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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: 70] [Impact Index Per Article: 10.0] [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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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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53
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Reutter H, Hilger AC, Hildebrandt F, Ludwig M. Underlying genetic factors of the VATER/VACTERL association with special emphasis on the "Renal" phenotype. Pediatr Nephrol 2016; 31:2025-33. [PMID: 26857713 PMCID: PMC5207487 DOI: 10.1007/s00467-016-3335-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/14/2016] [Accepted: 01/15/2016] [Indexed: 12/18/2022]
Abstract
The acronym VATER/VACTERL association (OMIM #192350) refers to the rare non-random co-occurrence of the following component features (CFs): vertebral defects (V), anorectal malformations (A), cardiac defects (C), tracheoesophageal fistula with or without esophageal atresia (TE), renal malformations (R), and limb defects (L). According to epidemiological studies, the majority of patients with VATER/VACTERL association present with a "Renal" phenotype comprising a large spectrum of congenital renal anomalies. This finding is supported by evidence linking all of the human disease genes for the VATER/VACTERL association identified to date, namely, FGF8, FOXF1, HOXD13, LPP, TRAP1, and ZIC3, with renal malformations. Here we review these genotype-phenotype correlations and suggest that the elucidation of the genetic causes of the VATER/VACTERL association will ultimately provide insights into the genetic causes of the complete spectrum of congenital renal anomalies per se.
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Affiliation(s)
- Heiko Reutter
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany. .,Department of Neonatology and Pediatric Intensive Care, Children's Hospital-University of Bonn, Bonn, Germany.
| | - Alina C Hilger
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital-Harvard Medical School, Boston, MA, USA
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
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54
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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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55
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Xiang F, Ma SY, Zhang DX, Zhang Q, Huang YS. Tumor necrosis factor receptor-associated protein 1 improves hypoxia-impaired energy production in cardiomyocytes through increasing activity of cytochrome c oxidase subunit II. Int J Biochem Cell Biol 2016; 79:239-248. [PMID: 27592455 DOI: 10.1016/j.biocel.2016.08.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 08/09/2016] [Accepted: 08/29/2016] [Indexed: 11/30/2022]
Abstract
Tumor necrosis factor receptor-associated protein 1 protects cardiomyocytes against hypoxia, but the underlying mechanisms are not completely understood. In the present study, we used gain- and loss-of-function approaches to explore the effects of tumor necrosis factor receptor-associated protein 1 and cytochrome c oxidase subunit II on energy production in hypoxic cardiomyocytes. Hypoxia repressed ATP production in cultured cardiomyocytes, whereas overexpression of tumor necrosis factor receptor-associated protein 1 significantly improved ATP production. Conversely, knockdown of tumor necrosis factor receptor-associated protein 1 facilitated the hypoxia-induced decrease in ATP synthesis. Further investigation revealed that tumor necrosis factor receptor-associated protein 1 induced the expression and activity of cytochrome c oxidase subunit II, a component of cytochrome c oxidase that is important in mitochondrial respiratory chain function. Moreover, lentiviral-mediated overexpression of cytochrome c oxidase subunit II antagonized the decrease in ATP synthesis caused by knockdown of tumor necrosis factor receptor-associated protein 1, whereas knockdown of cytochrome c oxidase subunit II attenuated the increase in ATP synthesis caused by overexpression of tumor necrosis factor receptor-associated protein 1. In addition, inhibition of cytochrome c oxidase subunit II by a specific inhibitor sodium azide suppressed the ATP sy nthesis induced by overexpressed tumor necrosis factor receptor-associated protein 1. Hence, tumor necrosis factor receptor-associated protein 1 protects cardiomyocytes from hypoxia at least partly via potentiation of energy generation, and cytochrome c oxidase subunit II is one of the downstream effectors that mediates the tumor necrosis factor receptor-associated protein 1-mediated energy generation program.
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Affiliation(s)
- Fei Xiang
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Si-Yuan Ma
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Dong-Xia Zhang
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Qiong Zhang
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Yue-Sheng Huang
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, Third Military Medical University, Chongqing 400038, China.
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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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57
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The expanding phenotypic spectra of kidney diseases: insights from genetic studies. Nat Rev Nephrol 2016; 12:472-83. [PMID: 27374918 DOI: 10.1038/nrneph.2016.87] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) has led to the identification of previously unrecognized phenotypes associated with classic kidney disease genes. In addition to improving diagnostics for genetically heterogeneous diseases and enabling a faster rate of gene discovery, NGS has enabled an expansion and redefinition of nephrogenetic disease categories. Findings from these studies raise the question of whether disease diagnoses should be made on clinical grounds, on genetic evidence or a combination thereof. Here, we discuss the major kidney disease-associated genes and gene categories for which NGS has expanded the phenotypic spectrum. For example, COL4A3-5 genes, which are classically associated with Alport syndrome, are now understood to also be involved in the aetiology of focal segmental glomerulosclerosis. DGKE, which is associated with nephrotic syndrome, is also mutated in patients with atypical haemolytic uraemic syndrome. We examine how a shared genetic background between diverse clinical phenotypes can provide insight into the function of genes and novel links with essential pathophysiological mechanisms. In addition, we consider genetic and epigenetic factors that contribute to the observed phenotypic heterogeneity of kidney diseases and discuss the challenges in the interpretation of genetic data. Finally, we discuss the implications of the expanding phenotypic spectra associated with kidney disease genes for clinical practice, genetic counselling and personalized care, and present our recommendations for the use of NGS-based tests in routine nephrology practice.
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58
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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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59
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Chen Y, Liu Z, Chen J, Zuo Y, Liu S, Chen W, Liu G, Qiu G, Giampietro PF, Wu N, Wu Z. The genetic landscape and clinical implications of vertebral anomalies in VACTERL association. J Med Genet 2016; 53:431-7. [PMID: 27084730 PMCID: PMC4941148 DOI: 10.1136/jmedgenet-2015-103554] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/17/2016] [Indexed: 01/22/2023]
Abstract
VACTERL association is a condition comprising multisystem congenital malformations, causing severe physical disability in affected individuals. It is typically defined by the concurrence of at least three of the following component features: vertebral anomalies (V), anal atresia (A), cardiac malformations (C), tracheo-oesophageal fistula (TE), renal dysplasia (R) and limb abnormalities (L). Vertebral anomaly is one of the most important and common defects that has been reported in approximately 60–95% of all VACTERL patients. Recent breakthroughs have suggested that genetic factors play an important role in VACTERL association, especially in those with vertebral phenotypes. In this review, we summarised the genetic studies of the VACTERL association, especially focusing on the genetic aetiology of patients with vertebral anomalies. Furthermore, genetic reports of other syndromes with vertebral phenotypes overlapping with VACTERL association are also included. We aim to provide a further understanding of the genetic aetiology and a better evidence for genetic diagnosis of the association and vertebral anomalies.
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Affiliation(s)
- Yixin Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhenlei Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jia Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuzhi Zuo
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Sen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Gang Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Philip F Giampietro
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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60
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Abstract
PURPOSE OF REVIEW Recent technological improvements have increased the use of genetic testing in the clinic. This review serves to summarize the many practical benefits of genetic testing, discusses various methodologies that can be used clinically, and exemplifies ways in which genetics is propelling the field forward in nephrology. RECENT FINDINGS The advent of next-generation sequencing and microarray technologies has heralded an unprecedented number of discoveries in the field of nephrology, providing many opportunities for incorporating genomic diagnostics into clinical care. The use of genetic testing, particularly in pediatrics, can provide accurate diagnoses in puzzling cases, resolve misclassification of disease, and identify subsets of individuals with treatable conditions. SUMMARY Genetic testing may have broad benefits for patients and their families. Knowing the precise molecular etiology of disease can help clinicians determine the exact therapeutic course, and counsel patients and their families about prognosis. Genetic discoveries can also improve the classification of kidney disease and identify new targets for therapy.
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61
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Elmakky A, Stanghellini I, Landi A, Percesepe A. Role of Genetic Factors in the Pathogenesis of Radial Deficiencies in Humans. Curr Genomics 2016; 16:264-78. [PMID: 26962299 PMCID: PMC4765521 DOI: 10.2174/1389202916666150528000412] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/20/2015] [Accepted: 05/27/2015] [Indexed: 01/09/2023] Open
Abstract
Radial deficiencies (RDs), defined as under/abnormal development or absence of any of the
structures of the forearm, radial carpal bones and thumb, occur with a live birth incidence ranging
from 1 out of 30,000 to 1 out 6,000 newborns and represent about one third/one fourth of all the congenital
upper limb anomalies. About half of radial disorders have a mendelian cause and pattern of
inheritance, whereas the remaining half appears sporadic with no known gene involved. In sporadic
forms certain anomalies, such as thumb or radial hypoplasia, may occur either alone or in association
with systemic conditions, like vertebral abnormalities or renal defects. All the cases with a mendelian inheritance are syndromic
forms, which include cardiac defects (in Holt-Oram syndrome), bone marrow failure (in Fanconi anemia), platelet
deficiency (in thrombocytopenia-absent-radius syndrome), ocular motility impairment (in Okihiro syndrome). The
genetics of radial deficiencies is complex, characterized by genetic heterogeneity and high inter- and intra-familial clinical
variability: this review will analyze the etiopathogenesis and the genotype/phenotype correlations of the main radial deficiency
disorders in humans.
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Affiliation(s)
- Amira Elmakky
- Medical Genetics, Department of Medical and Surgical Sciences, University Hospital of Modena, Italy
| | - Ilaria Stanghellini
- Medical Genetics, Department of Medical and Surgical Sciences, University Hospital of Modena, Italy
| | - Antonio Landi
- Hand Surgery and Microsurgery, Department of Locomotor System Diseases, University Hospital of Modena, Modena, Italy
| | - Antonio Percesepe
- Medical Genetics, Department of Medical and Surgical Sciences, University Hospital of Modena, Italy
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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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63
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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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64
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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: 224] [Impact Index Per Article: 28.0] [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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65
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Kosfeld A, Kreuzer M, Daniel C, Brand F, Schäfer AK, Chadt A, Weiss AC, Riehmer V, Jeanpierre C, Klintschar M, Bräsen JH, Amann K, Pape L, Kispert A, Al-Hasani H, Haffner D, Weber RG. Whole-exome sequencing identifies mutations of TBC1D1 encoding a Rab-GTPase-activating protein in patients with congenital anomalies of the kidneys and urinary tract (CAKUT). Hum Genet 2015; 135:69-87. [PMID: 26572137 DOI: 10.1007/s00439-015-1610-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/04/2015] [Indexed: 01/06/2023]
Abstract
Congenital anomalies of the kidneys and urinary tract (CAKUT) are genetically highly heterogeneous leaving most cases unclear after mutational analysis of the around 30 causative genes known so far. Assuming that phenotypes frequently showing dominant inheritance, such as CAKUT, can be caused by de novo mutations, de novo analysis of whole-exome sequencing data was done on two patient-parent-trios to identify novel CAKUT genes. In one case, we detected a heterozygous de novo frameshift variant in TBC1D1 encoding a Rab-GTPase-activating protein regulating glucose transporter GLUT4 translocation. Sequence analysis of 100 further CAKUT cases yielded three novel or rare inherited heterozygous TBC1D1 missense variants predicted to be pathogenic. TBC1D1 mutations affected Ser237-phosphorylation or protein stability and thereby act as hypomorphs. Tbc1d1 showed widespread expression in the developing murine urogenital system. A mild CAKUT spectrum phenotype, including anomalies observed in patients carrying TBC1D1 mutations, was found in kidneys of some Tbc1d1 (-/-) mice. Significantly reduced Glut4 levels were detected in kidneys of Tbc1d1 (-/-) mice and the dysplastic kidney of a TBC1D1 mutation carrier versus controls. TBC1D1 and SLC2A4 encoding GLUT4 were highly expressed in human fetal kidney. The patient with the truncating TBC1D1 mutation showed evidence for insulin resistance. These data demonstrate heterozygous deactivating TBC1D1 mutations in CAKUT patients with a similar renal and ureteral phenotype, and provide evidence that TBC1D1 mutations may contribute to CAKUT pathogenesis, possibly via a role in glucose homeostasis.
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Affiliation(s)
- Anne Kosfeld
- Department of Human Genetics, OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Martin Kreuzer
- Department of Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | - Christoph Daniel
- Department of Nephropathology, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Frank Brand
- Department of Human Genetics, OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | | | - Alexandra Chadt
- German Diabetes Center, Leibniz Center for Diabetes Research at the Heinrich-Heine-University, Düsseldorf, Germany.,German Center for Diabetes Research (DZD), Düsseldorf, Germany
| | - Anna-Carina Weiss
- Institute of Molecular Biology, Hannover Medical School, Hannover, Germany
| | - Vera Riehmer
- Department of Human Genetics, OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Cécile Jeanpierre
- Institut National de la Santé et de la Recherche Médicale UMR1163, Hôpital Necker-Enfants Malades, 75015, Paris, France.,Institut Imagine, Université Paris Descartes - Sorbonne Paris Cité, 75015, Paris, France
| | - Michael Klintschar
- Department of Legal Medicine, Hannover Medical School, Hannover, Germany
| | | | - Kerstin Amann
- Department of Nephropathology, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Lars Pape
- Department of Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | - Andreas Kispert
- Institute of Molecular Biology, Hannover Medical School, Hannover, Germany
| | - Hadi Al-Hasani
- German Diabetes Center, Leibniz Center for Diabetes Research at the Heinrich-Heine-University, Düsseldorf, Germany.,German Center for Diabetes Research (DZD), Düsseldorf, Germany
| | - Dieter Haffner
- Department of Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | - Ruthild G Weber
- Department of Human Genetics, OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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66
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Si T, Yang G, Qiu X, Luo Y, Liu B, Wang B. Expression of tumor necrosis factor receptor-associated protein 1 and its clinical significance in kidney cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:13090-13095. [PMID: 26722505 PMCID: PMC4680450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To investigate the expression and clinical significance of TRAP1 (tumor necrosis factor receptor-associated protein 1) in kidney cancer. METHODS TRAP1 expression was detected in kidney cancer and normal kidney tissues by qRT-PCR and immunohistochemistry (IHC), respectively. Then, the correlation of TRAP1 expression with clinicopathological characters and patients' prognosis was evaluated in kidney cancer. RESULTS IHC results revealed that the high-expression rates of TRAP1 in kidney cancer tissues and normal kidney tissues were 51.3% (41/80), 23.3% (7/30), and the difference was statistically significant (P=0.01). Also, TRAP1 mRNA level in kidney cancer was found to be significantly greater compared with those in normal kidney by qRT-PCR. In addition, TRAP1 expression in kidney cancer significantly correlated with lymph node metastasis and clinical stage (P<0.05). Kaplan-Meier survival analysis indicated that the mean survival time of patients with TRAP1 low-expression was significantly higher (56 months) than those patients with TRAP1 high-expression (47 months). Meanwhile, Kaplan-Meier and Cox survival analysis indicated that TRAP1, lymph node metastasis and clinical stage were correlated with patients' prognosis. CONCLUSION TRAP1 is highly expressed in kidney cancer and correlates with patients prognosis, which may be served as a potential marker for the diagnosis and treatment of kidney cancer.
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Affiliation(s)
- Tong Si
- Department of Urology, Guangdong No. 2 Provincial People's Hospital Guangzhou, China
| | - Guosheng Yang
- Department of Urology, Guangdong No. 2 Provincial People's Hospital Guangzhou, China
| | - Xiaofu Qiu
- Department of Urology, Guangdong No. 2 Provincial People's Hospital Guangzhou, China
| | - Youhua Luo
- Department of Urology, Guangdong No. 2 Provincial People's Hospital Guangzhou, China
| | - Baichuan Liu
- Department of Urology, Guangdong No. 2 Provincial People's Hospital Guangzhou, China
| | - Bingwei Wang
- Department of Urology, Guangdong No. 2 Provincial People's Hospital Guangzhou, China
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67
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Gassié L, Lombard A, Moraldi T, Bibonne A, Leclerc C, Moreau M, Marlier A, Gilbert T. Hspa9 is required for pronephros specification and formation inXenopus laevis. Dev Dyn 2015; 244:1538-49. [DOI: 10.1002/dvdy.24344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 07/29/2015] [Accepted: 08/17/2015] [Indexed: 01/13/2023] Open
Affiliation(s)
- Lionel Gassié
- Université Toulouse 3 Centre de Biologie du Développement; Toulouse France
| | | | - Tiphanie Moraldi
- Université Lyon 1 Institut Universitaire Technologique; Villeurbanne France
| | - Anne Bibonne
- Université Toulouse 3 Centre de Biologie du Développement; Toulouse France
- CNRS UMR 5547; Toulouse France
| | - Catherine Leclerc
- Université Toulouse 3 Centre de Biologie du Développement; Toulouse France
- CNRS UMR 5547; Toulouse France
| | - Marc Moreau
- Université Toulouse 3 Centre de Biologie du Développement; Toulouse France
- CNRS UMR 5547; Toulouse France
| | - Arnaud Marlier
- Yale' School of Medicine Department of Internal Medicine; New Haven Connecticut USA
| | - Thierry Gilbert
- Université Toulouse 3 Centre de Biologie du Développement; Toulouse France
- CNRS UMR 5547; Toulouse France
- Institut National de la Santé et de la Recherche Médicale; Toulouse France
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68
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Hilger AC, Halbritter J, Pennimpede T, van der Ven A, Sarma G, Braun DA, Porath JD, Kohl S, Hwang DY, Dworschak GC, Hermann BG, Pavlova A, El-Maarri O, Nöthen MM, Ludwig M, Reutter H, Hildebrandt F. Targeted Resequencing of 29 Candidate Genes and Mouse Expression Studies Implicate ZIC3 and FOXF1 in Human VATER/VACTERL Association. Hum Mutat 2015; 36:1150-4. [PMID: 26294094 DOI: 10.1002/humu.22859] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/06/2015] [Indexed: 01/14/2023]
Abstract
The VATER/VACTERL association describes the combination of congenital anomalies including vertebral defects, anorectal malformations, cardiac defects, tracheoesophageal fistula with or without esophageal atresia, renal malformations, and limb defects. As mutations in ciliary genes were observed in diseases related to VATER/VACTERL, we performed targeted resequencing of 25 ciliary candidate genes as well as disease-associated genes (FOXF1, HOXD13, PTEN, ZIC3) in 123 patients with VATER/VACTERL or VATER/VACTERL-like phenotype. We detected no biallelic mutation in any of the 25 ciliary candidate genes; however, identified an identical, probably disease-causing ZIC3 missense mutation (p.Gly17Cys) in four patients and a FOXF1 de novo mutation (p.Gly220Cys) in a further patient. In situ hybridization analyses in mouse embryos between E9.5 and E14.5 revealed Zic3 expression in limb and prevertebral structures, and Foxf1 expression in esophageal, tracheal, vertebral, anal, and genital tubercle tissues, hence VATER/VACTERL organ systems. These data provide strong evidence that mutations in ZIC3 or FOXF1 contribute to VATER/VACTERL.
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Affiliation(s)
- Alina C Hilger
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Jan Halbritter
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Internal Medicine, Division of Nephrology, University Clinic Leipzig, Leipzig, Germany
| | - Tracie Pennimpede
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.,Division of Cancer Biology and Genetics, Queen's University, Kingston, Ontario, Canada
| | - Amelie van der Ven
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Georgia Sarma
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan D Porath
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stefan Kohl
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daw-Yang Hwang
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gabriel C Dworschak
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bernhard G Hermann
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Anna Pavlova
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany
| | - Osman El-Maarri
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany.,Department of Natural Sciences, Lebanese American University, Byblos/Beirut, Lebanon
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - 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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69
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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: 66] [Impact Index Per Article: 7.3] [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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70
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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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71
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Vivante A, Kleppa MJ, Schulz J, Kohl S, Sharma A, Chen J, Shril S, Hwang DY, Weiss AC, Kaminski MM, Shukrun R, Kemper MJ, Lehnhardt A, Beetz R, Sanna-Cherchi S, Verbitsky M, Gharavi AG, Stuart HM, Feather SA, Goodship JA, Goodship THJ, Woolf AS, Westra SJ, Doody DP, Bauer SB, Lee RS, Adam RM, Lu W, Reutter HM, Kehinde EO, Mancini EJ, Lifton RP, Tasic V, Lienkamp SS, Jüppner H, Kispert A, Hildebrandt F. Mutations in TBX18 Cause Dominant Urinary Tract Malformations via Transcriptional Dysregulation of Ureter Development. Am J Hum Genet 2015; 97:291-301. [PMID: 26235987 DOI: 10.1016/j.ajhg.2015.07.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/07/2015] [Indexed: 12/22/2022] Open
Abstract
Congenital anomalies of the kidneys and urinary tract (CAKUT) are the most common cause of chronic kidney disease in the first three decades of life. Identification of single-gene mutations that cause CAKUT permits the first insights into related disease mechanisms. However, for most cases the underlying defect remains elusive. We identified a kindred with an autosomal-dominant form of CAKUT with predominant ureteropelvic junction obstruction. By whole exome sequencing, we identified a heterozygous truncating mutation (c.1010delG) of T-Box transcription factor 18 (TBX18) in seven affected members of the large kindred. A screen of additional families with CAKUT identified three families harboring two heterozygous TBX18 mutations (c.1570C>T and c.487A>G). TBX18 is essential for developmental specification of the ureteric mesenchyme and ureteric smooth muscle cells. We found that all three TBX18 altered proteins still dimerized with the wild-type protein but had prolonged protein half life and exhibited reduced transcriptional repression activity compared to wild-type TBX18. The p.Lys163Glu substitution altered an amino acid residue critical for TBX18-DNA interaction, resulting in impaired TBX18-DNA binding. These data indicate that dominant-negative TBX18 mutations cause human CAKUT by interference with TBX18 transcriptional repression, thus implicating ureter smooth muscle cell development in the pathogenesis of human CAKUT.
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Affiliation(s)
- Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Marc-Jens Kleppa
- Institut für Molekularbiologie, Medizinische Hochschule Hannover 30625, Germany
| | - Julian Schulz
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan Kohl
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amita Sharma
- Pediatric Nephrology Unit and Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jing Chen
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daw-Yang Hwang
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Nephrology, Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Anna-Carina Weiss
- Institut für Molekularbiologie, Medizinische Hochschule Hannover 30625, Germany
| | - Michael M Kaminski
- Department of Medicine, Renal Division, University of Freiburg Medical Center, 79106 Freiburg, Germany
| | - Rachel Shukrun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Markus J Kemper
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Anja Lehnhardt
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Rolf Beetz
- Center for Pediatric and Adolescent Medicine, University Medical Clinic, 55131 Mainz, Germany
| | | | - Miguel Verbitsky
- Department of Medicine, Columbia University, New York, NY 10023, USA
| | - Ali G Gharavi
- Department of Medicine, Columbia University, New York, NY 10023, USA
| | - Helen M Stuart
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre and the Royal Manchester Children's and St Mary's Hospitals, Manchester M13 9WL, UK
| | | | - Judith A Goodship
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Timothy H J Goodship
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Adrian S Woolf
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre and the Royal Manchester Children's and St Mary's Hospitals, Manchester M13 9WL, UK
| | - Sjirk J Westra
- Pediatric Radiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Daniel P Doody
- Department of Pediatric Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Richard S Lee
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rosalyn M Adam
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Weining Lu
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, MA 02118, USA
| | - Heiko M Reutter
- Department of Neonatology, Children's Hospital, University of Bonn, 53127 Bonn, Germany
| | - Elijah O Kehinde
- Division of Urology, Department of Surgery, Kuwait University, 13110 Safat, Kuwait
| | - Erika J Mancini
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK; School of Life Sciences, University of Sussex, Brighton BN1 9QD, UK
| | - Richard P Lifton
- Department of Human Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Howard Hughes Medical Institute
| | - Velibor Tasic
- Medical School Skopje, University Children's Hospital, 1000 Skopje, Macedonia
| | - Soeren S Lienkamp
- Department of Medicine, Renal Division, University of Freiburg Medical Center, 79106 Freiburg, Germany; Center for Biological Signaling Studies (BIOSS), 79104 Freiburg, Germany
| | - Harald Jüppner
- Pediatric Nephrology Unit and Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Andreas Kispert
- Institut für Molekularbiologie, Medizinische Hochschule Hannover 30625, Germany
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute.
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72
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Hwang DY, Kohl S, Fan X, Vivante A, Chan S, Dworschak GC, Schulz J, van Eerde AM, Hilger AC, Gee HY, Pennimpede T, Herrmann BG, van de Hoek G, Renkema KY, Schell C, Huber TB, Reutter HM, Soliman NA, Stajic N, Bogdanovic R, Kehinde EO, Lifton RP, Tasic V, Lu W, Hildebrandt F. Mutations of the SLIT2-ROBO2 pathway genes SLIT2 and SRGAP1 confer risk for congenital anomalies of the kidney and urinary tract. Hum Genet 2015; 134:905-16. [PMID: 26026792 PMCID: PMC4497857 DOI: 10.1007/s00439-015-1570-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/18/2015] [Indexed: 12/26/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) account for 40-50% of chronic kidney disease that manifests in the first two decades of life. Thus far, 31 monogenic causes of isolated CAKUT have been described, explaining ~12% of cases. To identify additional CAKUT-causing genes, we performed whole-exome sequencing followed by a genetic burden analysis in 26 genetically unsolved families with CAKUT. We identified two heterozygous mutations in SRGAP1 in 2 unrelated families. SRGAP1 is a small GTPase-activating protein in the SLIT2-ROBO2 signaling pathway, which is essential for development of the metanephric kidney. We then examined the pathway-derived candidate gene SLIT2 for mutations in cohort of 749 individuals with CAKUT and we identified 3 unrelated individuals with heterozygous mutations. The clinical phenotypes of individuals with mutations in SLIT2 or SRGAP1 were cystic dysplastic kidneys, unilateral renal agenesis, and duplicated collecting system. We show that SRGAP1 is expressed in early mouse nephrogenic mesenchyme and that it is coexpressed with ROBO2 in SIX2-positive nephron progenitor cells of the cap mesenchyme in developing rat kidney. We demonstrate that the newly identified mutations in SRGAP1 lead to an augmented inhibition of RAC1 in cultured human embryonic kidney cells and that the SLIT2 mutations compromise the ability of the SLIT2 ligand to inhibit cell migration. Thus, we report on two novel candidate genes for causing monogenic isolated CAKUT in humans.
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Affiliation(s)
- Daw-Yang Hwang
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Division of Nephrology, Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Stefan Kohl
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Xueping Fan
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, MA, USA
| | - Asaf Vivante
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Stefanie Chan
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, MA, USA
| | - Gabriel C Dworschak
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Julian Schulz
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Albertien M van Eerde
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alina C Hilger
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Heon Yung Gee
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tracie Pennimpede
- Max Planck Institute for Molecular Genetics, Developmental Genetics Department, Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Developmental Genetics Department, Berlin, Germany
| | - Glenn van de Hoek
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kirsten Y Renkema
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christoph Schell
- Renal Division, University Hospital Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Tobias B Huber
- Renal Division, University Hospital Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Germany
| | - Heiko M Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Neonatology, Children’s Hospital, University of Bonn, Bonn, Germany
| | - 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
| | - Natasa Stajic
- Medical Faculty, University of Belgrade, Belgrade, Serbia
- Institute of Mother and Child Healthcare of Serbia, Belgrade, Serbia
| | - Radovan Bogdanovic
- Medical Faculty, University of Belgrade, Belgrade, Serbia
- Institute of Mother and Child Healthcare of Serbia, Belgrade, Serbia
| | | | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Velibor Tasic
- Department of Pediatric Nephrology, University Children’s Hospital, Skopje, Macedonia
| | - Weining Lu
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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73
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Lubinsky M. The VACTERL Association as a disturbance of cell fate determination. Am J Med Genet A 2015; 167A:2582-8. [DOI: 10.1002/ajmg.a.37238] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/05/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Mark Lubinsky
- 6003 W. Washington Blvd.; Wauwatosa; Wisconsin 53213
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74
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Agliarulo I, Matassa DS, Amoroso MR, Maddalena F, Sisinni L, Sepe L, Ferrari MC, Arzeni D, Avolio R, Paolella G, Landriscina M, Esposito F. TRAP1 controls cell migration of cancer cells in metabolic stress conditions: Correlations with AKT/p70S6K pathways. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2570-9. [PMID: 26071104 DOI: 10.1016/j.bbamcr.2015.05.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/14/2015] [Accepted: 05/28/2015] [Indexed: 12/17/2022]
Abstract
Cell motility is a highly dynamic phenomenon that is essential to physiological processes such as morphogenesis, wound healing and immune response, but also involved in pathological conditions such as metastatic dissemination of cancers. The involvement of the molecular chaperone TRAP1 in the regulation of cell motility, although still controversial, has been recently investigated along with some well-characterized roles in cancer cell survival and drug resistance in several tumour types. Among different functions, TRAP1-dependent regulation of protein synthesis seems to be involved in the migratory behaviour of cancer cells and, interestingly, the expression of p70S6K, a kinase responsible for translation initiation, playing a role in cell motility, is regulated by TRAP1. In this study, we demonstrate that TRAP1 silencing enhances cell motility in vitro but compromises the ability of cells to overcome stress conditions, and that this effect is mediated by the AKT/p70S6K pathway. In fact: i) inhibition of p70S6K activity specifically reduces migration in TRAP1 knock-down cells; ii) nutrient deprivation affects p70S6K activity thereby impairing cell migration only in TRAP1-deficient cells; iii) TRAP1 regulates the expression of both AKT and p70S6K at post-transcriptional level; and iii) TRAP1 silencing modulates the expression of genes involved in cell motility and epithelial-mesenchymal transition. Notably, a correlation between TRAP1 and AKT expression is found in vivo in human colorectal tumours. These results provide new insights into TRAP1 role in the regulation of cell migration in cancer cells, tumour progression and metastatic mechanisms.
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Affiliation(s)
- Ilenia Agliarulo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Danilo Swann Matassa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Francesca Maddalena
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, Rionero in Vulture, PZ, Italy
| | - Lorenza Sisinni
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, Rionero in Vulture, PZ, Italy
| | - Leandra Sepe
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Ceinge Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Naples, Italy
| | - Maria Carla Ferrari
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Ceinge Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Naples, Italy
| | - Diana Arzeni
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Rosario Avolio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Giovanni Paolella
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Ceinge Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Naples, Italy
| | - Matteo Landriscina
- Clinical Oncology Unit, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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Nakamura Y, Kikugawa S, Seki S, Takahata M, Iwasaki N, Terai H, Matsubara M, Fujioka F, Inagaki H, Kobayashi T, Kimura T, Kurahashi H, Kato H. PCSK5 mutation in a patient with the VACTERL association. BMC Res Notes 2015; 8:228. [PMID: 26055999 PMCID: PMC4467638 DOI: 10.1186/s13104-015-1166-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/12/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The VACTERL association is a typically sporadic, non-random collection of congenital anomalies that includes vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula with esophageal atresia, renal anomalies, and limb abnormalities. Although several chromosomal aberrations and gene mutations have been reported as disease-causative, these findings have been sparsely replicated to date. CASE PRESENTATION In the present study, whole exome sequencing of a case with the VACTERL association uncovered a novel frameshift mutation in the PCSK5 gene, which has been reported as one of the causative genes for the VACTERL association. Although this mutation appears potentially pathogenic in its functional aspects, it was also carried by the healthy father. Furthermore, a database survey revealed several other deleterious variants in the PCSK5 gene in the general population. CONCLUSIONS Further studies are necessary to clarify the etiological role of the PCSK5 mutation in the VACTERL association.
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Affiliation(s)
- Yukio Nakamura
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Japan.
| | | | - Shoji Seki
- Department of Orthopaedic Surgery, Faculty of Medicine, University of Toyama, Toyama, Japan.
| | - Masahiko Takahata
- Department of Orthopaedic Surgery, Hokkaido University School of Medicine, Sapporo, Japan.
| | - Norimasa Iwasaki
- Department of Orthopaedic Surgery, Hokkaido University School of Medicine, Sapporo, Japan.
| | - Hidetomi Terai
- Department of Orthopaedic Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.
| | - Mitsuhiro Matsubara
- Department of Orthopaedic Surgery, Nagano Prefectural Children's Hospital, Azumino, Japan.
| | - Fumio Fujioka
- Department of Orthopaedic Surgery, Nagano Prefectural Children's Hospital, Azumino, Japan.
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan.
| | - Tatsuya Kobayashi
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Tomoatsu Kimura
- Department of Orthopaedic Surgery, Faculty of Medicine, University of Toyama, Toyama, Japan.
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan.
| | - Hiroyuki Kato
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Japan.
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Boles RG, Hornung HA, Moody AE, Ortiz TB, Wong SA, Eggington JM, Stanley CM, Gao M, Zhou H, McLaughlin S, Zare AS, Sheldon KM, Skolnick J, McKernan KJ. Hurt, tired and queasy: Specific variants in the ATPase domain of the TRAP1 mitochondrial chaperone are associated with common, chronic "functional" symptomatology including pain, fatigue and gastrointestinal dysmotility. Mitochondrion 2015; 23:64-70. [PMID: 26022780 DOI: 10.1016/j.mito.2015.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/15/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
Abstract
Functional disorders are common conditions with a substantial impact on a patients' wellbeing, and can be diagnostically elusive. There are bidirectional associations between functional disorders and mitochondrial dysfunction. In this study, provided clinical information and the exon sequence of the TRAP1 mitochondrial chaperone were retrospectively reviewed with a focus on the functional categories of chronic pain, fatigue and gastrointestinal dysmotility. Very-highly conserved TRAP1 variants were identified in 73 of 930 unrelated patients. Functional symptomatology is strongly associated with specific variants in the ATPase binding pocket. In particular, the combined presence of all three functional categories is strongly associated with p.Ile253Val (OR 7.5, P = 0.0001) and with two other interacting variants (OR 18, P = 0.0005). Considering a 1-2% combined variant prevalence and high odds ratios, these variants may be an important factor in the etiology of functional symptomatology.
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Affiliation(s)
- Richard G Boles
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Holly A Hornung
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Alastair E Moody
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Thomas B Ortiz
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Stacey A Wong
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Julie M Eggington
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Christine M Stanley
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Mu Gao
- Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th St, Atlanta, GA 30318, United States
| | - Hongyi Zhou
- Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th St, Atlanta, GA 30318, United States
| | - Stephen McLaughlin
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Amir S Zare
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Katherine M Sheldon
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th St, Atlanta, GA 30318, United States
| | - Kevin J McKernan
- Courtagen Life Sciences, 12 Gill St, Ste. 3700, Woburn, MA 01801, United States
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Skinner SJ, Doonanco KR, Boles RG, Chan AKJ. Homozygous TRAP1 sequence variant in a child with Leigh syndrome and normal kidneys. Kidney Int 2015; 86:860. [PMID: 25265962 DOI: 10.1038/ki.2014.208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stephanie J Skinner
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Kurston R Doonanco
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | | | - Alicia K J Chan
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
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Gurung N, Grosse G, Draaken M, Hilger AC, Nauman N, Müller A, Gembruch U, Merz WM, Reutter H, Ludwig M. Mutations in PTF1A are not a common cause for human VATER/VACTERL association or neural tube defects mirroring Danforth's short tail mouse. Mol Med Rep 2015; 12:1579-83. [PMID: 25775927 DOI: 10.3892/mmr.2015.3486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 02/27/2015] [Indexed: 11/05/2022] Open
Abstract
Danforth's short tail (Sd) mutant mice exhibit defects of the neural tube and other abnormalities, which are similar to the human vertebral anomalies, anal atresia, cardiac defects, tracheosophageal fistula and/or esophageal atresia, renal and radial abnormalities, and limb defects (VATER/VACTERL) association, including defects of the hindgut. Sd has been shown to underlie ectopic gene expression of murine Ptf1a, which encodes pancreas-specific transcription factor 1A, due to the insertion of a retrotansposon in its 5' regulatory domain. In order to investigate the possible involvement of this gene in human VATER/VACTERL association and human neural tube defects (NTDs), a sequence analysis was performed. DNA samples from 103 patients with VATER/VACTERL and VATER/VACTERL‑like association, all presenting with anorectal malformations, and 72 fetuses with NTDs, where termination of pregnancy had been performed, were included in the current study. The complete PTF1A coding region, splice sites and 1.5 kb of the 5' flanking promotor region was sequenced. However, no pathogenic alterations were detected. The results of the present study do not support the hypothesis that high penetrant mutations in these regions of PTF1A are involved in the development of human VATER/VACTERL association or NTDs, although rare mutations may be detectable in larger patient samples.
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Affiliation(s)
- Nirmala Gurung
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn D‑53127, Germany
| | - Greta Grosse
- Institute of Human Genetics, University of Bonn, Bonn D‑53127, Germany
| | - Markus Draaken
- Institute of Human Genetics, University of Bonn, Bonn D‑53127, Germany
| | - Alina C Hilger
- Institute of Human Genetics, University of Bonn, Bonn D‑53127, Germany
| | - Nuzhat Nauman
- Department of Pathology, Holy Family Hospital, Rawalpindi 46000, Pakistan
| | - Andreas Müller
- Department of Neonatology, Children's Hospital, University of Bonn, Bonn D‑53127, Germany
| | - Ulrich Gembruch
- Department of Obstetrics and Prenatal Medicine, University of Bonn, Bonn D‑53127, Germany
| | - Waltraut M Merz
- Department of Obstetrics and Prenatal Medicine, University of Bonn, Bonn D‑53127, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn D‑53127, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn D‑53127, Germany
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Copy-number variation associated with congenital anomalies of the kidney and urinary tract. Pediatr Nephrol 2015; 30:487-95. [PMID: 25270717 DOI: 10.1007/s00467-014-2962-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 09/03/2014] [Accepted: 09/05/2014] [Indexed: 12/19/2022]
Abstract
BACKGROUND The most common cause of end-stage renal disease in children can be attributed to congenital anomalies of the kidney and urinary tract (CAKUT). Despite this high incidence of disease, the genetic mutations responsible for the majority of CAKUT cases remain unknown. METHODS To identify novel genomic regions associated with CAKUT, we screened 178 children presenting with the entire spectrum of structural anomalies associated with CAKUT for submicroscopic chromosomal imbalances (deletions or duplications) using single-nucleotide polymorphism (SNP) microarrays. RESULTS Copy-number variation (CNV) was detected in 10.1 % (18/178) of the patients; in 6.2 % of the total cohort, novel duplications or deletions of unknown significance were identified, and the remaining 3.9 % harboured CNV of known pathogenicity. CNVs were inherited in 90 % (9/10) of the families tested. In this cohort, patients diagnosed with multicystic dysplastic kidney (30 %) and posterior urethral valves (24 %) had a higher incidence of CNV. CONCLUSIONS The genes contained in the altered genomic regions represent novel candidates for CAKUT. This study has demonstrated that a significant proportion of patients with CAKUT harbour submicroscopic chromosomal imbalances, warranting screening in clinics for CNV.
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SIX1 gene: absence of mutations in children with isolated congenital anomalies of kidney and urinary tract. J Nephrol 2014; 27:667-71. [DOI: 10.1007/s40620-014-0112-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 05/13/2014] [Indexed: 11/30/2022]
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Cunningham BK, Khromykh A, Martinez AF, Carney T, Hadley DW, Solomon BD. Analysis of renal anomalies in VACTERL association. ACTA ACUST UNITED AC 2014; 100:801-5. [PMID: 25196458 DOI: 10.1002/bdra.23302] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 08/01/2014] [Accepted: 08/04/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND VACTERL association refers to a combination of congenital anomalies that can include: vertebral anomalies, anal atresia, cardiac malformations, tracheo-esophageal fistula with esophageal atresia, renal anomalies (typically structural renal anomalies), and limb anomalies. METHODS We conducted a description of a case series to characterize renal findings in a cohort of patients with VACTERL association. Out of the overall cohort, 48 patients (with at least three component features of VACTERL and who had abdominal ultrasound performed) met criteria for analysis. Four other patients were additionally analyzed separately, with the hypothesis that subtle renal system anomalies may occur in patients who would not otherwise meet criteria for VACTERL association. RESULTS Thirty-three (69%) of the 48 patients had a clinical manifestation affecting the renal system. The most common renal manifestation (RM) was vesicoureteral reflux (VUR) in addition to a structural defect (present in 27%), followed by unilateral renal agenesis (24%), and then dysplastic/multicystic kidneys or duplicated collected system (18% for each). Twenty-two (88%) of the 25 patients with a structural RM had an associated anorectal malformation. Individuals with either isolated lower anatomic anomalies, or both upper and lower anatomic anomalies were not statistically more likely to have a structural renal defect than those with isolated upper anatomic anomalies (p = 0.22, p = 0.284, respectively). CONCLUSION Given the high prevalence of isolated VUR in our cohort, we recommend a screening VCUG or other imaging modality be obtained to evaluate for VUR if initial renal ultrasound shows evidence of obstruction or renal scarring, as well as ongoing evaluation of renal health.
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Affiliation(s)
- Bridget K Cunningham
- Department of Pediatrics, Walter Reed National Military Medical Center-Bethesda, Maryland; Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Zeidler C, Woelfle J, Draaken M, Mughal SS, Große G, Hilger AC, Dworschak GC, Boemers TM, Jenetzky E, Zwink N, Lacher M, Schmidt D, Schmiedeke E, Grasshoff-Derr S, Märzheuser S, Holland-Cunz S, Schäfer M, Bartels E, Keppler K, Palta M, Leonhardt J, Kujath C, Rißmann A, Nöthen MM, Reutter H, Ludwig M. Heterozygous FGF8 mutations in patients presenting cryptorchidism and multiple VATER/VACTERL features without limb anomalies. ACTA ACUST UNITED AC 2014; 100:750-9. [PMID: 25131394 DOI: 10.1002/bdra.23278] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/31/2014] [Accepted: 06/03/2014] [Indexed: 11/09/2022]
Abstract
BACKGROUND The acronym VATER/VACTERL association describes the combination of at least three of the following cardinal features: vertebral defects, anorectal malformations, cardiac defects, tracheoesophageal fistula with or without esophageal atresia, renal malformations, and limb defects. Although fibroblast growth factor-8 (FGF8) mutations have mainly found in patients with Kallmann syndrome, mice with a hypomorphic Fgf8 allele or complete gene invalidation display, aside from gonadotropin-releasing hormone deficiency, parts or even the entire spectrum of human VATER/VACTERL association. METHODS We performed FGF8 gene analysis in 49 patients with VATER/VACTERL association and 27 patients presenting with a VATER/VACTERL-like phenotype (two cardinal features). RESULTS We identified two heterozygous FGF8 mutations in patients displaying either VATER/VACTERL association (p.Gly29_Arg34dup) or a VATER/VACTERL-like phenotype (p.Pro26Leu) without limb anomalies. Whereas the duplication mutation has not been reported before, p.Pro26Leu was once observed in a Kallmann syndrome patient. Both our patients had additional bilateral cryptorchidism, a key phenotypic feature in males with FGF8 associated Kallmann syndrome. Each mutation was paternally inherited. Besides delayed puberty in both and additional unilateral cryptorchidism in one of the fathers, they were otherwise healthy. Serum hormone levels downstream the gonadotropin-releasing hormone in both patients and their fathers were within normal range. CONCLUSION Our results suggest FGF8 mutations to contribute to the formation of the VATER/VACTERL association. Further studies are needed to support this observation.
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Affiliation(s)
- Claudia Zeidler
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
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83
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Clinical and etiological heterogeneity in patients with tracheo-esophageal malformations and associated anomalies. Eur J Med Genet 2014; 57:440-52. [DOI: 10.1016/j.ejmg.2014.05.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/20/2014] [Indexed: 12/12/2022]
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Amoroso MR, Matassa DS, Sisinni L, Lettini G, Landriscina M, Esposito F. TRAP1 revisited: novel localizations and functions of a 'next-generation' biomarker (review). Int J Oncol 2014; 45:969-77. [PMID: 24990602 DOI: 10.3892/ijo.2014.2530] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/26/2014] [Indexed: 11/06/2022] Open
Abstract
In the last decade, the identification and characterization of novel molecular mechanisms and pathways involving the heat shock protein TRAP1/HSP75 in cancers and other diseases enhanced the scientific interest. Recent reports have shown that TRAP1 stays at the crossroad of multiple crucial processes in the onset of neoplastic transformation. In fact, TRAP1: i) contributes to the tumor's switch to aerobic glycolysis through the inhibition of succinate dehydrogenase, the complex II of the mitochondrial respiratory chain; ii) is part of a pro-survival signaling pathway aimed at evading the toxic effects of oxidants and anticancer drugs and protects mitochondria against damaging stimuli via a decrease of ROS generation; iii) controls protein homeostasis through a direct involvement in the regulation of protein synthesis and protein co-translational degradation. Therefore, TRAP1 seems to be a central regulatory protein with balancing functions at the intersection of different metabolic processes during the neoplastic transformation. For this reason, it can be considered at the same time an attractive target for the development of novel anticancer strategies and a promising study model to understand the biology of tumor cells at a systemic level. This review summarizes the most recent advances in TRAP1 biology and proposes a new comprehensive view of its functions.
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Affiliation(s)
| | - Danilo Swann Matassa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Lorenza Sisinni
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Centre of Basilicata, Rionero in Vulture, PZ, Italy
| | - Giacomo Lettini
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Centre of Basilicata, Rionero in Vulture, PZ, Italy
| | - Matteo Landriscina
- Clinical Oncology Unit, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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Renkema KY, Stokman MF, Giles RH, Knoers NVAM. Next-generation sequencing for research and diagnostics in kidney disease. Nat Rev Nephrol 2014; 10:433-44. [PMID: 24914583 DOI: 10.1038/nrneph.2014.95] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The advent of next-generation sequencing technologies has enabled genetic nephrology research to move beyond single gene analysis to the simultaneous investigation of hundreds of genes and entire pathways. These new sequencing approaches have been used to identify and characterize causal factors that underlie inherited heterogeneous kidney diseases such as nephronophthisis and congenital anomalies of the kidney and urinary tract. In this Review, we describe the development of next-generation sequencing in basic and clinical research and discuss the implementation of this novel technology in routine patient management. Widespread use of targeted and nontargeted approaches for gene identification in clinical practice will require consistent phenotyping, appropriate disease modelling and collaborative efforts to combine and integrate data analyses. Next-generation sequencing is an exceptionally promising technique that has the potential to improve the management of patients with inherited kidney diseases. However, identifying the molecular mechanisms that lead to renal developmental disorders and ciliopathies is difficult. A major challenge in the near future will be how best to integrate data obtained using next-generation sequencing with personalized medicine, including use of high-throughput disease modelling as a tool to support the clinical diagnosis of kidney diseases.
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Affiliation(s)
- Kirsten Y Renkema
- Department of Medical Genetics, University Medical Center Utrecht, KC04.048.02, PO Box 85090, Utrecht, 3508 AB, Netherlands
| | - Marijn F Stokman
- Department of Medical Genetics, University Medical Center Utrecht, KC04.048.02, PO Box 85090, Utrecht, 3508 AB, Netherlands
| | - Rachel H Giles
- Department of Nephrology and Hypertension, University Medical Center Utrecht, KC04.048.02, PO Box 85090, Utrecht, 3508 AB, Netherlands
| | - Nine V A M Knoers
- Department of Medical Genetics, University Medical Center Utrecht, KC04.048.02, PO Box 85090, Utrecht, 3508 AB, Netherlands
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Rasola A, Neckers L, Picard D. Mitochondrial oxidative phosphorylation TRAP(1)ped in tumor cells. Trends Cell Biol 2014; 24:455-63. [PMID: 24731398 DOI: 10.1016/j.tcb.2014.03.005] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 03/11/2014] [Accepted: 03/17/2014] [Indexed: 02/07/2023]
Abstract
Many tumors undergo a dramatic metabolic shift known as the Warburg effect in which glucose utilization is favored and oxidative phosphorylation is downregulated, even when oxygen availability is plentiful. However, the mechanistic basis for this switch has remained unclear. Recently several independent groups identified tumor necrosis factor receptor-associated protein 1 (TRAP1), a mitochondrial molecular chaperone of the heat shock protein 90 (Hsp90) family, as a key modulator of mitochondrial respiration. Although all reports agree that this activity of TRAP1 has important implications for neoplastic progression, data from the different groups only partially overlap, suggesting that TRAP1 may have complex and possibly contextual effects on tumorigenesis. In this review we analyze these recent findings and attempt to reconcile these observations.
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Affiliation(s)
- Andrea Rasola
- CNR Institute of Neuroscience, University of Padova, 35121 Padova, Italy; Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy.
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Didier Picard
- Department of Cell Biology, University of Geneva, CH-1211 Geneva 4, Switzerland
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Reutter H, Gurung N, Ludwig M. Evidence for annular pancreas as an associated anomaly in the VATER/VACTERL association and investigation of the gene encoding pancreas specific transcription factor 1A as a candidate gene. Am J Med Genet A 2014; 164A:1611-3. [PMID: 24668915 DOI: 10.1002/ajmg.a.36479] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/03/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany; Department of Neonatology, Children's Hospital, University of Bonn, Bonn, Germany
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