High frequency of kidney and urinary tract anomalies in asymptomatic first-degree relatives of patients with CAKUT

The dominant findings of a recessive man: from Mendel's kid pea to kidney

The research of Mendel, born two centuries ago, still has many direct implications for our everyday clinical work. He introduced the terms "dominant" and "recessive" characters and determined their 3:1 ratio in the offspring of heterozygous "hybrid" plants. This distribution allowed calculation of the number of the phenotype-determining "elements," i.e., the alleles, and has been used ever since to prove the monogenic origin of a disorder. The Mendelian inheritance of monogenic kidney disorders is still of great help in distinguishing them from those with multifactorial origin in clinical practice. Inheritance of most monogenic kidney disorders fits to Mendel's observations: the equal contribution of the two parents and the complete penetrance or the direct correlation between the frequency of the recessive character and the degree of inbreeding. Nevertheless, beyond the truth of these basic concepts, several observations have expanded their genetic characteristics. The extreme genetic heterogeneity, the pleiotropy of the causal genes and the role of modifiers in ciliopathies, the digenic inheritance and parental imprinting in some tubulopathies, and the incomplete penetrance and eventual interallelic interactions in podocytopathies, reflect this expansion. For all these reasons, the transmission pattern in a natural setting may depend not only on the "character" but also on the causal gene and the variant. Mendel's passion for research combined with his modest personality and meticulous approach can still serve as an example in the work required to understand the non-Mendelian universe of genetics.

Fetal Renal Duplicated Collecting System at 14-16 Weeks of Gestation

(1) Background: To examine the incidence of the prenatal diagnosis of the renal double-collecting system (rDCS) and describe its clinical outcome and associated genetic abnormalities. (2) Methods: This retrospective study included women who attended the obstetric clinic for early fetal anatomic sonography with findings of a renal DCS. Diagnosis was conducted by an expert sonographer using defined criteria. (3) Results: In total, 29,268 women underwent early ultrasound anatomical screening at 14-16 weeks, and 383 cases of rDCS were diagnosed (prevalence: 1:76). Associated abnormalities were diagnosed in eleven pregnancies; four had chromosomal aberrations. No chromosomal abnormalities were reported in isolated cases. Ectopic uretrocele and dysplastic kidney were diagnosed in 6 (1.5%) and 5 (1.3%) fetuses, respectively. One girl was diagnosed with vesicoureteral reflux and recurrent UTIs, and two boys were diagnosed with undescended testis. The recurrence rate of rDCS was 8% in subsequent pregnancies. (4) Conclusions: In light of its benign nature, we speculate that isolated rDCS may be considered a benign anatomic variant, but a repeat examination in the third trimester is recommended to assess hydronephrosis.

Genetic Spectrum of Congenital Anomalies of the Kidney and Urinary Tract in Chinese Newborn Genome Project

Introduction

Congenital anomalies of the kidney and urinary tract (CAKUT) corresponds to a spectrum of defects. Several large-cohort studies have used high-throughput sequencing to investigate the genetic risk of CAKUT during antenatal, childhood, and adulthood period. However, our knowledge of newborns with CAKUT is limited.

Methods

This multicenter retrospective cohort study explored the genetic spectrum of CAKUT in a Chinese neonatal cohort. Clinical data and whole exome sequencing (WES) data of 330 newborns clinically diagnosed with CAKUT were collected. WES data were analyzed for putative deleterious single nucleotide variants (SNVs) and potential disease-associated copy number variants (CNVs).

Results

In this study, pathogenic variants were identified in 61 newborns (18.5%, 61/330), including 35 patients (57.4%) with SNVs, 25 patients (41%) with CNVs, and 1 patient with both an SNV and a CNV. Genetic diagnosis rates were significantly higher in patients with extrarenal manifestations (P＜0.001), especially in those with cardiovascular malformations (P＜0.05). SNVs in genes related to syndromic disorders (CAKUT with extrarenal manifestations) were common, affecting 20 patients (57.1%, 20/35). KMT2D was the most common gene (5 patients) and 17q12 deletion was the most common CNV (4 patients). Patient 110 was detected with both a CNV (17q12 deletion) and an SNV (a homozygous variant of SLC25A13). Among the newborns with positive genetic results, 22 (36.1%, 22/61) patients may benefit from a molecular diagnosis and change in clinical management (including early multidisciplinary treatment, disease-specific follow-up, and familial genetic counseling).

Conclusion

This study shows the heterogeneous genetic etiologies in a Chinese CAKUT neonatal cohort by using WES. Patients with CAKUT who have extrarenal manifestations are more likely to harbor genetic diagnoses. Kabuki syndrome and 17q12 deletion syndrome were the most common genetic findings. Approximately 36.1% of the patients may benefit from molecular diagnoses and a change in clinical management.

Exome sequencing in individuals with congenital anomalies of the kidney and urinary tract (CAKUT): a single-center experience

Individuals with congenital anomalies of the kidney and urinary tract (CAKUT) show a broad spectrum of malformations. CAKUT can occur in an isolated fashion or as part of a syndromic disorder and can lead to end-stage kidney failure. A monogenic cause can be identified in ~12% of affected individuals. This study investigated a single-center CAKUT cohort analyzed by exome sequencing (ES). Emphasis was placed on the question whether diagnostic yield differs between certain CAKUT phenotypes (e.g., bilateral kidney affection, unilateral kidney affection or only urinary tract affection). 86 unrelated individuals with CAKUT were categorized according to their phenotype and analyzed by ES to identify a monogenic cause. Prioritized variants were rated according to the recommendations of the American College of Medical Genetics and Genomics and the Association for Clinical Genomic Science. Diagnostic yields of different phenotypic categories were compared. Clinical data were collected using a standardized questionnaire. In the study cohort, 7/86 individuals had a (likely) pathogenic variant in the genes PAX2, PBX1, EYA1, or SALL1. Additionally, in one individual, a 17q12 deletion syndrome (including HNF1B) was detected. 64 individuals had a kidney affection, which was bilateral in 36. All solved cases (8/86, 9%) had bilateral kidney affection (diagnostic yield in subcohort: 8/36, 22%). Although the diagnostic yield in CAKUT cohorts is low, our single-center experience argues, that, in individuals with bilateral kidney affection, monogenic burden is higher than in those with unilateral kidney or only urinary tract affection.

Fetal uropathies: pre- and postnatal imaging, management and follow-up

Congenital uropathies are the most common fetal anomalies. They include a wide spectrum of anomalies ranging from mild pelvis dilation to complex urinary tract malformations. Prenatal imaging not only allows for their diagnosis but, in experienced hands, it can differentiate obstructive from refluxing or malformative uropathies. Such precise prenatal information allows for intervention before birth in select cases or for adapting the postnatal workup to provide a better long-term outcome. For the different types of congenital uropathies, we describe their prenatal presentations on US and the complementary role of fetal MRI where indicated. We correlate these findings with postnatal workup and summarize the updated neonatal diagnostic and clinical/surgical management.

Maternal risk factors for congenital anomalies of the kidney and urinary tract: A case-control study

BACKGROUND

Congenital anomalies of the kidney and urinary tract (CAKUT) are significant causes of pediatric morbidity and mortality. The spectrum of CAKUT can be part of a syndrome, but most of these abnormalities occur as isolated and sporadic forms. The etiology of human CAKUT is unknown in the majority of cases. This case-control study aimed to investigate the association between maternal characteristics and the occurrence of CAKUT and specific CAKUT phenotypes.

METHODS

In this case-control study, 29,653 newborns were evaluated consecutively in a tertiary neonatal unit using the Latin American Collaborative Study of Congenital Malformations (ECLAMC) registry. Newborns without congenital anomalies were matched to CAKUT cases by sex, date, and place of birth at a ratio of 3:1. For analysis purposes, the cases were stratified into four subgroups: upper tract abnormalities (UTA), including ureteropelvic junction obstruction, vesicoureteral reflux, primary megaureter and others (n = 239), lower urinary tract obstruction (LUTO) (n = 79), cystic diseases (n = 59) and agenesis/hypodysplasia (n = 28). Multivariable logistic regression analyses were used to calculate crude and adjusted odds ratios (ORs) with 95% confidence intervals (CIs) for associations between the maternal risk factors and the presence of CAKUT.

RESULTS

The prevalence of non-syndromic CAKUT in our sample was 13 per 1000 live births. Data records allowed the analysis of 405 cases and 1208 controls. After adjustment by the binary regression logistic, three covariates remained associated as risk factors for the entire spectrum of CAKUT: consanguinity (Odds ratio [OR], 7.1, 95%CI, 2.4-20.4), family history of CAKUT (OR, 6.4, 95%CI, 1.9-21.3), and maternal chronic hypertension (OR, 14.69, 95%CI, 3.2-67.5) (Figure). These risk factors persisted consistently across the various CAKUT phenotypes with minor variations. Consanguinity was the only factor consistently associated with almost all CAKUT phenotypes. Maternal hypertension was associated with all phenotypes except for the agenesis/hypodysplasia group. The prevalence of CAKUT cases was 15 times higher in hypertensive mothers (3%) compared to normotensive mothers (0.2%).

CONCLUSION

Our study suggests that an increased risk of CAKUT is associated with consanguinity, a positive family history of CAKUT, and maternal hypertension. However, the prevalence of these risk factors in our cohort was rare and most cases presented as sporadic forms.

Maternal Chronic Disease and Congenital Anomalies of the Kidney and Urinary Tract in Offspring: A Japanese Cohort Study

RATIONALE & OBJECTIVE

Several maternal chronic diseases have been reported as risk factors for congenital anomalies of the kidney and urinary tract (CAKUT) in offspring. However, these investigations used case-control designs, and cases with isolated genitourinary CAKUT were not distinguished from cases in which CAKUT were present with extrarenal congenital anomalies (complicated CAKUT). We examined the association of maternal diseases with isolated and complicated CAKUT in offspring using data from a prospective cohort study.

STUDY DESIGN

A nationwide prospective birth cohort study.

SETTING & PARTICIPANTS

100,239 children enrolled in the Japan Environment and Children's Study between January 2011 and March 2014 at 15 research centers. Physicians' diagnoses in mothers and children were collected from medical record transcripts and questionnaires.

EXPOSURES

Medical histories of maternal noncommunicable diseases, including obesity, hypertension, diabetes mellitus, kidney disease, hyperthyroidism, hypothyroidism, psychiatric disease, epilepsy, cancer, and autoimmune disease.

OUTCOMES

CAKUT diagnosed during the first 3 years of life, classified as isolated or complicated.

ANALYTICAL APPROACH

Multivariable Poisson regression with generalized estimating equations accounting for clustering by clinical center.

RESULTS

Among the 100,239 children, 560 (0.6%) had CAKUT, comprising 454 (81%) isolated and 106 (19%) complicated forms. The risk of isolated CAKUT was increased in children of mothers who experienced kidney disease (adjusted risk ratio [RR], 1.80 [95% CI, 1.12-2.91]) or cancer (RR, 2.11 [95% CI, 1.15-3.86]). Furthermore, the risk of complicated CAKUT was increased in children of mothers with diabetes mellitus (RR, 3.04 [95% CI, 1.64-5.61]).

LIMITATIONS

Lack of standardization or prespecification of clinical definitions, diagnostic criteria, measurements, and testing. Genetic testing was not performed.

CONCLUSIONS

Isolated CAKUTs and complicated CAKUTs were associated with different maternal diseases. The results may inform clinical management of pregnancy and highlight potential differences in the genesis of isolated and complicated forms of CAKUT.

Disease mechanisms of monogenic congenital anomalies of the kidney and urinary tract American Journal of Medical Genetics Part C

Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) is a developmental disorder of the kidney and/or genito-urinary tract that results in end stage kidney disease (ESKD) in up to 50% of children. Despite the congenital nature of the disease, CAKUT accounts for almost 10% of adult onset ESKD. Multiple lines of evidence suggest that CAKUT is a Mendelian disorder, including the observation of familial clustering of CAKUT. Pathogenesis in CAKUT is embryonic in origin, with disturbances of kidney and urinary tract development resulting in a heterogeneous range of disease phenotypes. Despite polygenic and environmental factors being implicated, a significant proportion of CAKUT is monogenic in origin, with studies demonstrating single gene defects in 10%-20% of patients with CAKUT. Here, we review monogenic disease causation with emphasis on the etiological role of gene developmental pathways in CAKUT.

Definition, diagnosis and clinical management of non-obstructive kidney dysplasia: a consensus statement by the ERKNet Working Group on Kidney Malformations

Kidney dysplasia is one of the most frequent causes of chronic kidney failure in children. While dysplasia is a histological diagnosis, the term 'kidney dysplasia' is frequently used in daily clinical life without histopathological confirmation. Clinical parameters of kidney dysplasia have not been clearly defined, leading to imprecise communication amongst healthcare professionals and patients. This lack of consensus hampers precise disease understanding and the development of specific therapies. Based on a structured literature search, we here suggest a common basis for clinical, imaging, genetic, pathological and basic science aspects of non-obstructive kidney dysplasia associated with functional kidney impairment. We propose to accept hallmark sonographic findings as surrogate parameters defining a clinical diagnosis of dysplastic kidneys. We suggest differentiated clinical follow-up plans for children with kidney dysplasia and summarize established monogenic causes for non-obstructive kidney dysplasia. Finally, we point out and discuss research gaps in the field.

Multidisciplinary approaches for elucidating genetics and molecular pathogenesis of urinary tract malformations

Advances in clinical diagnostics and molecular tools have improved our understanding of the genetically heterogeneous causes underlying congenital anomalies of kidney and urinary tract (CAKUT). However, despite a sharp incline of CAKUT reports in the literature within the past 2 decades, there remains a plateau in the genetic diagnostic yield that is disproportionate to the accelerated ability to generate robust genome-wide data. Explanations for this observation include (i) diverse inheritance patterns with incomplete penetrance and variable expressivity, (ii) rarity of single-gene drivers such that large sample sizes are required to meet the burden of proof, and (iii) multigene interactions that might produce either intra- (e.g., copy number variants) or inter- (e.g., effects in trans) locus effects. These challenges present an opportunity for the community to implement innovative genetic and molecular avenues to explain the missing heritability and to better elucidate the mechanisms that underscore CAKUT. Here, we review recent multidisciplinary approaches at the intersection of genetics, genomics, in vivo modeling, and in vitro systems toward refining a blueprint for overcoming the diagnostic hurdles that are pervasive in urinary tract malformation cohorts. These approaches will not only benefit clinical management by reducing age at molecular diagnosis and prompting early evaluation for comorbid features but will also serve as a springboard for therapeutic development.

Targeted next-generation sequencing in a large series of fetuses with severe renal diseases

We report the screening of a large panel of genes in a series of 100 fetuses (98 families) affected with severe renal defects. Causative variants were identified in 22% of cases, greatly improving genetic counseling. The percentage of variants explaining the phenotype was different according to the type of phenotype. The highest diagnostic yield was found in cases affected with the ciliopathy-like phenotype (11/15 families and, in addition, a single heterozygous or a homozygous Class 3 variant in PKHD1 in three unrelated cases with autosomal recessive polycystic kidney disease). The lowest diagnostic yield was observed in cases with congenital anomalies of the kidney and urinary tract (9/78 families and, in addition, Class 3 variants in GREB1L in three unrelated cases with bilateral renal agenesis). Inheritance was autosomal recessive in nine genes (PKHD1, NPHP3, CEP290, TMEM67, DNAJB11, FRAS1, ACE, AGT, and AGTR1), and autosomal dominant in six genes (PKD1, PKD2, PAX2, EYA1, BICC1, and MYOCD). Finally, we developed an original approach of next-generation sequencing targeted RNA sequencing using the custom capture panel used for the sequencing of DNA, to validate one MYOCD heterozygous splicing variant identified in two male siblings with megabladder and inherited from their healthy mother.

The term CAKUT has outlived its usefulness: the case for the defense

Congenital anomalies of the kidney and urinary tract form a spectrum of congenital structural disorders that are generally known under the term CAKUT. The term CAKUT was introduced 20 years ago and has been used extensively in literature since. Prof. Woolf has made a plea for abandoning this term in his "case for the prosecution." Here, I advocate for the continued use of CAKUT as an umbrella term for these related congenital kidney and urinary tract abnormalities. I explain why the term CAKUT accurately and usefully defines this group of related structural disorders with prenatal origin and why it makes sense to continue grouping these disorders given accumulating evidence for shared etiology of CAKUT phenotypes and the importance of grouping CAKUT phenotypes in genetic counseling.

Genetic testing in the diagnosis of chronic kidney disease: recommendations for clinical practice

The overall diagnostic yield of massively parallel sequencing–based tests in patients with chronic kidney disease (CKD) is 30% for paediatric cases and 6–30% for adult cases. These figures should encourage nephrologists to frequently use genetic testing as a diagnostic means for their patients. However, in reality, several barriers appear to hinder the implementation of massively parallel sequencing–based diagnostics in routine clinical practice. In this article we aim to support the nephrologist to overcome these barriers. After a detailed discussion of the general items that are important to genetic testing in nephrology, namely genetic testing modalities and their indications, clinical information needed for high-quality interpretation of genetic tests, the clinical benefit of genetic testing and genetic counselling, we describe each of these items more specifically for the different groups of genetic kidney diseases and for CKD of unknown origin.

Australia and New Zealand renal gene panel testing in routine clinical practice of 542 families

Genetic testing in nephrology clinical practice has moved rapidly from a rare specialized test to routine practice both in pediatric and adult nephrology. However, clear information pertaining to the likely outcome of testing is still missing. Here we describe the experience of the accredited Australia and New Zealand Renal Gene Panels clinical service, reporting on sequencing for 552 individuals from 542 families with suspected kidney disease in Australia and New Zealand. An increasing number of referrals have been processed since service inception with an overall diagnostic rate of 35%. The likelihood of identifying a causative variant varies according to both age at referral and gene panel. Although results from high throughput genetic testing have been primarily for diagnostic purposes, they will increasingly play an important role in directing treatment, genetic counseling, and family planning.

Glomerular involvement in children with H syndrome

BACKGROUND

H syndrome is a multisystem inflammatory disease caused by mutations in the SLC29A3 gene (OMIM #602782). The protein product, hENT3, is a nucleoside transporter essential for DNA salvage synthesis. Clinical manifestations are hyperpigmentation, hypertrichosis, hepatosplenomegaly, hearing loss, heart anomalies, hypogonadism, short stature, skeletal deformities, and diabetes mellitus. Laboratory findings are consistent with inflammatory processes. Structural kidney anomalies have been described in 6% of patients.

CASE REPORTS

Three family members with genetically diagnosed H syndrome (c.1279G>A, p.Gly427Ser). Two of them presented with hypoalbuminemia and nephrotic range proteinuria. Kidney ultrasound was normal. Kidney biopsy performed in one patient presenting with generalized peripheral pitting edema revealed membranous nephropathy. Different treatments including ACE inhibitors, corticosteroids, and immunomodulatory agents failed to improve the clinical outcome.

CONCLUSIONS

Generalized peripheral pitting edema and glomerulopathy broaden the clinical spectrum of H syndrome. Periodic bloodwork and urinalysis are recommended.

Clinical Integration of Genome Diagnostics for Congenital Anomalies of the Kidney and Urinary Tract

Revolutions in genetics, epigenetics, and bioinformatics are currently changing the outline of diagnostics and clinical medicine. From a nephrologist's perspective, individuals with congenital anomalies of the kidney and urinary tract (CAKUT) are an important patient category: not only is CAKUT the predominant cause of kidney failure in children and young adults, but the strong phenotypic and genotypic heterogeneity of kidney and urinary tract malformations has hampered standardization of clinical decision making until now. However, patients with CAKUT may benefit from precision medicine, including an integrated diagnostics trajectory, genetic counseling, and personalized management to improve clinical outcomes of developmental kidney and urinary tract defects. In this review, we discuss the present understanding of the molecular etiology of CAKUT and the currently available genome diagnostic modalities in the clinical care of patients with CAKUT. Finally, we discuss how clinical integration of findings from large-scale genetic, epigenetic, and gene-environment interaction studies may improve the prognosis of all individuals with CAKUT.

Screening of renal anomalies in first-degree relatives of children diagnosed with non-syndromic congenital anomalies of kidney and urinary tract

BACKGROUND

Non-syndromic congenital anomalies of kidney and urinary tract (CAKUT) are usually sporadic in nature but familial clustering of cases have been observed suggesting a genetic predisposition to this condition. We aimed to determine the frequency and pattern of renal anomalies in first-degree relatives of children with non-syndromic CAKUT.

METHODS

We screened all the first-degree relatives of children with CAKUT. A total of 149 first-degree relatives, belonging to 62 families were screened with ultrasonography.

RESULTS

A renal anomaly was detected in 9 out of the 62 families. Two of these nine families had identical anomalies (child and a parent) indicating single-gene disorders with possible autosomal dominant inheritance, while the rest of families had a non-identical anomaly. The anomalies detected in the first-degree relatives were renal hypodysplasia (n = 2), multicystic dysplastic kidney (n = 3), pelviureteric junction obstruction (n = 2) and mild hydronephrosis (n = 2). The incidence of a sonographically detected anatomic renal anomaly in first-degree relatives of children with CAKUT was found to be 6.0%. Familial cystic kidney disease was found in two out of the 4 families with cystic kidney disease.

CONCLUSION

Significant renal anomalies were identified in first-degree relatives of children with non-syndromic CAKUT and hence, attempts must be made to screen the family members of children with non-syndromic CAKUT.

Screening for Renal and Urinary Tract Anomalies in Asymptomatic First Degree Relatives of Children with Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)

OBJECTIVE

To estimate the frequency of renal and urinary tract anomalies in first-degree relatives of children with Congenital anomalies of kidney and urinary tract (CAKUT).

METHODS

This descriptive study was conducted on parents and siblings of 138 children with CAKUT. Renal ultrasonogram, radionuclide diuretic renogram and micturating cysturethrogram were the tools used for screening these family members.

RESULTS

Asymptomatic first-degree relatives of 138 children [total of 270 first-degree relatives (95 fathers, 97 mothers and 78 siblings)] were screened, with new anomalies detected in 11 first-degree relatives (4% out of 270 first-degree relatives screened) from 11 families (7.9% out of 138 families screened). The anomalies detected were vesicoureteric reflux (VUR) (n = 2), non-obstructive non-refluxing hydronephrosis (n = 2), pelviureteral junction obstruction (PUJO) (n = 3), Duplex collecting system (n = 1), hypodysplastic kidney (n = 1), single kidney (n = 1) and horseshoe kidney (n = 1). Most of the anomalies were discordant to the index anomaly (66.6%). Among 95 fathers screened, 5 (5.2%) had renal anomalies. Among 97 mothers screened, 2 (2.1%) had renal anomalies. Among the 78 siblings screened, 4 (5.1%) had renal anomalies.

CONCLUSIONS

Familial clustering was noted in 7.9% of the 138 families (of the index cases) screened. The anomalies detected were mostly discordant to the index anomaly.

Mouse Models of Congenital Kidney Anomalies

Congenital anomalies of the kidney and urinary tract (CAKUT) are common birth defects, which cause the majority of chronic kidney diseases in children. CAKUT covers a wide range of malformations that derive from deficiencies in embryonic kidney and lower urinary tract development, including renal aplasia, hypodysplasia, hypoplasia, ectopia, and different forms of ureter abnormalities. The majority of the genetic causes of CAKUT remain unknown. Research on mutant mice has identified multiple genes that critically regulate renal differentiation. The data generated from this research have served as an excellent resource to identify the genetic bases of human kidney defects and have led to significantly improved diagnostics. Furthermore, genetic data from human CAKUT studies have also revealed novel genes regulating kidney differentiation.

The clinical characteristics of Chinese patients with unilateral renal agenesis

BACKGROUND

We aimed to investigate the clinical characteristics of Chinese patients with unilateral renal agenesis.

METHODS

We enrolled patients with unilateral renal agenesis diagnosed radiologically at the Department of Nephrology from January 2008 to January 2016. Patients with a solitary kidney due to nephrectomy or renal atrophy due to secondary factors were excluded. Clinical data were recorded and analyzed.

RESULTS

In this study, 118 Chinese patients with unilateral renal agenesis were recruited, and the gender ratio (male/female) was 1.11:1. A total of 14 (11.9%) patients had additional abnormalities, 15 (12.7%) had a family history, and 30 (25.4%) presented with renal insufficiency. Kidney length, serum creatinine level and estimated glomerular filtration rate were significantly different between patients with and without family history (P < 0.05, respectively). Gender showed a significant difference between patients with and without other abnormalities. Kidney length and the incidence of proteinuria, hematuria, hypertension, and hyperuricemia were significantly different between patients with and without renal insufficiency. Logistic regression analysis revealed that family history was associated with severe renal failure (OR = 7.11, 95% CI 1.52-33.25).

CONCLUSION

Renal insufficiency is common in patients with unilateral renal agenesis. Patients with renal insufficiency have shorter kidney lengths and a higher incidence of proteinuria, hypertension, hematuria, and hyperuricemia. Family history is considered a risk factor for severe renal failure.

Impact of next generation sequencing on our understanding of CAKUT

Congenital abnormalities of the kidney and urinary tract (CAKUT) form the leading cause of pediatric end-stage renal disease. Knowledge on the molecular mechanisms that underlie CAKUT leads to the improvement of DNA diagnostics and counseling regarding prognosis and recurrence risk estimation for CAKUT patients and their relatives. Implementation of next generation sequencing in research and diagnostic settings has led to the identification of the molecular basis of many developmental diseases. In this review, we summarize the efforts on next generation sequencing in CAKUT research and we discuss how next generation sequencing added to our understanding of CAKUT genetics. Although next generation sequencing has certainly proven to be a game changer in the field of disease gene identification and novel CAKUT-causing gene variants have been identified, most CAKUT cases still remain unsolved. Occurring with genetic and phenotypic heterogeneity along with incomplete penetrance, the identification of CAKUT etiology poses many challenges. We see great potential for combined -omics approaches that include next generation sequencing in the identification of CAKUT-specific biomarkers, which is necessary to optimize the care for CAKUT patients.

Targeted Exome Sequencing Identifies PBX1 as Involved in Monogenic Congenital Anomalies of the Kidney and Urinary Tract

Congenital anomalies of the kidney and urinary tract (CAKUT) occur in three to six of 1000 live births, represent about 20% of the prenatally detected anomalies, and constitute the main cause of CKD in children. These disorders are phenotypically and genetically heterogeneous. Monogenic causes of CAKUT in humans and mice have been identified. However, despite high-throughput sequencing studies, the cause of the disease remains unknown in most patients, and several studies support more complex inheritance and the role of environmental factors and/or epigenetics in the pathophysiology of CAKUT. Here, we report the targeted exome sequencing of 330 genes, including genes known to be involved in CAKUT and candidate genes, in a cohort of 204 unrelated patients with CAKUT; 45% of the patients were severe fetal cases. We identified pathogenic mutations in 36 of 204 (17.6%) patients. These mutations included five de novo heterozygous loss of function mutations/deletions in the PBX homeobox 1 gene (PBX1), a gene known to have a crucial role in kidney development. In contrast, the frequency of SOX17 and DSTYK variants recently reported as pathogenic in CAKUT did not indicate causality. These findings suggest that PBX1 is involved in monogenic CAKUT in humans and call into question the role of some gene variants recently reported as pathogenic in CAKUT. Targeted exome sequencing also proved to be an efficient and cost-effective strategy to identify pathogenic mutations and deletions in known CAKUT genes.

PBX1 haploinsufficiency leads to syndromic congenital anomalies of the kidney and urinary tract (CAKUT) in humans

BACKGROUND

Congenital anomalies of the kidney and urinary tract (CAKUT) represent a significant healthcare burden since it is the primary cause of chronic kidney in children. CNVs represent a recurrent molecular cause of CAKUT but the culprit gene remains often elusive. Our study aimed to define the gene responsible for CAKUT in patients with an 1q23.3q24.1 microdeletion.

METHODS

We describe eight patients presenting with CAKUT carrying an 1q23.3q24.1 microdeletion as identified by chromosomal microarray analysis (CMA). Clinical features were collected, especially the renal and urinary tract phenotype, and extrarenal features. We characterised PBX1 expression and localisation in fetal and adult kidneys using quantitative RT-PCR and immunohistochemistry.

RESULTS

We defined a 276-kb minimal common region (MCR) that only overlaps with the PBX1 gene. All eight patients presented with syndromic CAKUT. CAKUT were mostly bilateral renal hypoplasia (75%). The most frequent extrarenal symptoms were developmental delay and ear malformations. We demonstrate that PBX1 is strongly expressed in fetal kidneys and brain and expression levels decreased in adult samples. In control fetal kidneys, PBX1 was localised in nuclei of medullary, interstitial and mesenchymal cells, whereas it was present in endothelial cells in adult kidneys.

CONCLUSIONS

Our results indicate that PBX1 haploinsufficiency leads to syndromic CAKUT as supported by the Pbx1-null mice model. Correct PBX1 dosage appears to be critical for normal nephrogenesis and seems important for brain development in humans. CMA should be recommended in cases of fetal renal anomalies to improve genetic counselling and pregnancy management.

Genetics of Congenital Anomalies of the Kidney and Urinary Tract: The Current State of Play

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.

Hand2 inhibits kidney specification while promoting vein formation within the posterior mesoderm

Proper organogenesis depends upon defining the precise dimensions of organ progenitor territories. Kidney progenitors originate within the intermediate mesoderm (IM), but the pathways that set the boundaries of the IM are poorly understood. Here, we show that the bHLH transcription factor Hand2 limits the size of the embryonic kidney by restricting IM dimensions. The IM is expanded in zebrafish hand2 mutants and is diminished when hand2 is overexpressed. Within the posterior mesoderm, hand2 is expressed laterally adjacent to the IM. Venous progenitors arise between these two territories, and hand2 promotes venous development while inhibiting IM formation at this interface. Furthermore, hand2 and the co-expressed zinc-finger transcription factor osr1 have functionally antagonistic influences on kidney development. Together, our data suggest that hand2 functions in opposition to osr1 to balance the formation of kidney and vein progenitors by regulating cell fate decisions at the lateral boundary of the IM.

DOI:http://dx.doi.org/10.7554/eLife.19941.001

The human body is made up of many different types of cells, yet they are all descended from one single fertilized egg cell. The process by which cells specialize into different types is complex and has many stages. At each step of the process, the selection of cell types that a cell can eventually become is increasingly restricted. The entire system is controlled by switching different genes on and off in different groups of cells. Balancing the activity of these genes ensures that enough cells of each type are made in order to build a complete and healthy body. Upsetting this balance can result in organs that are too large, too small or even missing altogether.

The cells that form the kidneys and bladder originate within a tissue called the intermediate mesoderm. Controlling the size of this tissue is an important part of building working kidneys. Perens et al. studied how genes control the size of the intermediate mesoderm of zebrafish embryos, which is very similar to the intermediate mesoderm of humans. The experiments revealed that a gene called hand2, which is switched on in cells next to the intermediate mesoderm, restricts the size of this tissue in order to determine the proper size of the kidney. Switching off the hand2 gene resulted in zebrafish with abnormally large kidneys. Loss of hand2 also led to the loss of a different type of cell that forms veins. These findings suggest that cells with an active hand2 gene are unable to become intermediate mesoderm cells and instead go on to become part of the veins.

These experiments also demonstrated that a gene called osr1 works in opposition to hand2 to determine the right number of cells that are needed to build the kidneys. Further work will reveal how hand2 prevents cells from joining the intermediate mesoderm and how its role is balanced by the activity of osr1. Understanding how the kidneys form could eventually help to diagnose or treat several genetic diseases and may make it possible to grow replacement kidneys from unspecialized cells.

DOI:http://dx.doi.org/10.7554/eLife.19941.002

Functional and structural abnormalities of the kidney and urinary tract in severely malnourished children - A hospital based study

Objectives:

The association of malnutrition and systemic diseases like chronic kidney disease (CKD) is well known. Various urinary tract abnormalities may be associated with malnutrition. So objective of current study was to determine the frequency of functional and structural urinary tract abnormalities in severely malnourished children admitted in Nutritional Rehabilitation Unit (NRU) of a tertiary care facility, Karachi.

Methods:

This descriptive cases series of 78 children was conducted in NRU from October 2014 - March 2015. All newly admitted children aged 2-60 months, diagnosed as Severe Acute Malnutrition (SAM) were studied and children with known kidney and urinary tract disorders were excluded. Detailed history, examination and investigations like serum creatinine, ultrasound kidney and urinary tract in addition to routine tests for SAM, were done. A proforma was used to collect demographic data, clinical history, physical findings, and radio-imaging and biochemical investigations. Glomerular filtration rate (GFR) was calculated using Schwartz equation. Data was analyzed using descriptive statistics.

Results:

Among 78 children, male to female ratio was equal. Mean age was 18±15.53 months and majority (79.48%) of children were below 24 months. Majority (82%) of children with SAM had marasmus whereas 18% had edematous malnutrition. Out of 78, 57 (73%) children had either functional (80.7%) and or structural (19.3%) abnormalities whereas 21(36.84%) had normal functional and structural status. Most common functional abnormality was subnormal GFR (<90ml/min/1.73 m²) found in all 46 children. Functional abnormities were more common in children below 24 months. Other functional disorders were Bartter syndrome, renal tubular acidosis and urinary tract infection (UTI) found in two cases each. Common structural abnormalities were echogenic kidneys (n=4, 36%), hydronephrosis (n=3, 27%), hypoplastic kidneys (n=3, 27%) and calculi (n=1, 9%). Subnormal GFR was also found in all cases with structural abnormalities. UTI was observed exclusively in two children among 11 with structural abnormalities.

Conclusion:

A high frequency of functional abnormalities and noticeable proportion of structural abnormalities of urinary tract were detected in children with SAM. Current finding suggest that multicenter study at national level may be undertaken to generate better data about prevalence of renal diseases in SAM.

Maternal risk factors involved in specific congenital anomalies of the kidney and urinary tract: A case-control study

BACKGROUND

Congenital anomalies of the kidney and urinary tract (CAKUT) comprise a heterogeneous group of birth defects with a variety of genetic and nongenetic factors suspected of involvement in the etiology. However, little is known about risk factors in specific CAKUT phenotypes. Therefore, we studied potential maternal risk factors in individual phenotypes within the CAKUT spectrum.

METHODS

Questionnaire data were collected from parents of 562 children with CAKUT and 2139 healthy controls within the AGORA data- and biobank. Potential maternal risk factors investigated included folic acid use, overweight and obesity, smoking, alcohol consumption, subfertility, and diabetes mellitus. We performed logistic regression analyses to assess associations between these potential risk factors and CAKUT phenotypes.

RESULTS

Increased risks of CAKUT were observed for folic acid use and maternal obesity, while fertility treatment by in vitro fertilization or intrauterine insemination and diabetes diagnosed during pregnancy also seem to be associated with CAKUT. Use of multivitamins reduced the risk (odds ratio [OR], 0.5; 95% confidence interval [CI], 0.2-1.0) as opposed to use of folic acid supplements only (OR, 1.3; 95% CI, 1.0-1.8). Folic acid use was associated with duplex collecting systems (OR, 1.8; 95% CI, 1.0-3.4) and vesicoureteral reflux (OR, 1.8; 95% CI, 1.1-2.9) in particular. A relatively strong association was observed between diabetes during pregnancy and posterior urethral valves (OR, 2.6; 95% CI, 1.1-5.9).

CONCLUSION

Use of folic acid only seems to be counterproductive for prevention of CAKUT, in contrast to multivitamin use. Furthermore, we observed differences in risk factor patterns among CAKUT phenotypes, which stress the importance of separate analyses for each phenotype. Birth Defects Research (Part A) 106:596-603, 2016. © 2016 Wiley Periodicals, Inc.

Pattern of clinical presentation of congenital anomalies of the kidney and urinary tract among infants and children

AIM

Congenital anomalies of the kidneys and urinary tract (CAKUT) comprise various entities of structural malformations that result from defects in morphogenesis of the kidney and/or urinary tract. These anomalies are the most commonly diagnosed malformations in the prenatal period and constitute the leading cause of end-+stage renal disease (ESRD) in children, worldwide. This prospective study was performed to report the patterns of clinical presentation and diagnosis of infants and children with such malformations.

METHODS

Patients with suggestive features of CAKUT, presenting to Cairo University Children Hospital over one year duration were investigated and categorized based on underlying renal structural/functional malformation and associated extra-renal anomalies.

RESULTS

One hundred and seven CAKUT children were enrolled in the study. Familial clustering was identified in 14% of the cohort and syndromic CAKUT accounted for 31.8% of cases. Different anomaly entities have been identified; posterior urethral valves (PUV) being the commonest detected abnormality (36.4%). Of note, 9.3% of cohort patients had ESRD at presentation, of which 60% had PUV as their primary renal disease. Obstructive cases were noted to present significantly earlier and attain advanced CKD stages rather than non-obstructive ones.

CONCLUSION

CAKUT is a clinically heterogeneous group of diseases with diverse clinical phenotypes. More efforts should be aimed at improving antenatal detection as well as classification with comprehensive reference to the clinical, genetic and molecular features of the diseases. The high frequency of familial and syndromic CAKUT among studied patients is seemingly a convincing reason to pursue the underlying genetic defect in future studies.

Congenital anomalies of the kidney and urinary tract genetics in mice and men

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.

Developmental Genetics and Congenital Anomalies of the Kidney and Urinary Tract

Congenital anomalies of the kidney and urinary tract (CAKUT) are common birth defects and the leading cause of end-stage renal disease in children. There is a wide spectrum of renal abnormalities, from mild hydronephrosis to more severe cases, such as bilateral renal dysplasia. The etiology of the majority of cases of CAKUT remains unknown, but there is increasing evidence that genomic imbalance contributes to the pathogenesis of CAKUT. Advances in human and mouse genetics have contributed to increased understanding of the pathophysiology of CAKUT. Mutations in genes involved in both transcription factors and signal transduction pathways involved in renal development are associated with CAKUT. Large cohort studies suggest that copy number variants, genomic, or de novo mutations may explain up to one-third of all cases of CAKUT. One of the major challenges to the use of genetic information in the clinical setting remains the lack of strict genotype-phenotype correlation. However, identifying genetic causes of CAKUT may lead to improved diagnosis of extrarenal complications. With the advent of decreasing costs for whole genome and exome sequencing, future studies focused on genotype-phenotype correlations, gene modifiers, and animal models of gene mutations will be needed to translate genetic advances into improved clinical care.

Genetic, environmental, and epigenetic factors involved in CAKUT

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.

Copy-number variation associated with congenital anomalies of the kidney and urinary tract

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.

A predictive model of chronic kidney disease in patients with congenital anomalies of the kidney and urinary tract

BACKGROUND

The antenatal detection of congenital anomalies of the kidney and urinary tract (CAKUT) has permitted early management of these conditions. The aim of this study was to identify predictive factors associated with chronic kidney disease (CKD) in CAKUT. We also propose a risk score of CKD.

METHODS

In this cohort study, 822 patients with prenatally detected CAKUT were followed up for a median time of 43 months. The primary outcome was CKD stage III or higher. A predictive model was developed using the Cox proportional hazards model and evaluated by using c statistics.

RESULTS

Chronic kidney disease occurred in 49 of the 822 (6 %) children with prenatally detected CAKUT. The most accurate model included bilateral hydronephrosis, oligohydramnios, estimated glomerular filtration rate and postnatal diagnosis. The accuracy of the score was 0.95 [95 % confidence interval (CI) 0.89-0.99] and 0.92 (95 % CI 0.86-0.95) after a follow-up of 2 and 10 years, respectively. Based on survival curves, we estimated that at 10 years of age, the probability of survival without CKD stage III was approximately 98 and 58 % for the patients assigned to the low-risk and high-risk groups, respectively (p < 0.001).

CONCLUSIONS

Our predictive model of CKD may contribute to an early identification of a subgroup of patients at high risk for renal impairment. It should be pointed out, however, that this model requires external validation in a different cohort.

Next-generation sequencing for research and diagnostics in kidney disease

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.

Single-gene causes of congenital anomalies of the kidney and urinary tract (CAKUT) in humans

Congenital anomalies of the kidney and urinary tract (CAKUT) cover a wide range of structural malformations that result from defects in the morphogenesis of the kidney and/or urinary tract. These anomalies account for about 40-50 % of children with chronic kidney disease worldwide. Knowledge from genetically modified mouse models suggests that single gene mutations in renal developmental genes may lead to CAKUT in humans. However, until recently, only a handful of CAKUT-causing genes were reported, most of them in familial syndromic cases. Recent findings suggest that CAKUT may arise from mutations in a multitude of different single gene causes. We focus here on single-gene causes of CAKUT and their developmental origin. Currently, more than 20 monogenic CAKUT-causing genes have been identified. High-throughput sequencing techniques make it likely that additional CAKUT-causing genes will be identified in the near future.

Mutations in 12 known dominant disease-causing genes clarify many congenital anomalies of the kidney and urinary tract

Congenital anomalies of the kidney and urinary tract (CAKUT) account for approximately half of children with chronic kidney disease. CAKUT can be caused by monogenic mutations, however, data are lacking on their frequency. Genetic diagnosis has been hampered by genetic heterogeneity and lack of genotype-phenotype correlation. To determine the percentage of cases with CAKUT that can be explained by mutations in known CAKUT genes, we analyzed the coding exons of the 17 known dominant CAKUT-causing genes in a cohort of 749 individuals from 650 families with CAKUT. The most common phenotypes in this CAKUT cohort were 288 with vesicoureteral reflux, 120 with renal hypodysplasia and 90 with unilateral renal agenesis. We identified 37 different heterozygous mutations (33 novel) in 12 of the 17 known genes in 47 patients from 41 of the 650 families (6.3%). These mutations include (number of families): BMP7 (1), CDC5L (1), CHD1L (5), EYA1 (3), GATA3 (2), HNF1B (6), PAX2 (5), RET (3), ROBO2 (4), SALL1 (9), SIX2 (1), and SIX5 (1). Furthermore, several mutations previously reported to be disease-causing are most likely benign variants. Thus, in a large cohort over 6% of families with isolated CAKUT are caused by a mutation in 12 of 17 dominant CAKUT genes. Our report represents one of the most in-depth diagnostic studies of monogenic causes of isolated CAKUT in children.