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Mitrovic K, Zivotic I, Kolic I, Zakula J, Zivkovic M, Stankovic A, Jovanovic I. A preliminary study of the miRNA restitution effect on CNV-induced miRNA downregulation in CAKUT. BMC Genomics 2024; 25:218. [PMID: 38413914 PMCID: PMC10900603 DOI: 10.1186/s12864-024-10121-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/14/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The majority of CAKUT-associated CNVs overlap at least one miRNA gene, thus affecting the cellular levels of the corresponding miRNA. We aimed to investigate the potency of restitution of CNV-affected miRNA levels to remediate the dysregulated expression of target genes involved in kidney physiology and development in vitro. METHODS Heterozygous MIR484 knockout HEK293 and homozygous MIR185 knockout HEK293 cell lines were used as models depicting the deletion of the frequently affected miRNA genes by CAKUT-associated CNVs. After treatment with the corresponding miRNA mimics, the levels of the target genes have been compared to the non-targeting control treatment. For both investigated miRNAs, MDM2 and PKD1 were evaluated as common targets, while additional 3 genes were investigated as targets of each individual miRNA (NOTCH3, FIS1 and APAF1 as hsa-miR-484 targets and RHOA, ATF6 and CDC42 as hsa-miR-185-5p targets). RESULTS Restitution of the corresponding miRNA levels in both knockout cell lines has induced a change in the mRNA levels of certain candidate target genes, thus confirming the potential to alleviate the CNV effect on miRNA expression. Intriguingly, HEK293 WT treatment with investigated miRNA mimics has triggered a more pronounced effect, thus suggesting the importance of miRNA interplay in different genomic contexts. CONCLUSIONS Dysregulation of multiple mRNA targets mediated by CNV-affected miRNAs could represent the underlying mechanism behind the unresolved CAKUT occurrence and phenotypic variability observed in CAKUT patients. Characterizing miRNAs located in CNVs and their potential to become molecular targets could eventually help in understanding and improving the management of CAKUT.
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Affiliation(s)
- Kristina Mitrovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Ivan Zivotic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Ivana Kolic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Jelena Zakula
- Department of Molecular Biology and Endocrinology, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Maja Zivkovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Aleksandra Stankovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Ivan Jovanovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia.
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Kolvenbach CM, Shril S, Hildebrandt F. The genetics and pathogenesis of CAKUT. Nat Rev Nephrol 2023; 19:709-720. [PMID: 37524861 DOI: 10.1038/s41581-023-00742-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2023] [Indexed: 08/02/2023]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) comprise a large variety of malformations that arise from defective kidney or urinary tract development and frequently lead to kidney failure. The clinical spectrum ranges from severe malformations, such as renal agenesis, to potentially milder manifestations, such as vesicoureteral reflux. Almost 50% of cases of chronic kidney disease that manifest within the first three decades of life are caused by CAKUT. Evidence suggests that a large number of CAKUT are genetic in origin. To date, mutations in ~54 genes have been identified as monogenic causes of CAKUT, contributing to 12-20% of the aetiology of the disease. Pathogenic copy number variants have also been shown to cause CAKUT and can be detected in 4-11% of patients. Furthermore, environmental and epigenetic factors can increase the risk of CAKUT. The discovery of novel CAKUT-causing genes is challenging owing to variable expressivity, incomplete penetrance and variable genotype-phenotype correlation. However, such a discovery could ultimately lead to improvements in the accurate molecular genetic diagnosis, assessment of prognosis and multidisciplinary clinical management of patients with CAKUT, potentially including personalized therapeutic approaches.
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Affiliation(s)
- Caroline M Kolvenbach
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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3
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Greenberg D, D’Cruz R, Lacanlale JL, Rowan CJ, Rosenblum ND. Hedgehog-GLI mediated control of renal formation and malformation. FRONTIERS IN NEPHROLOGY 2023; 3:1176347. [PMID: 37675356 PMCID: PMC10479618 DOI: 10.3389/fneph.2023.1176347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/31/2023] [Indexed: 09/08/2023]
Abstract
CAKUT is the leading cause of end-stage kidney disease in children and comprises a broad spectrum of phenotypic abnormalities in kidney and ureter development. Molecular mechanisms underlying the pathogenesis of CAKUT have been elucidated in genetic models, predominantly in the mouse, a paradigm for human renal development. Hedgehog (Hh) signaling is critical to normal embryogenesis, including kidney development. Hh signaling mediates the physiological development of the ureter and stroma and has adverse pathophysiological effects on the metanephric mesenchyme, ureteric, and nephrogenic lineages. Further, disruption of Hh signaling is causative of numerous human developmental disorders associated with renal malformation; Pallister-Hall Syndrome (PHS) is characterized by a diverse spectrum of malformations including CAKUT and caused by truncating variants in the middle-third of the Hh signaling effector GLI3. Here, we outline the roles of Hh signaling in regulating murine kidney development, and review human variants in Hh signaling genes in patients with renal malformation.
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Affiliation(s)
- Dina Greenberg
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Robert D’Cruz
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jon L. Lacanlale
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Christopher J. Rowan
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Norman D. Rosenblum
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Division of Nephrology, Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
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4
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van der Zanden LFM, Groen in ‘t Woud S, van Rooij IALM, Quaedackers JSLT, Steffens M, de Wall LLL, Schreuder MF, Feitz WFJ, Roeleveld N. Maternal risk factors for posterior urethral valves. Front Pediatr 2023; 11:1110117. [PMID: 37187579 PMCID: PMC10175587 DOI: 10.3389/fped.2023.1110117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Introduction Posterior urethral valves (PUV) is a congenital disorder causing an obstruction of the lower urinary tract that affects approximately 1 in 4,000 male live births. PUV is considered a multifactorial disorder, meaning that both genetic and environmental factors are involved in its development. We investigated maternal risk factors for PUV. Methods We included 407 PUV patients and 814 controls matched on year of birth from the AGORA data- and biobank and three participating hospitals. Information on potential risk factors (family history of congenital anomalies of the kidney and urinary tract (CAKUT), season of conception, gravidity, subfertility, and conception using assisted reproductive techniques (ART), plus maternal age, body mass index, diabetes, hypertension, smoking, and use of alcohol and folic acid) was derived from maternal questionnaires. After multiple imputation, adjusted odds ratios (aORs) were estimated using conditional logistic regression corrected for minimally sufficient sets of confounders determined using directed acyclic graphs. Results A positive family history and low maternal age (<25 years) were associated with PUV development [aORs: 3.3 and 1.7 with 95% confidence intervals (95% CI) 1.4-7.7 and 1.0-2.8, respectively], whereas higher maternal age (>35 years) was associated with a lower risk (aOR: 0.7 95% CI: 0.4-1.0). Maternal preexisting hypertension seemed to increase PUV risk (aOR: 2.1 95% CI: 0.9-5.1), while gestational hypertension seemed to decrease this risk (aOR: 0.6 95% CI: 0.3-1.0). Concerning use of ART, the aORs for the different techniques were all above one, but with very wide 95% CIs including one. None of the other factors studied were associated with PUV development. Conclusion Our study showed that family history of CAKUT, low maternal age, and potentially preexisting hypertension were associated with PUV development, whereas higher maternal age and gestational hypertension seemed to be associated with a lower risk. Maternal age and hypertension as well as the possible role of ART in the development of PUV require further research.
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Affiliation(s)
- Loes F. M. van der Zanden
- Department for Health Evidence, Radboud university medical center, Nijmegen, Netherlands
- Correspondence: Loes F. M. van der Zanden
| | | | | | | | | | - Liesbeth L. L. de Wall
- Division of Pediatric Urology, Department of Urology, Amalia Children's Hospital, Radboud university medical center, Nijmegen, Netherlands
| | - Michiel F. Schreuder
- Department of Pediatric Nephrology, Amalia Children's Hospital, Radboud university medical center, Nijmegen, Netherlands
| | - Wout F. J. Feitz
- Division of Pediatric Urology, Department of Urology, Amalia Children's Hospital, Radboud university medical center, Nijmegen, Netherlands
| | - Nel Roeleveld
- Department for Health Evidence, Radboud university medical center, Nijmegen, Netherlands
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5
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Mitrovic K, Zivotic I, Kolic I, Djordjevic A, Zakula J, Filipovic Trickovic J, Zivkovic M, Stankovic A, Jovanovic I. Identification and functional interpretation of miRNAs affected by rare CNVs in CAKUT. Sci Rep 2022; 12:17746. [PMID: 36273030 PMCID: PMC9587983 DOI: 10.1038/s41598-022-22749-1] [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: 02/10/2022] [Accepted: 10/19/2022] [Indexed: 01/18/2023] Open
Abstract
Rare copy number variants (CNVs) are among the most common genomic disorders underlying CAKUT. miRNAs located in rare CNVs represent well-founded functional variants for human CAKUT research. The study aimed to identify and functionally interpret miRNAs most frequently affected by rare CNVs in CAKUT and to estimate the overall burden of rare CNVs on miRNA genes in CAKUT. The additional aim of this study was to experimentally confirm the effect of a rare CNV in CAKUT on candidate miRNA's expression and the subsequent change in mRNA levels of selected target genes. A database of CAKUT-associated rare CNV regions, created by literature mining, was used for mapping of the miRNA precursors. miRNAs and miRNA families, most frequently affected by rare CAKUT-associated CNVs, have been subjected to bioinformatic analysis. CNV burden analysis was performed to identify chromosomes with over/underrepresentation of miRNA genes in rare CNVs associated with CAKUT. A functional study was performed on HEK293 MIR484+/- KO and HEK293 WT cell lines, followed by the analysis of relative miRNA and mRNA target gene levels. 80% of CAKUT patients with underlying rare CNV had at least one miRNA gene overlapping the identified CNV. Network analysis of the most frequently affected miRNAs has revealed the dominant regulation of the two miRNAs, hsa-miR-484 and hsa-miR-185-5p. Additionally, miR-548 family members have shown substantial enrichment in rare CNVs in CAKUT. An over/underrepresentation of miRNA genes in rare CNVs associated with CAKUT was observed in multiple chromosomes, such as chr16, chr20, and chr21. A significant 0.37 fold downregulation of hsa-miR-484, followed by a notable upregulation of MDM2 and APAF1 and downregulation of NOTCH3 was detected in HEK293 MIR484+/- KO compared to HEK293 WT cell lines, supporting the study hypothesis. miRNA genes are frequently affected by rare CNVs in CAKUT patients. Understanding the potential of CNV-affected miRNAs to participate in CAKUT as genetic drivers represent a crucial implication for the development of novel therapeutic approaches.
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Affiliation(s)
- Kristina Mitrovic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ivan Zivotic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ivana Kolic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ana Djordjevic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jelena Zakula
- grid.7149.b0000 0001 2166 9385Department of Molecular Biology and Endocrinology, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jelena Filipovic Trickovic
- grid.7149.b0000 0001 2166 9385Department of Physical Chemistry, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Maja Zivkovic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Stankovic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ivan Jovanovic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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6
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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: 15] [Impact Index Per Article: 7.5] [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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7
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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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8
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Claus LR, Snoek R, Knoers NVAM, van Eerde AM. Review of genetic testing in kidney disease patients: Diagnostic yield of single nucleotide variants and copy number variations evaluated across and within kidney phenotype groups. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:358-376. [PMID: 36161467 PMCID: PMC9828643 DOI: 10.1002/ajmg.c.31995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/02/2022] [Accepted: 08/18/2022] [Indexed: 01/29/2023]
Abstract
Genetic kidney disease comprises a diverse group of disorders. These can roughly be divided in the phenotype groups congenital anomalies of the kidney and urinary tract, ciliopathies, glomerulopathies, stone disorders, tubulointerstitial kidney disease, and tubulopathies. Many etiologies can lead to chronic kidney disease that can progress to end-stage kidney disease. Despite each individual disease being rare, together these genetic disorders account for a large proportion of kidney disease cases. With the introduction of massively parallel sequencing, genetic testing has become more accessible, but a comprehensive analysis of the diagnostic yield is lacking. This review gives an overview of the diagnostic yield of genetic testing across and within the full range of kidney disease phenotypes through a systematic literature search that resulted in 115 included articles. Patient, test, and cohort characteristics that can influence the diagnostic yield are highlighted. Detection of copy number variations and their contribution to the diagnostic yield is described for all phenotype groups. Also, the impact of a genetic diagnosis for a patient and family members, which can be diagnostic, therapeutic, and prognostic, is shown through the included articles. This review will allow clinicians to estimate an a priori probability of finding a genetic cause for the kidney disease in their patients.
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Affiliation(s)
- Laura R. Claus
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Rozemarijn Snoek
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Nine V. A. M. Knoers
- Department of GeneticsUniversity Medical Center GroningenGroningenThe Netherlands
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9
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Liu W, Shi X, Li Y, Qiao F, Chen S, Feng L, Zeng W, Deng D, Wu Y. The Evaluation of Genetic Diagnosis on High-Risk Fetal CAKUT. Front Genet 2022; 13:869525. [PMID: 35711925 PMCID: PMC9194390 DOI: 10.3389/fgene.2022.869525] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background: It is challenging to make an accurate prenatal diagnosis for congenital anomalies of the kidney and urinary tract (CAKUT) because of its pathologic diversity. This study aims to evaluate the performance of whole-exome sequencing (WES) combined with karyotype analysis and copy number variations (CNVs) in diagnosing high-risk fetal CAKUT. Methods: We conducted a retrospective study on prenatal diagnoses of CAKUT in our hospital from January 2020 to April 2021. The research studied 24 high-risk fetuses with CAKUT who were scanned by ultrasonography at the prenatal diagnosis center of Tongji Hospital affiliated to Tongji Medical College of Huazhong University of Science and Technology. The likely pathogenic gene variants were screened for the patients and their parents by multiple approaches, including karyotype analysis, CNVs and WES, and further verified with Sanger sequencing. Results: ①We detected abnormal CNVs in 20.8% (5/24) of the fetuses but only 8.3% (2/24) fetuses had abnormal karyotypes. ②Of the 15 CAKUT fetuses, positive findings (40%) were detected by WES. Of the 9 high-risk fetuses with CAKUT (negative findings in ultrasound scan but with family history), we found abnormal variants (77.8%) through WES. Conclusion: The application of CNVs and WES showed advance in prenatal diagnosis of CAKUT and the pathogenic gene variants were detectable especially for high-risk fetuses with negative ultrasound findings on CAKUT in the preliminary study. The applied strategy could be used to improve the accuracy of prenatal diagnosis for CAKUT in the future.
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Affiliation(s)
- Wanlu Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinwei Shi
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqi Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fuyuan Qiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Suhua Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Feng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wanjiang Zeng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dongrui Deng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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10
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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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11
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Hay E, Cullup T, Barnicoat A. A practical approach to the genomics of kidney disorders. Pediatr Nephrol 2022; 37:21-35. [PMID: 33675412 DOI: 10.1007/s00467-021-04995-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/30/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Rapid technological advances in genomic testing continue to increase our understanding of the genetic basis of a wide range of kidney disorders. Establishing a molecular diagnosis benefits the individual by bringing an end to what is often a protracted diagnostic odyssey, facilitates accurate reproductive counselling for families and, in the future, is likely to lead to the delivery of more targeted management and surveillance regimens. The selection of the most appropriate testing modality requires an understanding both of the technologies available and of the genetic architecture and heterogeneity of kidney disease. Whilst we are witnessing a far greater diagnostic yield with broader genetic testing, such approaches invariably generate variants of uncertain significance and secondary incidental findings, which are not only difficult to interpret but present ethical challenges with reporting and feeding back to patients and their families. Here, we review the spectrum of nephrogenetic disorders, consider the optimal approach to genetic testing, explore the clinical utility of obtaining a molecular diagnosis, reflect on the challenges of variant interpretation and look to the future of this dynamic field.
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Affiliation(s)
- Eleanor Hay
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK.
| | - Thomas Cullup
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK
| | - Angela Barnicoat
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
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12
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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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13
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Bartik Z, Sillén U, Östensson M, Fransson S, Djos A, Sjöberg R, Martinsson T. A genome‑wide scan to locate regions associated with familial vesicoureteral reflux. Exp Ther Med 2021; 23:92. [PMID: 34976134 PMCID: PMC8674978 DOI: 10.3892/etm.2021.11015] [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: 02/07/2021] [Accepted: 07/06/2021] [Indexed: 11/05/2022] Open
Abstract
Vesicoureteral reflux (VUR) is a congenital malformation carrying a high risk of recurrent urinary tract infections (UTI) and, at worst, chronic renal failure. Familial clustering implies a genetic etiology, but studies during the past few decades have demonstrated a causal gene variant in <10% of patients with VUR. The aim of the present study was to search for fully or partially shared ancestral haplotypes in 14 families from south-western Sweden with at least three affected members. High-density single nucleotide polymorphism microarray was used for genotyping prior to analysis with a compatibility matching method developed in-house, and the analysis of copy number variations (CNV). No single unique haplotype was revealed to be shared by the families, thereby excluding a common ancestry and founder mutations as a probable cause of VUR. After evaluation of haplotypes shared by subsets of families, a haplotype shared by nine families was found to be of particular interest. This haplotype, located at chromosomal region 4q21.21, harbours two tentative candidate genes (bone morphogenetic protein 3 and fibroblast growth factor 5), both expressed in metanephros and with known functions during nephrogenesis. As to CNV, only one family had a specific CNV shared by all affected members. This was a focal deletion at 5q31.1 including follistatin-like 4, a gene without a previous known connection to VUR. These data demonstrated the genetic heterogeneity of VUR and indicated that an interaction of environmental and genetic factors, including non-coding and epigenetic regulators, all contribute to the complexity of VUR.
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Affiliation(s)
- Zsuzsa Bartik
- Department of Pediatric Surgery, Pediatric Uronephrology Center, The Queen Silvia Children's Hospital, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, SE‑41685 Gothenburg, Sweden
| | - Ulla Sillén
- Department of Pediatric Surgery, Pediatric Uronephrology Center, The Queen Silvia Children's Hospital, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, SE‑41685 Gothenburg, Sweden
| | - Malin Östensson
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, SE‑40530 Gothenburg, Sweden
| | - Susanne Fransson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE‑40530 Gothenburg, Sweden
| | - Anna Djos
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE‑40530 Gothenburg, Sweden
| | - Rosmarie Sjöberg
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE‑40530 Gothenburg, Sweden
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE‑40530 Gothenburg, Sweden
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14
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Groopman EE, Povysil G, Goldstein DB, Gharavi AG. Rare genetic causes of complex kidney and urological diseases. Nat Rev Nephrol 2020; 16:641-656. [PMID: 32807983 PMCID: PMC7772719 DOI: 10.1038/s41581-020-0325-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 02/08/2023]
Abstract
Although often considered a single-entity, chronic kidney disease (CKD) comprises many pathophysiologically distinct disorders that result in persistently abnormal kidney structure and/or function, and encompass both monogenic and polygenic aetiologies. Rare inherited forms of CKD frequently span diverse phenotypes, reflecting genetic phenomena including pleiotropy, incomplete penetrance and variable expressivity. Use of chromosomal microarray and massively parallel sequencing technologies has revealed that genomic disorders and monogenic aetiologies contribute meaningfully to seemingly complex forms of CKD across different clinically defined subgroups and are characterized by high genetic and phenotypic heterogeneity. Investigations of prevalent genomic disorders in CKD have integrated genetic, bioinformatic and functional studies to pinpoint the genetic drivers underlying their renal and extra-renal manifestations, revealing both monogenic and polygenic mechanisms. Similarly, massively parallel sequencing-based analyses have identified gene- and allele-level variation that contribute to the clinically diverse phenotypes observed for many monogenic forms of nephropathy. Genome-wide sequencing studies suggest that dual genetic diagnoses are found in at least 5% of patients in whom a genetic cause of disease is identified, highlighting the fact that complex phenotypes can also arise from multilocus variation. A multifaceted approach that incorporates genetic and phenotypic data from large, diverse cohorts will help to elucidate the complex relationships between genotype and phenotype for different forms of CKD, supporting personalized medicine for individuals with kidney disease.
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Affiliation(s)
- Emily E Groopman
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
- Institute for Genomic Medicine, Columbia University, New York, NY, USA.
- Center for Precision Medicine and Genomics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
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15
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Cocchi E, Nestor JG, Gharavi AG. Clinical Genetic Screening in Adult Patients with Kidney Disease. Clin J Am Soc Nephrol 2020; 15:1497-1510. [PMID: 32646915 PMCID: PMC7536756 DOI: 10.2215/cjn.15141219] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Expanded accessibility of genetic sequencing technologies, such as chromosomal microarray and massively parallel sequencing approaches, is changing the management of hereditary kidney diseases. Genetic causes account for a substantial proportion of pediatric kidney disease cases, and with increased utilization of diagnostic genetic testing in nephrology, they are now also detected at appreciable frequencies in adult populations. Establishing a molecular diagnosis can have many potential benefits for patient care, such as guiding treatment, familial testing, and providing deeper insights on the molecular pathogenesis of kidney diseases. Today, with wider clinical use of genetic testing as part of the diagnostic evaluation, nephrologists have the challenging task of selecting the most suitable genetic test for each patient, and then applying the results into the appropriate clinical contexts. This review is intended to familiarize nephrologists with the various technical, logistical, and ethical considerations accompanying the increasing utilization of genetic testing in nephrology care.
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Affiliation(s)
- Enrico Cocchi
- Division of Nephrology and Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, New York
- Department of Pediatrics, Universita' degli Studi di Torino, Torino, Italy
| | - Jordan Gabriela Nestor
- Division of Nephrology and Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, New York
| | - Ali G Gharavi
- Division of Nephrology and Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, New York
- Insititute of Genomic Medicine, Columbia University, New York, New York
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16
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The genomic landscape of CAKUT; you gain some, you lose some. Kidney Int 2020; 96:267-269. [PMID: 31331462 DOI: 10.1016/j.kint.2019.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/22/2019] [Indexed: 11/20/2022]
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17
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Human and mouse studies establish TBX6 in Mendelian CAKUT and as a potential driver of kidney defects associated with the 16p11.2 microdeletion syndrome. Kidney Int 2020; 98:1020-1030. [PMID: 32450157 DOI: 10.1016/j.kint.2020.04.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/03/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUTs) are the most common cause of chronic kidney disease in children. Human 16p11.2 deletions have been associated with CAKUT, but the responsible molecular mechanism remains to be illuminated. To explore this, we investigated 102 carriers of 16p11.2 deletion from multi-center cohorts, among which we retrospectively ascertained kidney morphologic and functional data from 37 individuals (12 Chinese and 25 Caucasian/Hispanic). Significantly higher CAKUT rates were observed in 16p11.2 deletion carriers (about 25% in Chinese and 16% in Caucasian/Hispanic) than those found in the non-clinically ascertained general populations (about 1/1000 found at autopsy). Furthermore, we identified seven additional individuals with heterozygous loss-of-function variants in TBX6, a gene that maps to the 16p11.2 region. Four of these seven cases showed obvious CAKUT. To further investigate the role of TBX6 in kidney development, we engineered mice with mutated Tbx6 alleles. The Tbx6 heterozygous null (i.e., loss-of-function) mutant (Tbx6+/‒) resulted in 13% solitary kidneys. Remarkably, this incidence increased to 29% in a compound heterozygous model (Tbx6mh/‒) that reduced Tbx6 gene dosage to below haploinsufficiency, by combining the null allele with a novel mild hypomorphic allele (mh). Renal hypoplasia was also frequently observed in these Tbx6-mutated mouse models. Thus, our findings in patients and mice establish TBX6 as a novel gene involved in CAKUT and its gene dosage insufficiency as a potential driver for kidney defects observed in the 16p11.2 microdeletion syndrome.
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18
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Ahn YH, Lee C, Kim NKD, Park E, Kang HG, Ha IS, Park WY, Cheong HI. Targeted Exome Sequencing Provided Comprehensive Genetic Diagnosis of Congenital Anomalies of the Kidney and Urinary Tract. J Clin Med 2020; 9:jcm9030751. [PMID: 32164334 PMCID: PMC7141392 DOI: 10.3390/jcm9030751] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/28/2020] [Accepted: 03/08/2020] [Indexed: 12/13/2022] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of chronic kidney disease in children. The search for genetic causes of CAKUT has led to genetic diagnosis in approximately 5-20 % of CAKUT patients from Western countries. In this study, genetic causes of CAKUT in Korean children were sought using targeted exome sequencing (TES) of 60 genes reported to cause CAKUT in human or murine models. We identified genetic causes in 13.8% of the 94 recruited patients. Pathogenic single nucleotide variants of five known disease-causing genes, HNF1B, PAX2, EYA1, UPK3A, and FRAS1 were found in 7 cases. Pathogenic copy number variations of 6 patients were found in HNF1B, EYA1, and CHD1L. Genetic abnormality types did not significantly differ according to CAKUT phenotypes. Patients with pathogenic variants of targeted genes had syndromic features more frequently than those without (p < 0.001). This is the first genetic analysis study of Korean patients with CAKUT. Only one-seventh of patients were found to have pathogenic mutations in known CAKUT-related genes, indicating that there are more CAKUT-causing genes or environmental factors to discover.
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Affiliation(s)
- Yo Han Ahn
- Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Korea; (Y.H.A.); (E.P.); (I.-S.H.); (H.I.C.)
- Department of Pediatrics, Seoul National University Children’s Hospital, Seoul 03080, Korea
| | - Chung Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea; (C.L.); (N.K.D.K.); (W.-Y.P.)
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Korea
| | - Nayoung K. D. Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea; (C.L.); (N.K.D.K.); (W.-Y.P.)
| | - Eujin Park
- Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Korea; (Y.H.A.); (E.P.); (I.-S.H.); (H.I.C.)
- Department of Pediatrics, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, Korea
| | - Hee Gyung Kang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Korea; (Y.H.A.); (E.P.); (I.-S.H.); (H.I.C.)
- Department of Pediatrics, Seoul National University Children’s Hospital, Seoul 03080, Korea
- Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul 03080, Korea
- Correspondence:
| | - Il-Soo Ha
- Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Korea; (Y.H.A.); (E.P.); (I.-S.H.); (H.I.C.)
- Department of Pediatrics, Seoul National University Children’s Hospital, Seoul 03080, Korea
- Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea; (C.L.); (N.K.D.K.); (W.-Y.P.)
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Korea; (Y.H.A.); (E.P.); (I.-S.H.); (H.I.C.)
- Department of Pediatrics, Seoul National University Children’s Hospital, Seoul 03080, Korea
- Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul 03080, Korea
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19
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Winberg J, Gustavsson P, Sahlin E, Larsson M, Ehrén H, Fossum M, Wester T, Nordgren A, Nordenskjöld A. Pathogenic copy number variants are detected in a subset of patients with gastrointestinal malformations. Mol Genet Genomic Med 2019; 8:e1084. [PMID: 31837127 PMCID: PMC7005659 DOI: 10.1002/mgg3.1084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 12/14/2022] Open
Abstract
Background Gastrointestinal atresias and urological defects are main causes of pediatric surgery in infants. As copy number variants (CNVs) have been shown to be involved in the development of congenital malformations, the aim of our study was to investigate the presence of CNVs in patients with gastrointestinal and urological malformations as well as the possibility of tissue‐specific mosaicism for CNVs in the cohort. Methods We have collected tissue and/or blood samples from 25 patients with anorectal malformations, esophageal atresia, or hydronephrosis, and screened for pathogenic CNVs using array comparative genomic hybridization (array‐CGH). Results We detected pathogenic aberrations in 2/25 patients (8%) and report a novel possible susceptibility region for esophageal atresia on 15q26.3. CNV analysis in different tissues from the same patients did not reveal evidence of tissue‐specific mosaicism. Conclusion Our study shows that it is important to perform clinical genetic investigations, including CNV analysis, in patients with congenital gastrointestinal malformations since this leads to improved information to families as well as an increased understanding of the pathogenesis.
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Affiliation(s)
- Johanna Winberg
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ellika Sahlin
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Larsson
- Pediatric Surgery, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Woman and Child Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Ehrén
- Pediatric Surgery, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Woman and Child Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magdalena Fossum
- Pediatric Surgery, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Woman and Child Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Wester
- Pediatric Surgery, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Woman and Child Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Agneta Nordenskjöld
- Pediatric Surgery, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Woman and Child Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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20
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Yu M, Tan L, Li Y, Chen J, Zhai Y, Rao J, Fang X, Wu X, Xu H, Shen Q. Intrauterine low-protein diet aggravates developmental abnormalities of the urinary system via the Akt/Creb3 pathway in Robo2 mutant mice. Am J Physiol Renal Physiol 2019; 318:F43-F52. [PMID: 31630547 DOI: 10.1152/ajprenal.00405.2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The offspring of Robo2 mutant mice usually present with variable phenotypes of congenital anomalies of the kidney and urinary tract (CAKUT). An intrauterine low-protein diet can also cause CAKUT in offspring, dominated by the duplicated collecting system phenotype. A single genetic or environment factor can only partially explain the pathogenesis of CAKUT. The present study aimed to establish an intrauterine low-protein diet roundabout 2 (Robo2) mutant mouse model and found that the intrauterine low-protein diet led to significantly increased CAKUT phenotypes in Robo2PB/+ mice offspring, dominant by a duplicated collecting system. At the same time, more ectopic and lower located ureteric buds (UBs) were observed in the intrauterine low-protein diet-fed Robo2 mutant mouse model, and the number of UB branches was reduced in the serum-free culture. During UB protrusion, intrauterine low-protein diet reduced the expression of Slit2/Robo2 in Robo2 mutant mice and affected the expression of glial cell-derived neurotrophic factor/Ret, which is a key molecule for metanephric development, with increasing phospho-Akt and phospho-cAMP responsive element-binding protein 3 activity and a reduction of apoptotic cells in embryonic day 11.5 UB tissues. The mechanism by which an intrauterine low-protein diet aggravates CAKUT in Robo2 mutant mice may be related to the disruption of Akt/cAMP responsive element-binding protein 3 signaling and a reduction in apoptosis in UB tissue.
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Affiliation(s)
- Minghui Yu
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Lihong Tan
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Yaxin Li
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Jing Chen
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Yihui Zhai
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Jia Rao
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Xiaoyan Fang
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Xiaohui Wu
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China.,State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Qian Shen
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
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Cai M, Lin N, Su L, Wu X, Xie X, Li Y, Chen X, Dai Y, Lin Y, Huang H, Xu L. Detection of copy number disorders associated with congenital anomalies of the kidney and urinary tract in fetuses via single nucleotide polymorphism arrays. J Clin Lab Anal 2019; 34:e23025. [PMID: 31506986 PMCID: PMC6977156 DOI: 10.1002/jcla.23025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/11/2019] [Accepted: 08/12/2019] [Indexed: 12/17/2022] Open
Abstract
Background While congenital anomalies of the kidney and urinary tract (CAKUT) constitute one‐third of all congenital malformations, the mechanisms underlying their development are poorly understood. Some studies have reported an association between CAKUT and copy number variations (CNVs) in children and adults, but few have focused on chromosomal microarray analysis (CMA) findings in fetuses with CAKUT. Therefore, we aimed to perform a CMA on fetuses with CAKUT and normal karyotypes in the presence and absence of other structural anomalies. Method The study was conducted in 147 fetuses with CAKUT and normal karyotypes between January 2016 and January 2019 in the Fujian Provincial Maternal and Child Health Hospital. Single nucleotide polymorphism (SNP) analysis was performed using the Affymetrix CytoScan HD platform. Results The SNP array identified abnormal CNVs in 13 cases (8.8%): Six were pathogenic, and seven were variations of uncertain clinical significance (VOUS). The detection rate of abnormal CNVs in non‐isolated CAKUT was higher than that in isolated CAKUT (22.7% vs 6.4%, P = .038). Within the abnormal CNV groups, the highest frequency of CNVs was identified in fetuses with polycystic kidney dysplasia (13.5%), followed by those with renal agenesis (10.5%). Conclusion SNP array is effective for identifying chromosomal abnormalities in CNVs in fetuses with CAKUT and normal karyotypes, and help counseling.
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Affiliation(s)
- Meiying Cai
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Linjuan Su
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaoqing Wu
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaorui Xie
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Ying Li
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xuemei Chen
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yifang Dai
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yuan Lin
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Department of the Prenatal Diagnosis Center, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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22
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Hu T, Zhang Z, Wang J, Li Q, Zhu H, Lai Y, Wang H, Liu S. Prenatal diagnosis of chromosomal aberrations by chromosomal microarray analysis in fetuses with ultrasound anomalies in the urinary system. Prenat Diagn 2019; 39:1096-1106. [PMID: 31461547 DOI: 10.1002/pd.5550] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 08/18/2019] [Accepted: 08/20/2019] [Indexed: 12/27/2022]
Abstract
OBJECTIVES This study aimed to explore the relationships between urinary anomalies and copy number variations (CNVs) in fetuses and provide information for prenatal diagnosis and genetic counseling for parents. METHODS Three hundred seventeen fetuses with urinary system anomalies detected by prenatal ultrasound were enrolled; 251 had isolated urinary system anomalies, and 66 had nonisolated system anomalies. CMA was performed on the Affymetrix 750K platform. RESULTS The frequency of chromosomal aberrations in fetuses with urinary system anomalies was 11.04%, including 6.31% with pathogenic CNVs (pCNVs). The detection rate of chromosomal abnormalities was significantly higher for the fetuses with nonisolated urinary system anomalies than for those with isolated urinary system anomalies. Seven fetuses (25.93%) with echogenic kidneys were identified with pCNVs; this detection rate was significantly higher than that for fetuses with other urinary anomalies. A 17q12 deletion was detected in eight fetuses with urinary anomalies, accounting for 40% of pCNVs. CONCLUSION CMA is especially valuable in the prenatal diagnosis of fetuses with urinary system anomalies. The pCNV rates differed between the isolated and nonisolated subgroups of urinary anomalies. Fetuses with echogenic kidneys had the highest rate of pCNVs. The 17q12 deletion was the most frequent pCNV in fetuses with urinary anomalies.
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Affiliation(s)
- Ting Hu
- Department of Obstetrics and Gynecology, West China Second University Hospital Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Zhu Zhang
- Department of Obstetrics and Gynecology, West China Second University Hospital Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Jiamin Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Qinqin Li
- Department of Obstetrics and Gynecology, West China Second University Hospital Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Hongmei Zhu
- Department of Obstetrics and Gynecology, West China Second University Hospital Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yi Lai
- Department of Obstetrics and Gynecology, West China Second University Hospital Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - He Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Shanling Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
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23
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Anderson K, Cañadas-Garre M, Chambers R, Maxwell AP, McKnight AJ. The Challenges of Chromosome Y Analysis and the Implications for Chronic Kidney Disease. Front Genet 2019; 10:781. [PMID: 31552093 PMCID: PMC6737325 DOI: 10.3389/fgene.2019.00781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
The role of chromosome Y in chronic kidney disease (CKD) remains unknown, as chromosome Y is typically excluded from genetic analysis in CKD. The complex, sex-specific presentation of CKD could be influenced by chromosome Y genetic variation, but there is limited published research available to confirm or reject this hypothesis. Although traditionally thought to be associated with male-specific disease, evidence linking chromosome Y genetic variation to common complex disorders highlights a potential gap in CKD research. Chromosome Y variation has been associated with cardiovascular disease, a condition closely linked to CKD and one with a very similar sexual dimorphism. Relatively few sources of genetic variation in chromosome Y have been examined in CKD. The association between chromosome Y aneuploidy and CKD has never been explored comprehensively, while analyses of microdeletions, copy number variation, and single-nucleotide polymorphisms in CKD have been largely limited to the autosomes or chromosome X. In many studies, it is unclear whether the analyses excluded chromosome Y or simply did not report negative results. Lack of imputation, poor cross-study comparability, and requirement for separate or additional analyses in comparison with autosomal chromosomes means that chromosome Y is under-investigated in the context of CKD. Limitations in genotyping arrays could be overcome through use of whole-chromosome sequencing of chromosome Y that may allow analysis of many different types of genetic variation across the chromosome to determine if chromosome Y genetic variation is associated with CKD.
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Affiliation(s)
- Kerry Anderson
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Marisa Cañadas-Garre
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Robyn Chambers
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Alexander Peter Maxwell
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom.,Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
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24
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Lin S, Shi S, Huang L, Lei T, Cai D, Hu W, Zhou Y, Luo Y. Is an analysis of copy number variants necessary for various types of kidney ultrasound anomalies in fetuses? Mol Cytogenet 2019; 12:31. [PMID: 31312255 PMCID: PMC6610977 DOI: 10.1186/s13039-019-0443-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/10/2019] [Indexed: 12/13/2022] Open
Abstract
Background This study aimed to estimate the associations of copy number variants (CNVs) with fetal kidney ultrasound anomalies. A total of 331 fetuses with kidney ultrasound anomalies who underwent prenatal chromosomal microarray analyses were enrolled. The fetuses were classified into groups with isolated and nonisolated anomalies or according to the types of kidney anomalies. Results Clinically significant CNVs were identified in 3.4% or 7.3% of fetuses with isolated or nonisolated kidney anomalies, respectively. CNVs were more frequently identified in fetuses with abnormal embryonic migration of the kidneys (6.6%) than in fetuses with malformations of the renal parenchyma (4.7%) or anomalies of the urinary collecting system (3.4%). In particular, CNVs were most frequently detected in fetuses with ectopic kidneys (9.5%) but not in fetuses with horseshoe kidneys or isolated duplex kidneys. Among these CNVs, the most common were del(17)(q12q12) (1.2%) and del(22)(q11q11) (0.6%). The dup(17)(p12p12) and del(15)(q11.2q11.2) CNVs were identified in this study but not in previous studies. The del(X)(p11.4p11.4) and del(16)(p13.3p13.3) CNVs were further implicated as associated with kidney anomalies. Conclusions Fetuses with abnormal embryonic migration of the kidneys (particularly ectopic kidneys) showed a higher frequency of clinically significant CNVs, whereas fetuses with horseshoe kidneys or duplex kidneys were less frequently associated with these CNVs.
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Affiliation(s)
- Shaobin Lin
- 1Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, 58 Zhong Shan Er Road, Guangzhou, 510080 Guangdong China
| | - Shanshan Shi
- 2Fetal Medicine Center, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Linhuan Huang
- 1Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, 58 Zhong Shan Er Road, Guangzhou, 510080 Guangdong China
| | - Ting Lei
- 3Department of Ultrasonic Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Danlei Cai
- 3Department of Ultrasonic Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenlong Hu
- 4Clinical Medical Research Center, Shenzhen people' s hospital, Shenzhen, China
| | - Yi Zhou
- 1Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, 58 Zhong Shan Er Road, Guangzhou, 510080 Guangdong China
| | - Yanmin Luo
- 1Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, 58 Zhong Shan Er Road, Guangzhou, 510080 Guangdong China
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25
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Cañadas-Garre M, Anderson K, Cappa R, Skelly R, Smyth LJ, McKnight AJ, Maxwell AP. Genetic Susceptibility to Chronic Kidney Disease - Some More Pieces for the Heritability Puzzle. Front Genet 2019; 10:453. [PMID: 31214239 PMCID: PMC6554557 DOI: 10.3389/fgene.2019.00453] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022] Open
Abstract
Chronic kidney disease (CKD) is a major global health problem with an increasing prevalence partly driven by aging population structure. Both genomic and environmental factors contribute to this complex heterogeneous disease. CKD heritability is estimated to be high (30-75%). Genome-wide association studies (GWAS) and GWAS meta-analyses have identified several genetic loci associated with CKD, including variants in UMOD, SHROOM3, solute carriers, and E3 ubiquitin ligases. However, these genetic markers do not account for all the susceptibility to CKD, and the causal pathways remain incompletely understood; other factors must be contributing to the missing heritability. Less investigated biological factors such as telomere length; mitochondrial proteins, encoded by nuclear genes or specific mitochondrial DNA (mtDNA) encoded genes; structural variants, such as copy number variants (CNVs), insertions, deletions, inversions and translocations are poorly covered and may explain some of the missing heritability. The sex chromosomes, often excluded from GWAS studies, may also help explain gender imbalances in CKD. In this review, we outline recent findings on molecular biomarkers for CKD (telomeres, CNVs, mtDNA variants, sex chromosomes) that typically have received less attention than gene polymorphisms. Shorter telomere length has been associated with renal dysfunction and CKD progression, however, most publications report small numbers of subjects with conflicting findings. CNVs have been linked to congenital anomalies of the kidney and urinary tract, posterior urethral valves, nephronophthisis and immunoglobulin A nephropathy. Information on mtDNA biomarkers for CKD comes primarily from case reports, therefore the data are scarce and diverse. The most consistent finding is the A3243G mutation in the MT-TL1 gene, mainly associated with focal segmental glomerulosclerosis. Only one GWAS has found associations between X-chromosome and renal function (rs12845465 and rs5987107). No loci in the Y-chromosome have reached genome-wide significance. In conclusion, despite the efforts to find the genetic basis of CKD, it remains challenging to explain all of the heritability with currently available methods and datasets. Although additional biomarkers have been investigated in less common suspects such as telomeres, CNVs, mtDNA and sex chromosomes, hidden heritability in CKD remains elusive, and more comprehensive approaches, particularly through the integration of multiple -"omics" data, are needed.
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Affiliation(s)
- Marisa Cañadas-Garre
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Kerry Anderson
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Ruaidhri Cappa
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Ryan Skelly
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Laura Jane Smyth
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Alexander Peter Maxwell
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
- Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom
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Li S, Han X, Wang Y, Chen S, Niu J, Qian Z, Li P, Jin L, Xu C. Chromosomal microarray analysis in fetuses with congenital anomalies of the kidney and urinary tract: A prospective cohort study and meta-analysis. Prenat Diagn 2019; 39:165-174. [PMID: 30650192 DOI: 10.1002/pd.5420] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/24/2018] [Accepted: 01/07/2019] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To evaluate the usefulness and incremental diagnostic yield of chromosomal microarray analysis (CMA) compared with standard karyotyping in fetuses with congenital anomalies of the kidney and urinary tract (CAKUT). METHODS A prospective cohort study and systematic review of the literature were conducted. In the prospective cohort study, 123 fetuses with CAKUT, as detected by prenatal ultrasound at our center, were enrolled and evaluated using karyotyping and CMA. In the meta-analysis, articles in PubMed and ISI Web of Knowledge databases describing copy number variations (CNVs) in prenatal cases of CAKUT were included. RESULTS Among the 123 fetuses in our prospective cohort study, 13 fetuses were detected with chromosomal abnormalities or submicroscopic chromosomal abnormalities by both karyotyping and CMA. In the remaining 110 fetuses, four pathogenic CNVs in four fetuses were only detected by CMA, indicating an excess diagnostic yield of 3.6%. Six publications and our own study met the inclusion criteria for the meta-analysis. In total, 615 fetuses with CAKUT were included. The pooled data from all of the reviewed studies indicate that the incremental yield of CMA over karyotyping was 3.8%. CONCLUSION The use of CMA provides a 3.8% incremental yield of detecting pathogenic CNVs in fetuses with CAKUT and normal karyotype.
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Affiliation(s)
- Shuyuan Li
- Institute of Embryo-Fetal Original Adult Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xu Han
- Institute of Embryo-Fetal Original Adult Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanlin Wang
- Institute of Embryo-Fetal Original Adult Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Songchang Chen
- Institute of Embryo-Fetal Original Adult Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianmei Niu
- Institute of Embryo-Fetal Original Adult Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaoxia Qian
- Institute of Embryo-Fetal Original Adult Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pin Li
- Department of Pediatric Endocrinology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Li Jin
- Institute of Embryo-Fetal Original Adult Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenming Xu
- Institute of Embryo-Fetal Original Adult Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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27
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Impact of next generation sequencing on our understanding of CAKUT. Semin Cell Dev Biol 2018; 91:104-110. [PMID: 30172048 DOI: 10.1016/j.semcdb.2018.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 08/16/2018] [Accepted: 08/28/2018] [Indexed: 12/29/2022]
Abstract
Congenital abnormalities of the kidney and urinary tract (CAKUT) form the leading cause of pediatric end-stage renal disease. Knowledge on the molecular mechanisms that underlie CAKUT leads to the improvement of DNA diagnostics and counseling regarding prognosis and recurrence risk estimation for CAKUT patients and their relatives. Implementation of next generation sequencing in research and diagnostic settings has led to the identification of the molecular basis of many developmental diseases. In this review, we summarize the efforts on next generation sequencing in CAKUT research and we discuss how next generation sequencing added to our understanding of CAKUT genetics. Although next generation sequencing has certainly proven to be a game changer in the field of disease gene identification and novel CAKUT-causing gene variants have been identified, most CAKUT cases still remain unsolved. Occurring with genetic and phenotypic heterogeneity along with incomplete penetrance, the identification of CAKUT etiology poses many challenges. We see great potential for combined -omics approaches that include next generation sequencing in the identification of CAKUT-specific biomarkers, which is necessary to optimize the care for CAKUT patients.
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28
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Predictors of poor neonatal outcomes in prenatally diagnosed multicystic dysplastic kidney disease. J Perinatol 2018; 38:658-664. [PMID: 29572458 DOI: 10.1038/s41372-018-0093-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/15/2018] [Accepted: 02/20/2018] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Multicystic dysplastic kidney (MCDK) is one of the most common anomalies detected by prenatal ultrasound. Our objective was to identify factors associated with severe adverse neonatal outcomes of prenatally diagnosed MCDK STUDY DESIGN: A retrospective review of prenatally diagnosed MCDK (1 January 2009 to 30 December 2014) from a single academic center was conducted. The primary outcome was death or need for dialysis among live-born infants. Associations between prenatal characteristics and outcome were analyzed by Fisher's exact test and Mann-Whitney test. RESULTS A total of 53 cases of prenatally suspected MCDK were included, of which 46 cases were live-born and confirmed postnatally (38 survivors, 8 non-survivors). Prenatally diagnosed extrarenal anomalies, bilateral MCDK, contralateral renal anomalies, and anhydramnios were significantly associated with death or need for dialysis (all p < 0.0001). CONCLUSIONS Prenatally identified findings are associated with adverse neonatal outcome, and can guide counseling and management planning. In the absence of significant associated findings, prenatally diagnosed unilateral MCDK has a benign neonatal course.
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Iskander SM, Feeney MM, Yee K, Rosenblum ND. Protein Kinase 2 β Is Expressed in Neural Crest-Derived Urinary Pacemaker Cells and Required for Pyeloureteric Contraction. J Am Soc Nephrol 2018; 29:1198-1209. [PMID: 29436516 DOI: 10.1681/asn.2017090951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/10/2018] [Indexed: 01/31/2023] Open
Abstract
Nonobstructive hydronephrosis, defined as dilatation of the renal pelvis with or without dilatation of the ureter, is the most common antenatal abnormality detected by fetal ultrasound. Yet, the etiology of nonobstructive hydronephrosis is poorly defined. We previously demonstrated that defective development of urinary tract pacemaker cells (utPMCs) expressing hyperpolarization-activated cyclic nucleotide-gated channel 3 (HCN3) and the stem cell marker cKIT causes abnormal ureteric peristalsis and nonobstructive hydronephrosis. However, further investigation of utPMC development and function is limited by lack of knowledge regarding the embryonic derivation, development, and molecular apparatus of these cells. Here, we used lineage tracing in mice to identify cells that give rise to utPMCs. Neural crest cells (NCCs) indelibly labeled with tdTomato expressed HCN3 and cKIT. Furthermore, purified HCN3+ and cKIT+ utPMCs were enriched in Sox10 and Tfap-2α, markers of NCCs. Sequencing of purified RNA from HCN3+ cells revealed enrichment of a small subset of RNAs, including RNA encoding protein kinase 2β (PTK2β), a Ca2+-dependent tyrosine kinase that regulates ion channel activity in neurons. Immunofluorescence analysis in situ revealed PTK2β expression in NCCs as early as embryonic day 12.5 and in HCN3+ and cKIT+ utPMCs as early as embryonic day 15.5, with sustained expression in HCN3+ utPMCs until postnatal week 8. Pharmacologic inhibition of PTK2β in murine pyeloureteral tissue explants inhibited contraction frequency. Together, these results demonstrate that utPMCs are derived from NCCs, identify new markers of utPMCs, and demonstrate a functional contribution of PTK2β to utPMC function.
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Affiliation(s)
- Samir M Iskander
- Program in Developmental and Stem Cell Biology and.,Departments of Laboratory Medicine and Pathobiology and
| | - Meghan M Feeney
- Program in Developmental and Stem Cell Biology and.,Departments of Laboratory Medicine and Pathobiology and
| | - Kirby Yee
- Program in Developmental and Stem Cell Biology and
| | - Norman D Rosenblum
- Program in Developmental and Stem Cell Biology and .,Departments of Laboratory Medicine and Pathobiology and.,Division of Nephrology, The Hospital for Sick Children, Toronto, Ontario, Canada; and.,Paediatrics, University of Toronto, Toronto, Ontario, Canada
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30
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Abstract
Technologies such as next-generation sequencing and chromosomal microarray have advanced the understanding of the molecular pathogenesis of a variety of renal disorders. Genetic findings are increasingly used to inform the clinical management of many nephropathies, enabling targeted disease surveillance, choice of therapy, and family counselling. Genetic analysis has excellent diagnostic utility in paediatric nephrology, as illustrated by sequencing studies of patients with congenital anomalies of the kidney and urinary tract and steroid-resistant nephrotic syndrome. Although additional investigation is needed, pilot studies suggest that genetic testing can also provide similar diagnostic insight among adult patients. Reaching a genetic diagnosis first involves choosing the appropriate testing modality, as guided by the clinical presentation of the patient and the number of potential genes associated with the suspected nephropathy. Genome-wide sequencing increases diagnostic sensitivity relative to targeted panels, but holds the challenges of identifying causal variants in the vast amount of data generated and interpreting secondary findings. In order to realize the promise of genomic medicine for kidney disease, many technical, logistical, and ethical questions that accompany the implementation of genetic testing in nephrology must be addressed. The creation of evidence-based guidelines for the utilization and implementation of genetic testing in nephrology will help to translate genetic knowledge into improved clinical outcomes for patients with kidney disease.
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Affiliation(s)
- Emily E Groopman
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
| | - Hila Milo Rasouly
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
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31
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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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32
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Nestor JG, Groopman EE, Gharavi AG. Towards precision nephrology: the opportunities and challenges of genomic medicine. J Nephrol 2017; 31:47-60. [PMID: 29043570 DOI: 10.1007/s40620-017-0448-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/10/2017] [Indexed: 12/28/2022]
Abstract
The expansion of genomic medicine is furthering our understanding of many human diseases. This is well illustrated in the field of nephrology, through the characterization, discovery, and growing insight into various renal diseases through use of Next Generation Sequencing (NGS) technologies. This review will provide an overview of the diagnostic opportunities of using genetic testing in the clinical setting by describing notable discoveries regarding inherited forms of renal disease that have advanced the field and by highlighting some of the potential benefits of establishing a molecular diagnosis in a clinical practice. In addition, it will discuss some of the challenges associated with the expansion of genetic testing into the clinical setting, including clinical variant interpretation and return of genetic results.
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Affiliation(s)
- Jordan G Nestor
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA
| | - Emily E Groopman
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA.
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33
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Mallett AJ, McCarthy HJ, Ho G, Holman K, Farnsworth E, Patel C, Fletcher JT, Mallawaarachchi A, Quinlan C, Bennetts B, Alexander SI. Massively parallel sequencing and targeted exomes in familial kidney disease can diagnose underlying genetic disorders. Kidney Int 2017; 92:1493-1506. [PMID: 28844315 DOI: 10.1016/j.kint.2017.06.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 10/19/2022]
Abstract
Inherited kidney disease encompasses a broad range of disorders, with both multiple genes contributing to specific phenotypes and single gene defects having multiple clinical presentations. Advances in sequencing capacity may allow a genetic diagnosis for familial renal disease, by testing the increasing number of known causative genes. However, there has been limited translation of research findings of causative genes into clinical settings. Here, we report the results of a national accredited diagnostic genetic service for familial renal disease. An expert multidisciplinary team developed a targeted exomic sequencing approach with ten curated multigene panels (207 genes) and variant assessment individualized to the patient's phenotype. A genetic diagnosis (pathogenic genetic variant[s]) was identified in 58 of 135 families referred in two years. The genetic diagnosis rate was similar between families with a pediatric versus adult proband (46% vs 40%), although significant differences were found in certain panels such as atypical hemolytic uremic syndrome (88% vs 17%). High diagnostic rates were found for Alport syndrome (22 of 27) and tubular disorders (8 of 10), whereas the monogenic diagnostic rate for congenital anomalies of the kidney and urinary tract was one of 13. Quality reporting was aided by a strong clinical renal and genetic multidisciplinary committee review. Importantly, for a diagnostic service, few variants of uncertain significance were found with this targeted, phenotype-based approach. Thus, use of targeted massively parallel sequencing approaches in inherited kidney disease has a significant capacity to diagnose the underlying genetic disorder across most renal phenotypes.
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Affiliation(s)
- Andrew J Mallett
- Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia; Faculty of Medicine, University of Queensland, Brisbane, Australia; KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia.
| | - Hugh J McCarthy
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Gladys Ho
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Katherine Holman
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Elizabeth Farnsworth
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Chirag Patel
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Jeffery T Fletcher
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatrics, The Canberra Hospital, Canberra, Australia
| | - Amali Mallawaarachchi
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Clinical Genetics, Liverpool Hospital, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Catherine Quinlan
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Department of Pediatric Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Bruce Bennetts
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Stephen I Alexander
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia; Centre for Kidney Research, University of Sydney, Sydney, Australia.
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34
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Le Tanno P, Breton J, Bidart M, Satre V, Harbuz R, Ray PF, Bosson C, Dieterich K, Jaillard S, Odent S, Poke G, Beddow R, Digilio MC, Novelli A, Bernardini L, Pisanti MA, Mackenroth L, Hackmann K, Vogel I, Christensen R, Fokstuen S, Béna F, Amblard F, Devillard F, Vieville G, Apostolou A, Jouk PS, Guebre-Egziabher F, Sartelet H, Coutton C. PBX1 haploinsufficiency leads to syndromic congenital anomalies of the kidney and urinary tract (CAKUT) in humans. J Med Genet 2017; 54:502-510. [PMID: 28270404 DOI: 10.1136/jmedgenet-2016-104435] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/03/2017] [Accepted: 01/17/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Congenital anomalies of the kidney and urinary tract (CAKUT) represent a significant healthcare burden since it is the primary cause of chronic kidney in children. CNVs represent a recurrent molecular cause of CAKUT but the culprit gene remains often elusive. Our study aimed to define the gene responsible for CAKUT in patients with an 1q23.3q24.1 microdeletion. METHODS We describe eight patients presenting with CAKUT carrying an 1q23.3q24.1 microdeletion as identified by chromosomal microarray analysis (CMA). Clinical features were collected, especially the renal and urinary tract phenotype, and extrarenal features. We characterised PBX1 expression and localisation in fetal and adult kidneys using quantitative RT-PCR and immunohistochemistry. RESULTS We defined a 276-kb minimal common region (MCR) that only overlaps with the PBX1 gene. All eight patients presented with syndromic CAKUT. CAKUT were mostly bilateral renal hypoplasia (75%). The most frequent extrarenal symptoms were developmental delay and ear malformations. We demonstrate that PBX1 is strongly expressed in fetal kidneys and brain and expression levels decreased in adult samples. In control fetal kidneys, PBX1 was localised in nuclei of medullary, interstitial and mesenchymal cells, whereas it was present in endothelial cells in adult kidneys. CONCLUSIONS Our results indicate that PBX1 haploinsufficiency leads to syndromic CAKUT as supported by the Pbx1-null mice model. Correct PBX1 dosage appears to be critical for normal nephrogenesis and seems important for brain development in humans. CMA should be recommended in cases of fetal renal anomalies to improve genetic counselling and pregnancy management.
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Affiliation(s)
- Pauline Le Tanno
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Julie Breton
- Département d'Anatomie et Cytologie Pathologiques, CHU Grenoble Alpes, Grenoble, France
| | - Marie Bidart
- Université Grenoble Alpes, Grenoble, France
- UF Clinatec, Pôle Recherche, CHU Grenoble Alpes, Grenoble, France
| | - Véronique Satre
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
- Equipe "Génétique, Epigénétique et Thérapies de l'Infertilité", Institut Albert Bonniot, La Tronche, France
| | - Radu Harbuz
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Pierre F Ray
- Université Grenoble Alpes, Grenoble, France
- Equipe "Génétique, Epigénétique et Thérapies de l'Infertilité", Institut Albert Bonniot, La Tronche, France
- Laboratoire de Biochimie Génétique et Moléculaire, Institut de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
| | - Caroline Bosson
- Laboratoire de Biochimie Génétique et Moléculaire, Institut de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
| | - Klaus Dieterich
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
| | - Sylvie Jaillard
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, Université de Rennes, Rennes, France
| | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du Développement CLAD-Ouest, Hôpital Sud, Rennes, France
| | - Gemma Poke
- Genetic Health Service New Zealand Central Hub, Wellington, New Zealand
| | - Rachel Beddow
- Genetic Health Service New Zealand Central Hub, Wellington, New Zealand
| | | | - Antonio Novelli
- Department of Medical Genetics, Bambino Gesù Children's Hospital, Rome, Italy
| | - Laura Bernardini
- Mendel Laboratory IRCCS "Casa Sollievo della Sofferenza" Hospital, Foggia, Italy
| | | | - Luisa Mackenroth
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany
| | - Karl Hackmann
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany
| | - Ida Vogel
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Christensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Siv Fokstuen
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Frédérique Béna
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Florence Amblard
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Francoise Devillard
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Gaelle Vieville
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Alexia Apostolou
- Département d'Anatomie et Cytologie Pathologiques, CHU Grenoble Alpes, Grenoble, France
| | - Pierre-Simon Jouk
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
| | | | - Hervé Sartelet
- Département d'Anatomie et Cytologie Pathologiques, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
| | - Charles Coutton
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Equipe "Génétique, Epigénétique et Thérapies de l'Infertilité", Institut Albert Bonniot, La Tronche, France
- Université Grenoble Alpes, Grenoble, France
- Génétique et Procréation, Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
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Siomou E, Mitsioni AG, Giapros V, Bouba I, Noutsopoulos D, Georgiou I. Copy-number variation analysis in familial nonsyndromic congenital anomalies of the kidney and urinary tract: Evidence for the causative role of a transposable element-associated genomic rearrangement. Mol Med Rep 2017; 15:3631-3636. [PMID: 28440405 PMCID: PMC5436203 DOI: 10.3892/mmr.2017.6462] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/23/2017] [Indexed: 12/20/2022] Open
Abstract
Most congenital anomalies of the kidney and urinary tract (CAKUT) are sporadic, but familial occurrence has been described, suggesting a genetic contribution. Copy-number variations (CNVs) were detected in patients with CAKUT to identify possible novel genomic regions associated with CAKUT. CNVs were investigated in 7 children with CAKUT from three unrelated families using array comparative genomic hybridization: female monozygotic twins with bilateral duplex collecting system/vesicoureteral reflux (VUR)/unilateral renal hypodyspasia (URHD); two male siblings with VUR/URHD; 3 male second cousins, one with bilateral VUR/URHD, one with bilateral VUR and one with ureterovesical junction obstruction (UVJO). Five patients had a normal constitution of CNVs, one had a duplication of 0.2 Mb on the 5q-arm (5q23.3), probably unrelated to CAKUT, and one with UVJO had a 1.4 Mb deletion on the 17q-arm (17q12) which includes a known CAKUT gene, HNF1B. The phenotype of HNF1B deletion was extended including renal magnesium wasting. A higher coverage in transposable elements (TEs) was found in the deleted region compared with the expected density in any random genomic region. Notably, the 5′ breakpoint was mapped within a solo long terminal repeat (LTR) sequence. Moreover, highly similar members of solo LTR and mammalian interspersed repetitive (MIR) elements, as well as nucleotide sequence microhomology were detected at the breakpoint regions. In conclusion, the deletion detected in one patient suggests this genomic imbalance as causative for UVJO. A not very well known phenotype of HNF1B deletion resulting in both low urinary tract malformations and renal wasting of magnesium was described. The high load in TEs of the deleted region, the presence of highly similar elements, and the microhomology found at breakpoint regions may have contributed to the generation of the deletion. CNV analysis could reveal novel causative genomic regions in patients with CAKUT, and further studies in larger cohorts are needed.
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Affiliation(s)
- Ekaterini Siomou
- Department of Pediatrics, University Hospital of Ioannina, Ioannina 45500, Greece
| | - Artemis G Mitsioni
- Laboratory of Medical Genetics and Human Reproduction, Faculty of Medicine, University of Ioannina, Ioannina 45500, Greece
| | - Vasileios Giapros
- Neonatal Intensive Care Unit, University Hospital of Ioannina, Ioannina 45500, Greece
| | - Ioanna Bouba
- Laboratory of Medical Genetics and Human Reproduction, Faculty of Medicine, University of Ioannina, Ioannina 45500, Greece
| | - Dimitrios Noutsopoulos
- Laboratory of General Biology, Faculty of Medicine, University of Ioannina, Ioannina 45500, Greece
| | - Ioannis Georgiou
- Laboratory of Medical Genetics and Human Reproduction, Faculty of Medicine, University of Ioannina, Ioannina 45500, Greece
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36
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Genetics of Congenital Anomalies of the Kidney and Urinary Tract: The Current State of Play. Int J Mol Sci 2017; 18:ijms18040796. [PMID: 28398236 PMCID: PMC5412380 DOI: 10.3390/ijms18040796] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 01/13/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are the most frequent form of malformation at birth and represent the cause of 40–50% of pediatric and 7% of adult end-stage renal disease worldwide. The pathogenesis of CAKUT is based on the disturbance of normal nephrogenesis, secondary to environmental and genetic causes. Often CAKUT is the first clinical manifestation of a complex systemic disease, so an early molecular diagnosis can help the physician identify other subtle clinical manifestations, significantly affecting the management and prognosis of patients. The number of sporadic CAKUT cases explained by highly penetrant mutations in a single gene may have been overestimated over the years and a genetic diagnosis is missed in most cases, hence the importance of identifying new genetic approaches which can help unraveling the vast majority of unexplained CAKUT cases. The aim of our review is to clarify the current state of play and the future perspectives of the genetic bases of CAKUT.
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37
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Abstract
Congenital abnormalities of the kidney and urinary tract (CAKUT) are one of the leading congenital defects to be identified on prenatal ultrasound. CAKUT represent a broad spectrum of abnormalities, from transient hydronephrosis to severe bilateral renal agenesis. CAKUT are a major contributor to chronic and end stage kidney disease (CKD/ESKD) in children. Prenatal imaging is useful to identify CAKUT, but will not detect all defects. Both genetic abnormalities and the fetal environment contribute to CAKUT. Monogenic gene mutations identified in human CAKUT have advanced our understanding of molecular mechanisms of renal development. Low nephron number and solitary kidneys are associated with increased risk of adult onset CKD and ESKD. Premature and low birth weight infants represent a high risk population for low nephron number. Additional research is needed to identify biomarkers and appropriate follow-up of premature and low birth weight infants into adulthood.
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Affiliation(s)
- Stacy Rosenblum
- Department of Pediatrics/Neonatology, Children's Hospital of Montefiore/Einstein, Bronx, NY, USA
| | - Abhijeet Pal
- Department of Pediatrics/Nephrology, Children's Hospital of Montefiore/Einstein, Bronx, NY, USA
| | - Kimberly Reidy
- Department of Pediatrics/Nephrology, Children's Hospital of Montefiore/Einstein, Bronx, NY, USA.
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38
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Li M, Carey J, Cristiano S, Susztak K, Coresh J, Boerwinkle E, Kao WHL, Beaty TH, Köttgen A, Scharpf RB. Genome-Wide Association of Copy Number Polymorphisms and Kidney Function. PLoS One 2017; 12:e0170815. [PMID: 28135296 PMCID: PMC5279752 DOI: 10.1371/journal.pone.0170815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 01/11/2017] [Indexed: 01/08/2023] Open
Abstract
Genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) have identified more than 50 loci associated with estimated glomerular filtration rate (eGFR), a measure of kidney function. However, significant SNPs account for a small proportion of eGFR variability. Other forms of genetic variation have not been comprehensively evaluated for association with eGFR. In this study, we assess whether changes in germline DNA copy number are associated with GFR estimated from serum creatinine, eGFRcrea. We used hidden Markov models (HMMs) to identify copy number polymorphic regions (CNPs) from high-throughput SNP arrays for 2,514 African (AA) and 8,645 European ancestry (EA) participants in the Atherosclerosis Risk in Communities (ARIC) study. Separately for the EA and AA cohorts, we used Bayesian Gaussian mixture models to estimate copy number at regions identified by the HMM or previously reported in the HapMap Project. We identified 312 and 464 autosomal CNPs among individuals of EA and AA, respectively. Multivariate models adjusted for SNP-derived covariates of population structure identified one CNP in the EA cohort near genome-wide statistical significance (Bonferroni-adjusted p = 0.067) located on chromosome 5 (876-880kb). Overall, our findings suggest a limited role of CNPs in explaining eGFR variability.
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Affiliation(s)
- Man Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Jacob Carey
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Stephen Cristiano
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology and Clinical Research, Baltimore, Maryland, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Wen Hong L. Kao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology and Clinical Research, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Division of Genetic Epidemiology, Medical Center–University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Robert B. Scharpf
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
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39
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Abstract
Renal anomalies are common birth defects that may manifest as a wide spectrum of anomalies from hydronephrosis (dilation of the renal pelvis and calyces) to renal aplasia (complete absence of the kidney(s)). Aneuploidies and mosaicisms are the most common syndromes associated with CAKUT. Syndromes with single gene and renal developmental defects are less common but have facilitated insight into the mechanism of renal and other organ development. Analysis of underlying genetic mutations with transgenic and mutant mice has also led to advances in our understanding of mechanisms of renal development.
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40
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Array comparative genomic hybridization and genomic sequencing in the diagnostics of the causes of congenital anomalies. J Appl Genet 2016; 58:185-198. [PMID: 27858254 DOI: 10.1007/s13353-016-0376-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/19/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
The aim of this review is to provide the current state of knowledge about the usefulness of modern genetic technologies in uncovering the causality of isolated and multiple congenital anomalies. Array comparative genomic hybridization and next-generation sequencing have revolutionized the clinical approach to patients with these phenotypes. Both technologies enable early diagnosis, especially in clinically challenging newborn populations, and help to uncover genetic defects associated with various phenotypes. The application of both complementary methods could assist in identifying many variants that may simultaneously be involved in the development of a number of isolated or multiple congenital anomalies. Both technologies carry serious variant misinterpretation risks as well. Therefore, the methods of variant classification and accessible variant databases are mentioned. A useful strategy of clinical genetic testing with the application of both methodologies is presented. Finally, future directions and challenges are briefly commented on in this review.
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Faure A, Bouty A, Caruana G, Williams L, Burgess T, Wong MN, James PA, O'Brien M, Walker A, Bertram JF, Heloury Y. DNA copy number variants: A potentially useful predictor of early onset renal failure in boys with posterior urethral valves. J Pediatr Urol 2016; 12:227.e1-7. [PMID: 27160979 DOI: 10.1016/j.jpurol.2016.02.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/29/2016] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Posterior urethral valves (PUV) are among the most common urological causes of chronic kidney disease (CKD) in childhood. Recently, genomic imbalances have been cited as potential risk factors for altered kidney function and have been associated with CKD. The phenotypic effects of a copy number variant (CNV) in boys with PUV are unknown. Here, it was hypothesised that the progression to early renal failure in PUV patients may be influenced by genetic aberrations. OBJECTIVE To assess the relationship between CNVs and renal outcomes. PATIENTS AND METHODS Between September 2012 and July 2015, 45 children with PUV were recruited to evaluate the presence of CNVs in their DNA. The patients' medical records were retrospectively reviewed. The criteria for outcomes of renal function included: assessments of the nadir serum creatinine in the first year of life, the estimated glomerular filtration rate at 1 and 5 years, and the requirement for renal replacement. RESULTS Thirteen CNVs were identified in 12 boys (29% of the cohort). Microarray analysis revealed two pathogenic CNVs (well-established CNVs known to be associated with genetic disease) and 11 of unknown significance (CNVs with insufficient current available evidence for unequivocal determination of clinical significance), including genes that have been previously implicated in kidney diseases and urogenital disorders. The median follow-up was 10.2 years (range 3-17.5) in the group of patients with CNV compared with 5.8 years (range 1-16.6) in those CNV-. The nadir creatinine values were significantly higher in boys with CNVs than in those without CNVs (57.5 μmol/L (range 23-215) and 28 μmol/L (range 18-155), respectively (P = 0.05) (Figure). Boys CNV+ had a worse prognosis, with a higher incidence of Stage-V CKD compared with the control group (33% with CNVs vs. 9% in CNV-, P = 0.06) at a median age of 22 months (range 8 months-16 years). Four (33%) patients CNV+ underwent renal transplantation. DISCUSSION The role of CNVs in the deterioration of renal function remains unknown. It can be hypothesised that CNVs could be a contributing factor or may serve as an accelerant for the progression to renal failure. CONCLUSION The CNVs >100 Kb were significantly associated with early onset renal failure in children with PUV. Prenatal detection of CNV could help to identify foetuses at high risk of severe renal impairment in cases of suspected PUV, especially in cases without oligohydramnios or severe pulmonary hypoplasia. These preliminary results should be confirmed in a larger cohort of patients.
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Affiliation(s)
- A Faure
- Department of Urology, Royal Children's Hospital, Parkville, VIC 3052, Australia.
| | - A Bouty
- Department of Urology, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - G Caruana
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, and Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - L Williams
- Royal Children's Hospital, VCGS, Parkville, VIC 3052, Australia
| | - T Burgess
- Royal Children's Hospital, VCGS, Parkville, VIC 3052, Australia; Department of Paediatrics, Royal Children's Hospital, University of Melbourne, Parkville, VIC 3010, Australia
| | - M N Wong
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, and Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - P A James
- Royal Children's Hospital, VCGS, Parkville, VIC 3052, Australia
| | - M O'Brien
- Department of Urology, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - A Walker
- Department of Paediatric Nephrology, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - J F Bertram
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, and Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Y Heloury
- Department of Urology, Royal Children's Hospital, Parkville, VIC 3052, Australia
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Xi Q, Zhu X, Wang Y, Ru T, Dai C, Wang Z, Li J, Hu Y. Copy number variations in multicystic dysplastic kidney: update for prenatal diagnosis and genetic counseling. Prenat Diagn 2016; 36:463-8. [PMID: 26941192 DOI: 10.1002/pd.4807] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Qi Xi
- Department of Obstetrics and Gynecology; Drum Tower Hospital, Medical School of Nanjing University; Nanjing Jiangsu China
| | - Xiangyu Zhu
- Department of Obstetrics and Gynecology; Drum Tower Hospital, Medical School of Nanjing University; Nanjing Jiangsu China
| | - Yaping Wang
- Department of Medical Genetics, Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University; Nanjing Jiangsu China
| | - Tong Ru
- Department of Obstetrics and Gynecology; Drum Tower Hospital, Medical School of Nanjing University; Nanjing Jiangsu China
| | - Chenyan Dai
- Department of Obstetrics and Gynecology; Drum Tower Hospital, Medical School of Nanjing University; Nanjing Jiangsu China
| | - Zhiqun Wang
- Department of Obstetrics and Gynecology; Drum Tower Hospital, Medical School of Nanjing University; Nanjing Jiangsu China
| | - Jie Li
- Centre of Prenatal Diagnosis of Jiangsu Province, Drum Tower Hospital; Medical School of Nanjing University; Nanjing Jiangsu China
| | - Yali Hu
- Department of Obstetrics and Gynecology; Drum Tower Hospital, Medical School of Nanjing University; Nanjing Jiangsu China
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Boghossian NS, Sicko RJ, Kay DM, Rigler SL, Caggana M, Tsai MY, Yeung EH, Pankratz N, Cole BR, Druschel CM, Romitti PA, Browne ML, Fan R, Liu A, Brody LC, Mills JL. Rare copy number variants implicated in posterior urethral valves. Am J Med Genet A 2016; 170:622-33. [PMID: 26663319 PMCID: PMC6205289 DOI: 10.1002/ajmg.a.37493] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/13/2015] [Indexed: 11/07/2022]
Abstract
The cause of posterior urethral valves (PUV) is unknown, but genetic factors are suspected given their familial occurrence. We examined cases of isolated PUV to identify novel copy number variants (CNVs). We identified 56 cases of isolated PUV from all live-births in New York State (1998-2005). Samples were genotyped using Illumina HumanOmni2.5 microarrays. Autosomal and sex-linked CNVs were identified using PennCNV and cnvPartition software. CNVs were prioritized for follow-up if they were absent from in-house controls, contained ≥ 10 consecutive probes, were ≥ 20 Kb in size, had ≤ 20% overlap with variants detected in other birth defect phenotypes screened in our lab, and were rare in population reference controls. We identified 47 rare candidate PUV-associated CNVs in 32 cases; one case had a 3.9 Mb deletion encompassing BMP7. Mutations in BMP7 have been associated with severe anomalies in the mouse urethra. Other interesting CNVs, each detected in a single PUV case included: a deletion of PIK3R3 and TSPAN1, duplication/triplication in FGF12, duplication of FAT1--a gene essential for normal growth and development, a large deletion (>2 Mb) on chromosome 17q that involves TBX2 and TBX4, and large duplications (>1 Mb) on chromosomes 3q and 6q. Our finding of previously unreported novel CNVs in PUV suggests that genetic factors may play a larger role than previously understood. Our data show a potential role of CNVs in up to 57% of cases examined. Investigation of genes in these CNVs may provide further insights into genetic variants that contribute to PUV.
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Affiliation(s)
- Nansi S. Boghossian
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Robert J. Sicko
- Department of Health, Division of Genetics, Wadsworth Center, Albany, New York
| | - Denise M. Kay
- Department of Health, Division of Genetics, Wadsworth Center, Albany, New York
| | - Shannon L. Rigler
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Michele Caggana
- Department of Health, Division of Genetics, Wadsworth Center, Albany, New York
| | - Michael Y. Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Edwina H. Yeung
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Benjamin R. Cole
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Charlotte M. Druschel
- Department of Health, Congenital Malformations Registry, Albany, New York
- University at Albany School of Public Health, Rensselaer, New York
| | - Paul A. Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa
| | - Marilyn L. Browne
- Department of Health, Congenital Malformations Registry, Albany, New York
- University at Albany School of Public Health, Rensselaer, New York
| | - Ruzong Fan
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Aiyi Liu
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Lawrence C. Brody
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - James L. Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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Fu F, Chen F, Li R, Zhang Y, Pan M, Li D, Liao C. Prenatal diagnosis of fetal multicystic dysplastic kidney via high-resolution whole-genome array. Nephrol Dial Transplant 2016; 31:1693-8. [PMID: 26932690 DOI: 10.1093/ndt/gfv465] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/25/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Women with fetal multicystic dysplastic kidneys (MCDK) are commonly referred for genetic counseling, for which identification of the correct etiology is a prerequisite. METHODS A total of 72 women with fetal MCDK at Guangzhou Women and Children's Medical Center were examined via invasive prenatal diagnosis from May 2010 to June 2015. Standard karyotyping analysis was provided to all fetuses, and chromosomal microarray with Affymetrix CytoSan HD arrays was offered to cases whose DNA samples were available. RESULTS Abnormal karyotypes were detected in 3 of 72 (4.17%) fetuses. Of the 69 (95.8%, 69/72) fetuses with normal karyotypes, 30 (42%, 30/69) underwent chromosome microarray analysis (CMA) testing. The CMA identified pathogenic copy number variations in five fetuses, leading to a pathogenic detection rate of 16.7% (5/30). Well-known microdeletion or microduplication syndromes including renal cysts and diabetes (RCAD) syndrome and Williams-Beuren syndrome (WBS) were identified in three cases. Moreover, four chromosomal imbalanced regions were also identified in our MCDK fetuses: 22q11.1 duplication, 4q35.2 deletion, 22q13.33 duplication and 1p33 duplication. Genes PEX26, ELN, HNF1B, ALG12, FRG1, FRG2 and CYP4A11 were possible candidates for fetal MCDK. The proportions of variants of unknown significance before and after parental analysis were 13.3% (4/30) and 3.3% (1/30), respectively. CONCLUSIONS In the present study, the frequency of chromosomal abnormalities in MCDK fetuses was 4.17% and all rearrangements were imbalanced aberrations. CMA was able to increase the pathogenic detection rate to 16.7% in MCDK fetuses with normal karyotype. Critical regions for RCAD syndrome, WBS and copy number variants of 22q11.1 duplication, 4q35.2 deletion, 22q13.33 duplication and 1p33 duplication were associated with fetal MCDK. Genes PEX26, ELN, HNF1B, ALG12, FRG1, FRG2 and CYP4A11 were possible candidates for fetal MCDK.
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Affiliation(s)
- Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Feifei Chen
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yongling Zhang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Min Pan
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Can Liao
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
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Prioritization and burden analysis of rare variants in 208 candidate genes suggest they do not play a major role in CAKUT. Kidney Int 2016; 89:476-86. [DOI: 10.1038/ki.2015.319] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/19/2015] [Accepted: 08/20/2015] [Indexed: 12/24/2022]
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Caruana G, Bertram JF. Congenital anomalies of the kidney and urinary tract genetics in mice and men. Nephrology (Carlton) 2016; 20:309-11. [PMID: 25605230 DOI: 10.1111/nep.12402] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2015] [Indexed: 01/03/2023]
Abstract
The most common cause of paediatric end-stage kidney disease results from congenital anomalies of the kidney and urinary tract (CAKUT). Genetic manipulation in mice has provided insight into the developmental events that give rise to the broad spectrum of malformations associated with CAKUT. Despite the increase in the number of identified CAKUT-causing genes, the underlying genetic cause for the majority of patients with CAKUT remains unknown. In this mini-review, we provide an overview of the genetic causes of CAKUT based on current mouse mutant models, as well as next-generation sequencing approaches in humans that are helping to bridge the gaps in our understanding.
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Affiliation(s)
- Georgina Caruana
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
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Westland R, Verbitsky M, Vukojevic K, Perry BJ, Fasel DA, Zwijnenburg PJG, Bökenkamp A, Gille JJP, Saraga-Babic M, Ghiggeri GM, D'Agati VD, Schreuder MF, Gharavi AG, van Wijk JAE, Sanna-Cherchi S. Copy number variation analysis identifies novel CAKUT candidate genes in children with a solitary functioning kidney. Kidney Int 2015; 88:1402-1410. [PMID: 26352300 PMCID: PMC4834924 DOI: 10.1038/ki.2015.239] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 05/28/2015] [Accepted: 06/12/2015] [Indexed: 12/29/2022]
Abstract
Copy number variations associate with different developmental phenotypes and represent a major cause of congenital anomalies of the kidney and urinary tract (CAKUT). Because rare pathogenic copy number variations are often large and contain multiple genes, identification of the underlying genetic drivers has proven to be difficult. Here we studied the role of rare copy number variations in 80 patients from the KIMONO-study cohort for which pathogenic mutations in three genes commonly implicated in CAKUT were excluded. In total, 13 known or novel genomic imbalances in 11 of 80 patients were absent or extremely rare in 23,362 population controls. To identify the most likely genetic drivers for the CAKUT phenotype underlying these rare copy number variations, we used a systematic in silico approach based on frequency in a large dataset of controls, annotation with publicly available databases for developmental diseases, tolerance and haploinsufficiency scores, and gene expression profile in the developing kidney and urinary tract. Five novel candidate genes for CAKUT were identified that showed specific expression in the human and mouse developing urinary tract. Among these genes, DLG1 and KIF12 are likely novel susceptibility genes for CAKUT in humans. Thus, there is a significant role of genomic imbalance in the determination of kidney developmental phenotypes. Additionally, we defined a systematic strategy to identify genetic drivers underlying rare copy number variations.
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Affiliation(s)
- Rik Westland
- Division of Nephrology, Columbia University, New York, New York, USA.,Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
| | - Miguel Verbitsky
- Division of Nephrology, Columbia University, New York, New York, USA
| | - Katarina Vukojevic
- Division of Nephrology, Columbia University, New York, New York, USA.,Department of Anatomy, Histology, and Embryology, School of Medicine, University of Split, Split, Croatia
| | - Brittany J Perry
- Division of Nephrology, Columbia University, New York, New York, USA
| | - David A Fasel
- Division of Nephrology, Columbia University, New York, New York, USA
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Arend Bökenkamp
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
| | - Johan J P Gille
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Mirna Saraga-Babic
- Department of Anatomy, Histology, and Embryology, School of Medicine, University of Split, Split, Croatia
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Vivette D D'Agati
- Department of Pathology, Columbia University, New York, New York, USA
| | - Michiel F Schreuder
- Department of Pediatric Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, New York, New York, USA
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, The Netherlands
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Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) refer to a spectrum of structural renal malformations and are the leading cause of end-stage renal disease in children. The genetic diagnosis of CAKUT has proven to be challenging due to genetic and phenotypic heterogeneity and incomplete genetic penetrance. Monogenic causes of CAKUT have been identified using different approaches, including single gene screening, and gene panel and whole exome sequencing. The majority of the identified mutations, however, lack substantial evidence to support a pathogenic role in CAKUT. Copy number variants or single nucleotide variants that are associated with CAKUT have also been identified. Numerous studies support the influence of epigenetic and environmental factors on kidney development and the natural history of CAKUT, suggesting that the pathogenesis of this syndrome is multifactorial. In this Review we describe the current knowledge regarding the genetic susceptibility underlying CAKUT and the approaches used to investigate the genetic basis of CAKUT. We outline the associated environmental risk factors and epigenetic influences on CAKUT and discuss the challenges and strategies used to fully address the involvement and interplay of these factors in the pathogenesis of the disease.
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