CNV frequency in the database of genomic variants, gene content and final visual inspection detecting 37 ultra-rare CNVs. After, prioritization qPCR analysis confirmed 3 microduplications, all detected in PUV patients. One microduplication (5q23.2) occurred de novo in the two remaining microduplications found on chromosome 1p36.21 and 10q23.31. Parental DNA was not available for segregation analysis. All three duplications comprised 11 coding genes: four human specific lncRNA and one microRNA. Three coding genes (FBLIM1, SLC16A12, SNCAIP) and the microRNA MIR107 have previously been shown to be expressed in the developing urinary tract of mouse embryos. We propose that duplications, rare or de novo, contribute to PUV formation, a male-limited phenotype.
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Affiliation(s)
- Luca M. Schierbaum
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
| | - Sophia Schneider
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
| | - Stefan Herms
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
- Human Genomics Research Group, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Sugirthan Sivalingam
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany;
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, 53127 Bonn, Germany
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Julia Fabian
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
| | - Heiko Reutter
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
- Department of Neonatology and Pediatric Intensive Care, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Stefanie Weber
- Department of Pediatrics, University Hospital Marburg, 35033 Marburg, Germany;
| | - Waltraut M. Merz
- Department of Obstetrics and Prenatal Medicine, University of Bonn, 53127 Bonn, Germany;
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute of Lodz, 93-428 Łódź, Poland;
- Department of Pediatrics, Cardiology and Immunology, Medical University of Łódź, 93-428 Łódź, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, 31-007 Krakow, Poland; (M.M.); (K.Z.)
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology Medical University of Lublin, 20-059 Lublin, Poland;
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, 02-091 Warsaw, Poland; (A.S.); (G.K.)
| | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, 02-091 Warsaw, Poland; (A.S.); (G.K.)
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, 31-007 Krakow, Poland; (M.M.); (K.Z.)
| | - Maria Szczepanska
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, 40-055 Katowice, Poland;
| | - Katarzyna Taranta-Janusz
- Department of Pediatrics and Nephrology, Medical University of Białystok, 15-089 Białystok, Poland;
| | - Pawel Kroll
- Neurourology Unit, Pediatric Surgery and Urology Clinic, 61-701 Poznań, Poland;
- Neurourology Unit, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Marcin Polok
- Department of Pediatric Surgery and Urology, University of Zielona Góra, 65-417 Zielona Góra, Poland;
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, 65-417 Zielona Góra, Poland;
| | - Alina C. Hilger
- Institute of Human Genetics, University Hospital of Bonn, 53127 Bonn, Germany; (L.M.S.); (S.S.); (S.H.); (J.F.); (H.R.)
- Department of Neonatology and Pediatric Intensive Care, University Hospital Erlangen, 91054 Erlangen, Germany
- Correspondence:
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17
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Rieke JM, Zhang R, Braun D, Yilmaz Ö, Japp AS, Lopes FM, Pleschka M, Hilger AC, Schneider S, Newman WG, Beaman GM, Nordenskjöld A, Ebert AK, Promm M, Rösch WH, Stein R, Hirsch K, Schäfer FM, Schmiedeke E, Boemers TM, Lacher M, Kluth D, Gosemann JH, Anderberg M, Barker G, Holmdahl G, Läckgren G, Keene D, Cervellione RM, Giorgio E, Di Grazia M, Feitz WFJ, Marcelis CLM, Van Rooij IALM, Bökenkamp A, Beckers GMA, Keegan CE, Sharma A, Dakal TC, Wittler L, Grote P, Zwink N, Jenetzky E, Brusco A, Thiele H, Ludwig M, Schweizer U, Woolf AS, Odermatt B, Reutter H. SLC20A1 Is Involved in Urinary Tract and Urorectal Development. Front Cell Dev Biol 2020; 8:567. [PMID: 32850778 PMCID: PMC7426641 DOI: 10.3389/fcell.2020.00567] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/15/2020] [Indexed: 02/04/2023] Open
Abstract
Previous studies in developing Xenopus and zebrafish reported that the phosphate transporter slc20a1a is expressed in pronephric kidneys. The recent identification of SLC20A1 as a monoallelic candidate gene for cloacal exstrophy further suggests its involvement in the urinary tract and urorectal development. However, little is known of the functional role of SLC20A1 in urinary tract development. Here, we investigated this using morpholino oligonucleotide knockdown of the zebrafish ortholog slc20a1a. This caused kidney cysts and malformations of the cloaca. Moreover, in morphants we demonstrated dysfunctional voiding and hindgut opening defects mimicking imperforate anus in human cloacal exstrophy. Furthermore, we performed immunohistochemistry of an unaffected 6-week-old human embryo and detected SLC20A1 in the urinary tract and the abdominal midline, structures implicated in the pathogenesis of cloacal exstrophy. Additionally, we resequenced SLC20A1 in 690 individuals with bladder exstrophy-epispadias complex (BEEC) including 84 individuals with cloacal exstrophy. We identified two additional monoallelic de novo variants. One was identified in a case-parent trio with classic bladder exstrophy, and one additional novel de novo variant was detected in an affected mother who transmitted this variant to her affected son. To study the potential cellular impact of SLC20A1 variants, we expressed them in HEK293 cells. Here, phosphate transport was not compromised, suggesting that it is not a disease mechanism. However, there was a tendency for lower levels of cleaved caspase-3, perhaps implicating apoptosis pathways in the disease. Our results suggest SLC20A1 is involved in urinary tract and urorectal development and implicate SLC20A1 as a disease-gene for BEEC.
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Affiliation(s)
- Johanna Magdalena Rieke
- Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
- Institute for Anatomy and Cell Biology, University Hospital Bonn, University of Bonn, Bonn, Germany
- Department of Pediatrics, Children’s Hospital Medical Center, University Hospital Bonn, Bonn, Germany
| | - Rong Zhang
- Institut für Biochemie und Molekularbiologie, Universitätsklinikum Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Doreen Braun
- Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
| | - Öznur Yilmaz
- Institute for Anatomy and Cell Biology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Anna S. Japp
- Institute of Neuropathology, University of Bonn Medical Center, Bonn, Germany
- Institute of Pathology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Filipa M. Lopes
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Michael Pleschka
- Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
- Institute for Anatomy and Cell Biology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Alina C. Hilger
- Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
- Department of Pediatrics, Children’s Hospital Medical Center, University Hospital Bonn, Bonn, Germany
| | - Sophia Schneider
- Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
- Department of Neonatology and Pediatric Intensive Care, Children’s Hospital Medical Center, University Hospital Bonn, Bonn, Germany
| | - William G. Newman
- Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Glenda M. Beaman
- Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Agneta Nordenskjöld
- Department of Women’s and Children’s Health, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Pediatric Surgery, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Anne-Karoline Ebert
- Department of Urology and Pediatric Urology, University Hospital of Ulm, Ulm, Germany
| | - Martin Promm
- Department of Pediatric Urology, Clinic St. Hedwig, University Medical Center Regensburg, Regensburg, Germany
| | - Wolfgang H. Rösch
- Department of Pediatric Urology, Clinic St. Hedwig, University Medical Center Regensburg, Regensburg, Germany
| | - Raimund Stein
- Medical Faculty Mannheim, Centre for Pediatric, Adolescent and Reconstructive Urology, University Medical Center Mannheim, Heidelberg University, Mannheim, Germany
| | - Karin Hirsch
- Division of Pediatric Urology, Department of Urology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Frank-Mattias Schäfer
- Department of Pediatric Surgery and Urology, Cnopfsche Kinderklinik, Nürnberg, Germany
| | - Eberhard Schmiedeke
- Department of Pediatric Surgery and Urology, Center for Child and Youth Health, Klinikum Bremen-Mitte, Bremen, Germany
| | - Thomas M. Boemers
- Department of Pediatric Surgery and Pediatric Urology, Children’s Hospital of Cologne, Cologne, Germany
| | - Martin Lacher
- Department of Pediatric Surgery, University of Leipzig, Leipzig, Germany
| | - Dietrich Kluth
- Department of Pediatric Surgery, University of Leipzig, Leipzig, Germany
| | | | - Magnus Anderberg
- Department of Pediatric Surgery, Skane University Hospital Lund, Lund, Sweden
| | - Gillian Barker
- Department of Women’s and Children’s Health, Uppsala Academic Children Hospital, Uppsala, Sweden
| | - Gundela Holmdahl
- Department of Pediatric Surgery, Queen Silvias Children’s Hospital, Gothenburg, Sweden
| | - Göran Läckgren
- Pediatric Urology, University Children’s Hospital, Uppsala, Sweden
| | - David Keene
- Pediatric Urology, Royal Manchester Children’s Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Raimondo M. Cervellione
- Pediatric Urology, Royal Manchester Children’s Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Massimo Di Grazia
- Pediatric Urology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca’ Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Wouter F. J. Feitz
- Division of Pediatric Urology, Department of Urology, Radboudumc Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Carlo L. M. Marcelis
- Department of Genetics, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands
| | - Iris A. L. M. Van Rooij
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Arend Bökenkamp
- Emma Children’s Hospital, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Goedele M. A. Beckers
- Department of Urology, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Catherine E. Keegan
- Division of Genetics, Department of Pediatrics, University of Michigan, Ann Arbor, MI, United States
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
| | - Amit Sharma
- Department of Neurology, University Hospital Bonn, Bonn, Germany
- Department of Ophthalmology, University Hospital Bonn, Bonn, Germany
| | - Tikam Chand Dakal
- Department of Biotechnology, Mohanlal Sukhadia University Udaipur, Udaipur, India
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University, Frankfurt am Main, Germany
| | - Nadine Zwink
- Department of Pediatric and Adolescent Psychiatry and Psychotherapy, University Medical Centre, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Ekkehart Jenetzky
- Department of Pediatric and Adolescent Psychiatry and Psychotherapy, University Medical Centre, Johannes Gutenberg University of Mainz, Mainz, Germany
- Institute of Integrative Medicine, Witten/Herdecke University, Herdecke, Germany
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Ulrich Schweizer
- Institut für Biochemie und Molekularbiologie, Universitätsklinikum Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Adrian S. Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
- Royal Manchester Children’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Benjamin Odermatt
- Institute for Anatomy and Cell Biology, University Hospital Bonn, University of Bonn, Bonn, Germany
- Institute for Neuroanatomy, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
- Department of Neonatology and Pediatric Intensive Care, Children’s Hospital Medical Center, University Hospital Bonn, Bonn, Germany
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18
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Jackson AR, Ching CB, McHugh KM, Becknell B. Roles for urothelium in normal and aberrant urinary tract development. Nat Rev Urol 2020; 17:459-468. [PMID: 32647226 DOI: 10.1038/s41585-020-0348-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/11/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUTs) represent the leading cause of chronic kidney disease and end-stage kidney disease in children. Increasing evidence points to critical roles for the urothelium in the developing urinary tract and in the genesis of CAKUTs. The involvement of the urothelium in patterning the urinary tract is supported by evidence that CAKUTs can arise as a result of abnormal urothelial development. Emerging evidence indicates that congenital urinary tract obstruction triggers urothelial remodelling that stabilizes the obstructed kidney and limits renal injury. Finally, the diagnostic potential of radiological findings and urinary biomarkers derived from the urothelium of patients with CAKUTs might aid their contribution to clinical care.
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Affiliation(s)
- Ashley R Jackson
- Nephrology and Urology Research Affinity Group, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Center for Clinical and Translational Research, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Christina B Ching
- Nephrology and Urology Research Affinity Group, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Center for Clinical and Translational Research, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Division of Pediatric Urology, Department of Surgery, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Kirk M McHugh
- Nephrology and Urology Research Affinity Group, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Center for Clinical and Translational Research, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Department of Anatomy, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Brian Becknell
- Nephrology and Urology Research Affinity Group, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA. .,Center for Clinical and Translational Research, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA. .,Nephrology Division, Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
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19
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Fernandez-Prado R, Kanbay M, Ortiz A, Perez-Gomez MV. Expanding congenital abnormalities of the kidney and urinary tract (CAKUT) genetics: basonuclin 2 (BNC2) and lower urinary tract obstruction. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:S226. [PMID: 31656805 DOI: 10.21037/atm.2019.08.73] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Raul Fernandez-Prado
- Division of Nephrology and Hypertension, Dialysis Unit, School of Medicine, IIS-Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Mehmet Kanbay
- Division of Nephrology, Department of Medicine, Koc University School of Medicine, Istanbul, Turkey
| | - Alberto Ortiz
- Division of Nephrology and Hypertension, Dialysis Unit, School of Medicine, IIS-Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Maria Vanessa Perez-Gomez
- Division of Nephrology and Hypertension, Dialysis Unit, School of Medicine, IIS-Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
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