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Kosfeld A, Brand F, Weiss AC, Kreuzer M, Goerk M, Martens H, Schubert S, Schäfer AK, Riehmer V, Hennies I, Bräsen JH, Pape L, Amann K, Krogvold L, Bjerre A, Daniel C, Kispert A, Haffner D, Weber RG. Mutations in the leukemia inhibitory factor receptor (LIFR) gene and Lifr deficiency cause urinary tract malformations. Hum Mol Genet 2017; 26:1716-1731. [DOI: 10.1093/hmg/ddx086] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/02/2017] [Indexed: 02/01/2023] Open
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52
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Bashamboo A, Eozenou C, Rojo S, McElreavey K. Anomalies in human sex determination provide unique insights into the complex genetic interactions of early gonad development. Clin Genet 2017; 91:143-156. [DOI: 10.1111/cge.12932] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/10/2016] [Accepted: 11/10/2016] [Indexed: 12/19/2022]
Affiliation(s)
- A. Bashamboo
- Human Developmental Genetics Unit; Institut Pasteur; Paris France
| | - C. Eozenou
- Human Developmental Genetics Unit; Institut Pasteur; Paris France
| | - S. Rojo
- Human Developmental Genetics Unit; Institut Pasteur; Paris France
| | - K. McElreavey
- Human Developmental Genetics Unit; Institut Pasteur; Paris France
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Whole-exome sequencing in the molecular diagnosis of individuals with congenital anomalies of the kidney and urinary tract and identification of a new causative gene. Genet Med 2016; 19:412-420. [PMID: 27657687 PMCID: PMC5362362 DOI: 10.1038/gim.2016.131] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/20/2016] [Indexed: 12/19/2022] Open
Abstract
Purpose To investigate the utility of whole-exome sequencing (WES) to define a molecular diagnosis in patients clinically diagnosed with congenital anomalies of kidney and urinary tract (CAKUT). Methods WES was performed in 62 families with CAKUT. WES data were analyzed for Single Nucleotide Variants (SNVs) in 35 known CAKUT genes, putatively deleterious sequence changes in new candidate genes, and potentially disease-associated copy-number variants (CNVs). Results In approximately 5% of families, pathogenic SNVs were identified in PAX2, HNF1B, and EYA1. Observed phenotypes in these families expand the current understanding about the role of these genes in CAKUT. Four pathogenic CNVs were also identified using two CNV detection tools. In addition, we found one deleterious de novo SNV in FOXP1 among the 62 families with CAKUT. Database of clinical BMGL laboratory was queried and seven additional unrelated individuals with novel de novo SNVs in FOXP1 were identified. Six of these 8 individuals with FOXP1 SNVs, have syndromic urinary tract defects, implicating this gene in urinary tract development. Conclusion We conclude that WES can be used to identify the molecular etiology (SNVs, CNVs) in a subset of individuals with CAKUT. WES can also help identify novel CAKUT genes.
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Bashamboo A, McElreavey K. The role of next generation sequencing in understanding male and female sexual development: clinical implications. Expert Rev Endocrinol Metab 2016; 11:433-443. [PMID: 30058910 DOI: 10.1080/17446651.2016.1220299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Next Generation Sequencing is revolutionising our understanding of variation in the human genome and as costs reduce the sequencing of patient's genomes is become more routine. Areas covered: Here, we review the current challenges in the field and some of the efforts that are underway to resolve them. We describe how these technologies are impacting on our understanding of human sex development and the profound clinical implications of these technologies on conditions such as Disorders of Sex Development (DSD). Expert commentary: The sheer wealth of genomic data is generating new challenges-some are technical such as variant calling, or predicting the functional consequence of a variant-whereas others are more profound, such as establishing the link between extensive genomic information and the clinical presentation. Predicting disease phenotypes from genetic sequences is often extremely difficult because the genotype-phenotype relationship has proven to be far more complex than anticipated.
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Affiliation(s)
- Anu Bashamboo
- a Human Developmental Genetics , Institut Pasteur , Paris , France
| | - Ken McElreavey
- a Human Developmental Genetics , Institut Pasteur , Paris , France
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Abstract
T-box (Tbx) genes encode an ancient group of transcription factors that play important roles in patterning, specification, proliferation, and differentiation programs in vertebrate organogenesis. This is testified by severe organ malformation syndromes in mice homozygous for engineered null alleles of specific T-box genes and by the large number of human inherited organ-specific diseases that have been linked to mutations in these genes. One of the organ systems that has not been associated with loss of specific T-box gene function in human disease for long is the excretory system. However, this has changed with the finding that mutations in TBX18, a member of a vertebrate-specific subgroup within the Tbx1-subfamily of T-box transcription factor genes, cause congenital anomalies of the kidney and urinary tract, predominantly hydroureter and ureteropelvic junction obstruction. Gene expression analyses, loss-of-function studies, and lineage tracing in the mouse suggest a primary role for this transcription factor in specifying the ureteric mesenchyme in the common anlage of the kidney, the ureter, and the bladder. We review the function of Tbx18 in ureterogenesis and discuss the body of evidence that Tbx18 and other members of the T-box gene family, namely, Tbx1, Tbx2, Tbx3, and Tbx20, play additional roles in development and homeostasis of other components of the excretory system in vertebrates.
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Vivante A, Hwang DY, Kohl S, Chen J, Shril S, Schulz J, van der Ven A, Daouk G, Soliman NA, Kumar AS, Senguttuvan P, Kehinde EO, Tasic V, Hildebrandt F. Exome Sequencing Discerns Syndromes in Patients from Consanguineous Families with Congenital Anomalies of the Kidneys and Urinary Tract. J Am Soc Nephrol 2016; 28:69-75. [PMID: 27151922 DOI: 10.1681/asn.2015080962] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/16/2016] [Indexed: 12/22/2022] Open
Abstract
Congenital anomalies of the kidneys and urinary tract (CAKUT) are the leading cause of CKD in children, featuring a broad variety of malformations. A monogenic cause can be detected in around 12% of patients. However, the morphologic clinical phenotype of CAKUT frequently does not indicate specific genes to be examined. To determine the likelihood of detecting causative recessive mutations by whole-exome sequencing (WES), we analyzed individuals with CAKUT from 33 different consanguineous families. Using homozygosity mapping and WES, we identified the causative mutations in nine of the 33 families studied (27%). We detected recessive mutations in nine known disease-causing genes: ZBTB24, WFS1, HPSE2, ATRX, ASPH, AGXT, AQP2, CTNS, and PKHD1 Notably, when mutated, these genes cause multiorgan syndromes that may include CAKUT as a feature (syndromic CAKUT) or cause renal diseases that may manifest as phenocopies of CAKUT. None of the above monogenic disease-causing genes were suspected on clinical grounds before this study. Follow-up clinical characterization of those patients allowed us to revise and detect relevant new clinical features in a more appropriate pathogenetic context. Thus, applying WES to the diagnostic approach in CAKUT provides opportunities for an accurate and early etiology-based diagnosis and improved clinical management.
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Affiliation(s)
- Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel
| | - Daw-Yang Hwang
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Division of Nephrology, Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Stefan Kohl
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Pediatrics, Cologne Children's Hospital, Cologne, Germany
| | - Jing Chen
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Julian Schulz
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amelie van der Ven
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ghaleb Daouk
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Neveen A Soliman
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt.,Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Aravind Selvin Kumar
- Pediatric Nephrology Department, Institute of Child Health and Hospital for Children, Chennai, Tamil Nadu, India
| | - Prabha Senguttuvan
- Pediatric Nephrology Department, Institute of Child Health and Hospital for Children, Chennai, Tamil Nadu, India
| | - Elijah O Kehinde
- Division of Urology, Department of Surgery, Kuwait University, Safat, Kuwait
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia; and
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; .,Howard Hughes Medical Institute, Chevy Chase, Maryland
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Abstract
PURPOSE OF REVIEW The prenatal detection of congenital anomalies of the kidney and urinary tract (CAKUT) has permitted the early management of these conditions. The aim of this review is to provide an overview of the management of neonates with antenatal hydronephrosis (ANH). RECENT FINDINGS In spite of the continuous advances in the understanding of the genetic basis, clinical course, and outcomes of CAKUT, there are still many controversies regarding the clinical significance, postnatal evaluation, and management of neonates with ANH. Mild ANH will often resolve spontaneously, whereas moderate to severe ANH is frequently associated with CAKUT. SUMMARY ANH is a surrogate marker of potential congenital renal anomalies, but usually cannot identify a specific disease. A multidisciplinary team approach is required to diagnose and treat these complex disorders. Currently nonsurgical management of CAKUT should be considered whenever possible for infants with ANH.
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Kohl S, Chen J, Vivante A, Hwang DY, Shril S, Dworschak GC, Van Der Ven A, Sanna-Cherchi S, Bauer SB, Lee RS, Soliman NA, Kehinde EO, Reutter HM, Tasic V, Hildebrandt F. Targeted sequencing of 96 renal developmental microRNAs in 1213 individuals from 980 families with congenital anomalies of the kidney and urinary tract. Nephrol Dial Transplant 2016; 31:1280-3. [PMID: 26908769 DOI: 10.1093/ndt/gfv447] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 12/15/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of chronic kidney diseases in children and young adults, accounting for ∼50% of cases. These anomalies represent maldevelopment of the genitourinary system and can be genetically explained in only 10-16% of cases by mutations or by copy number variations in protein coding sequences. Knock-out mouse models, lacking components of the microRNA (miRNA) processing machinery (i.e. Dicer, Drosha, Dgcr8), exhibit kidney malformations resembling human CAKUT. METHODS Given the Dicer-null mouse phenotype, which implicates a central role for miRNAs gene regulation during kidney development, we hypothesized that miRNAs expressed during kidney development may cause CAKUT in humans if mutated. To evaluate this possibility we carried out Next-Generation sequencing of 96 stem-loop regions of 73 renal developmental miRNA genes in 1248 individuals with non-syndromic CAKUT from 980 families. RESULTS We sequenced 96 stem-loop regions encoded by 73 miRNA genes that are expressed during kidney development in humans, mice and rats. Overall, we identified in 31/1213 individuals from 26 families with 17 different single nucleotide variants. Two variants did not segregate with the disease and hence were not causative. Thirteen variants were likely benign variants because they occurred in control populations and/or they affected nucleotides of weak evolutionary conservation. Two out of 1213 unrelated individuals had potentially pathogenic variants with unknown biologic relevance affecting miRNAs MIR19B1 and MIR99A. CONCLUSIONS Our results indicate that mutations affecting mature microRNAs in individuals with CAKUT are rare and thus most likely not a common cause of CAKUT in humans.
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Affiliation(s)
- Stefan Kohl
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA Department of Pediatrics, Cologne Children's Hospital, Cologne, Germany
| | - Jing Chen
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel
| | - Daw-Yang Hwang
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA Division of Nephrology, Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gabriel C Dworschak
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Amelie Van Der Ven
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Richard S Lee
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Neveen A Soliman
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Elijah O Kehinde
- Division of Urology, Department of Surgery, Kuwait University, Safat, Kuwait
| | - Heiko M Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany Department of Neonatology, Children's Hospital, University of Bonn, Bonn, Germany
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA Howard Hughes Medical Institute, Chevy Chase, MD, USA
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Vivante A, Hildebrandt F. Exploring the genetic basis of early-onset chronic kidney disease. Nat Rev Nephrol 2016; 12:133-46. [PMID: 26750453 DOI: 10.1038/nrneph.2015.205] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The primary causes of chronic kidney disease (CKD) in children differ from those of CKD in adults. In the USA the most common diagnostic groups of renal disease that manifest before the age of 25 years are congenital anomalies of the kidneys and urinary tract, steroid-resistant nephrotic syndrome, chronic glomerulonephritis and renal cystic ciliopathies, which together encompass >70% of early-onset CKD diagnoses. Findings from the past decade suggest that early-onset CKD is caused by mutations in any one of over 200 different monogenic genes. Developments in high-throughput sequencing in the past few years has rendered identification of causative mutations in this high number of genes feasible. Use of genetic analyses in patients with early onset-CKD will provide patients and their families with a molecular genetic diagnosis, generate new insights into disease mechanisms, facilitate aetiology-based classifications of patient cohorts for clinical studies, and might have consequences for personalized approaches to the prevention and treatment of CKD. In this Review, we discuss the implications of next-generation sequencing in clinical genetic diagnostics and the discovery of novel genes in early-onset CKD. We also delineate the resulting opportunities for deciphering disease mechanisms and the therapeutic implications of these findings.
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Affiliation(s)
- Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA.,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
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