The genetic basis of congenital anomalies of the kidney and urinary tract

Kidney Transplantation in Congenital Abnormalities of Kidney and Urinary Tract (CAKUT)

Congenital anomalies of the kidney and urinary tract (CAKUT) are a common cause of chronic kidney disease in children. Most patients will reach end-stage renal function and dialysis or transplantation in childhood or early adulthood. Patients with CAKUT deserve a careful evaluation before a kidney transplant; detailed imaging and functional studies are necessary, particularly in the presence of lower urinary tract abnormalities, and surgical procedures are advisable in selected cases. A higher incidence of complications has been reported after a kidney transplant in CAKUT, mainly urinary tract infections. However, in the long term, the prognosis seems to be comparable to other kidney diseases. A large number of reports are available in the literature on medical and surgical management of patients with CAKUT before, during, and after a kidney transplant; almost all recommendations of surgical procedures before a kidney transplantation are based on retrospective not controlled studies or personal opinions; prospective controlled studies are needed. In this narrative, nonsystematic review, we report the results of recently published selected studies and underline questions that should be addressed in future guidelines.

Extrarenal Clinical Features are Reported for Most Genes Implicated in Genetic Kidney Disease

Introduction

Genetic kidney disease is often suspected based on a family history of the disease or the presence of extrarenal features. This study examined how often a positive family history or syndromic features are found.

Methods

A total of 255 genes from the Genomics England "green" lists for congenital anomalies of the kidney and urinary tract (CAKUT) (n = 57), ciliopathies and cystic kidney diseases (n = 90), hematuria (n = 5), renal proteinuria (n = 55), and renal tubulopathies (n = 48) were examined for mode of inheritance and, in the Online Mendelian Inheritance in Man (OMIM), for reported clinical features in different systems (neurological, cardiac, etc.) that would be obvious on a history or physical examination.

Results

Autosomal recessive (AR) inheritance was recorded for 148 of the 248 genes (60%) with an OMIM entry. Extrarenal features were associated with 221 genes (89%), including those causing hematuria (5, 100%), renal ciliopathies (86, 97%), CAKUT (52, 91%), renal tubulopathies (41, 85%), and proteinuric renal diseases (37, 76%).The median number of affected systems was 4 (range: 0-10). More extrarenal features were associated with CAKUT (4, 0-10) and the ciliopathies (5, 0-9) than with hematuria (2, 2-5), proteinuria (3, 0-7), and the tubulopathies (3, 0-7) (P < 0.00001). The most commonly-affected systems were growth and musculoskeletal (164, 66%), neurological (147, 59%), and ocular (133, 54%).

Conclusion

Extrarenal associations have been reported for most genes affected in genetic kidney disease, and are more common with pediatric-onset conditions with recessive inheritance. However, information is limited for how often extrarenal features are found in any individual.

Ureter development and associated congenital anomalies

Malformations of the ureter are among the most common birth defects in humans. Although some of these anomalies are asymptomatic, others are clinically relevant, causing perinatal lethality or progressing to kidney failure in childhood. The genetic causes and developmental aetiology of ureteral anomalies are difficult to study in humans; however, embryological and genetic analyses in the mouse have provided insights into the complex developmental programmes that govern ureter formation from simple tissue primordia, and the pathological consequences that result from disruption of these programmes. Abnormalities in the formation of the nephric duct and ureteric bud lead to changes in the number of ureters (and kidneys), whereas the formation of ectopic ureteric buds, failure of the nephric duct to target the cloaca or failure of the distal ureter to mature underlie vesicoureteral reflux, ureter ectopia, ureterocoele and subsequent hydroureter. Alterations in ureter specification, early growth or cyto-differentiation programmes have now also been associated with various forms of perinatal hydroureter and hydronephrosis as a consequence of functional obstruction. The characterization of cellular processes and molecular drivers of ureterogenesis in the mouse may not only aid understanding of the aetiology of human ureteral anomalies, improve prognostication and benefit the development of therapeutic strategies, but may also prove important for efforts to generate a bioartificial organ.

Extrarenal manifestations in inherited kidney diseases

Monogenic kidney diseases result from an abundance of potential genes carrying pathogenic variants. These conditions are primarily recognized for manifesting as kidney disorders, defined as an impairment of the structure and/or function of the kidneys. However, the impact of these genetic disorders extends far beyond the kidneys, giving rise to a diverse spectrum of extrarenal manifestations. These manifestations can affect any organ system throughout the body, leading to a complex clinical presentation that demands a comprehensive understanding and interdisciplinary management of affected persons. The intricate interplay between genetic variants, molecular pathways, and systemic interactions underscores the importance of exploring the extrarenal aspects of inherited kidney diseases. This exploration not only deepens our comprehension of the diseases themselves but also opens avenues for more holistic diagnostics, treatment strategies, and improved interdisciplinary patient care. This article delves into the intricate realm of extrarenal manifestations in inherited kidney diseases, shedding light on the far-reaching effects that these genetic conditions can exert beyond the confines of the kidney system.

Heterozygous variants in the teashirt zinc finger homeobox 3 (TSHZ3) gene in human congenital anomalies of the kidney and urinary tract

Around 180 genes have been associated with congenital anomalies of the kidney and urinary tract (CAKUT) in mice, and represent promising novel candidate genes for human CAKUT. In whole-exome sequencing data of two siblings with genetically unresolved multicystic dysplastic kidneys (MCDK), prioritizing variants in murine CAKUT-associated genes yielded a rare variant in the teashirt zinc finger homeobox 3 (TSHZ3) gene. Therefore, the role of TSHZ3 in human CAKUT was assessed. Twelve CAKUT patients from 9/301 (3%) families carried five different rare heterozygous TSHZ3 missense variants predicted to be deleterious. CAKUT patients with versus without TSHZ3 variants were more likely to present with hydronephrosis, hydroureter, ureteropelvic junction obstruction, MCDK, and with genital anomalies, developmental delay, overlapping with the previously described phenotypes in Tshz3-mutant mice and patients with heterozygous 19q12-q13.11 deletions encompassing the TSHZ3 locus. Comparable with Tshz3-mutant mice, the smooth muscle layer was disorganized in the renal pelvis and thinner in the proximal ureter of the nephrectomy specimen of a TSHZ3 variant carrier compared to controls. TSHZ3 was expressed in the human fetal kidney, and strongly at embryonic day 11.5-14.5 in mesenchymal compartments of the murine ureter, kidney, and bladder. TSHZ3 variants in a 5' region were more frequent in CAKUT patients than in gnomAD samples (p < 0.001). Mutant TSHZ3 harboring N-terminal variants showed significantly altered SOX9 and/or myocardin binding, possibly adversely affecting smooth muscle differentiation. Our results provide evidence that heterozygous TSHZ3 variants are associated with human CAKUT, particularly MCDK, hydronephrosis, and hydroureter, and, inconsistently, with specific extrarenal features, including genital anomalies.

Reviewing the complexities of horseshoe kidney: insights into embryogenesis and surgical considerations

Horseshoe kidney (HSK) is a common renal malformation with unique and complex characteristics. A systematic literature search was conducted using PubMed and ScienceDirect databases. Several theories have been proposed regarding HSK formation, such as the close apposition of the kidneys during ascent through an arterial fork, lateral flexion of the trunk, and caudal embryonic rotation. Emerging evidence from animal models implicates notochord signaling and the sonic hedgehog pathway in HSK formation. The isthmus, a defining feature of HSK, is hypothesized to arise from ectopic mesenchymal tissue. The surgical anatomy of HSK is complex, given the variability in location, orientation, and blood supply. Both arterial and venous anatomy exhibit significant variability, raising questions about whether anomalous blood supply is a cause or a consequence of abnormal renal position. The isthmus usually contains functional renal parenchyma and fusion between the kidneys, primarily at the lower pole. While it is often stated that the inferior mesenteric artery is "held back" at the L3 level, this anatomical configuration is present in only 40% of cases. The review highlights the need for further research and provides a comprehensive overview of HSK knowledge.

Swiss Consensus on Prenatal and Early Postnatal Urinary Tract Dilation: Practical Approach and When to Refer

Urinary tract dilations (UTDs) are the most frequent prenatal renal anomaly. The spectrum of etiologies causing UTD ranges from mild spontaneously resolving obstruction to severe upper and lower urinary tract obstruction or reflux. The early recognition and management of these anomalies allows for improved renal endowment prenatally and ultimately better outcome for the child. The role of the general obstetrician and pediatrician is to recognize potential prenatal and postnatal cases addressed to their practice and to refer patients to specialized pediatric nephrology and urology centers with a sense of the urgency of such a referral. The aim of this paper is to offer clinical recommendations to clinicians regarding the management of neonates and children born with prenatally detected UTD, based on a consensus between Swiss pediatric nephrology centers. The aim is to give suggestions and recommendations based on the currently available literature regarding classifications and definitions of prenatal and postnatal UTD, etiologies, prenatal and postnatal renal function evaluation, investigations, antibiotic prophylaxis, and the need for referral to a pediatric nephrologist and/or urologist. The overarching goal of a systematic approach to UTD is to ultimately optimize kidney health during childhood and improve long-term renal function prognosis.

Kidney development at a glance: metabolic regulation of renal progenitor cells

The aberrant regulation of renal progenitor cells during kidney development leads to congenital kidney anomalies and dysplasia. Recently, significant progress has been made in understanding the metabolic needs of renal progenitor cells during mammalian kidney development, with evidence indicating that multiple metabolic pathways play essential roles in determining the cell fates of distinct renal progenitor populations. This review summarizes recent findings and explores the prospects of integrating this novel information into current diagnostic and treatment strategies for renal diseases. Reciprocal interactions between various embryonic kidney progenitor populations establish the foundation for normal kidney organogenesis, with the three principal kidney structures-the nephrons, the collecting duct network, and the stroma-being generated by nephron progenitor cells, ureteric bud/collecting duct progenitor cells, and interstitial progenitor cells. While energy metabolism is well recognized for its importance in organism development, physiological function regulation, and responses to environmental stimuli, research has primarily focused on nephron progenitor metabolism, highlighting its role in maintaining self-renewal. In contrast, studies on the metabolic requirements of ureteric bud/collecting duct and stromal progenitors remain limited. Given the importance of interactions between progenitor populations during kidney development, further research into the metabolic regulation of self-renewal and differentiation in ureteric bud and stromal progenitor cells will be critical.

Evaluation of normal and abnormal fetal renal microvascular flow characteristics of three-dimensional MV-flow imaging

OBJECTIVE

To evaluate the applicability of three-dimensional MV-Flow imaging for prenatal renal diagnosis.

METHOD

This prospective study included normal and abnormal kidneys ranging from 20 to 40 weeks gestation between April and July 2023. All participants underwent conventional ultrasound and three-dimensional MV-Flow examinations. The renal volume and microvascular indexes were obtained by the three-dimensional MV-Flow.

RESULTS

A total of 207 normal kidneys from 154 fetuses and 67 abnormal kidneys from 53 fetuses, with conditions such as renal cystic diseases, hyperechoic kidney, large kidney, and small kidney were included. Normal renal volume, vascularization index, and vascularization-flow index increased slightly with gestational age (p < 0.001). No correlation was found between gestational age and flow index (p = 0.604). The microvascular indexes decreased in the fetal renal cystic disease group while renal volume increased. Higher vascularization index and vascularization-flow index were observed in the hyperechoic kidney group. The microvascular indexes of the large and small kidney groups were within the reference range for normal kidneys. Only the autosomal dominant polycystic kidney disease exhibited an absence of distinct subcapsular microvascular flow in the MV-Flow image, referred to as the "thick shell sign".

CONCLUSION

Fetal renal volume, vascularization index, and vascularization-flow index increase with gestational age. Quantitative evaluation using 3D MV-Flow imaging reveals varying renal volume and microvascular perfusion characteristics among different fetal renal abnormalities.

Maternal and fetal risk factors for congenital anomalies of the kidney and urinary tract: a birth cohort study in urban China

BACKGROUND

Congenital anomalies of the kidney and urinary tract (CAKUT) are among the most common causes of kidney diseases in children. Previous studies on CAKUT etiologies have been predominantly focused on non-modifiable genetic risk factors. The existing nongenetic studies are limited by lack of comprehensive investigation of potentially modifiable risk factors and the inability to distinguish among various phenotypes of CAKUT. Therefore, this study aimed to comprehensively evaluate both maternal and fetal risk factors of CAKUT, sorted by disease phenotype.

METHODS

A prospective birth cohort study was conducted among 10,179 women who delivered a singleton live newborn in Lanzhou, China, between 2010 and 2012. Face-to-face interviews were conducted among the participants within 1-3 days after delivery using standard questionnaires to collect information on maternal demographics and characteristics. All newborns underwent postnatal renal ultrasonographic screening during their routine 1-month checkup. Clinical data, including birth outcomes and maternal complications, were confirmed by reviewing their medical records. Maternal and fetal risk factors were compared in children with and without CAKUT. Multivariable logistic regression analysis was performed to identify independent risk factors of CAKUT and their phenotypes, respectively.

RESULTS

A total of 489 (4.8%) cases of CAKUT were identified. Logistic regression revealed that maternal overweight (pre-pregnancy), gestational diabetes, preterm birth, and low birth weight were independent risk factors for CAKUT. Maternal overweight increased the risk of vesicoureteral reflux (VUR, odds ratio (OR) = 1.441, 95% confidence interval (CI) 1.010-2.057) and posterior urethral valves (PUV, OR = 1.868, 95% CI 1.074-3.249). Gestational diabetes increased the risk of ureteropelvic junction obstruction (UPJO, OR = 1.269; 95% CI 1.044-1.543) and posterior urethral valves (OR = 1.794; 95% CI 1.302-2.474). Preterm birth increased the risk of ureteropelvic junction obstruction (OR = 1.056; 95% CI 1.004-1.111).

CONCLUSIONS

Our study identified various risk factors associated with different CAKUT phenotypes, stressing the importance of separate analyses for each phenotype. Our findings may provide helpful guidance on developing targeted and effective CAKUT prevention programs in the future.

Risks of Renal Anomalies and Urinary Tract Infections in Neonates With Single Umbilical Artery

Background Our study aims to evaluate the characteristics of congenital anomalies of kidneys and urinary tracts (CAKUT) and urinary tract infection (UTI) in babies with single umbilical artery (SUA) and to identify factors associated with these outcomes. Methods We performed a 15-year retrospective analysis on babies who were born ≥34 weeks with SUA between 2006 and 2020. Relevant clinical information on obstetrics and neonatal examinations, UTIs, and imaging of the urinary systems was evaluated. Results The frequency of SUA in newborns was 3.28 per 1,000 deliveries. The majority (271/291; 93.1%) of patients had kidney ultrasound, and 19 (7.0%) had CAKUT. Hydronephrosis (n = 11, 57.9%) was the commonest CAKUT, followed by unilateral kidney agenesis (n = 3, 15.8%), horseshoe kidney (n = 2, 10.5%), and right low-lying kidney (n = 2, 10.5%). Most significant CAKUT (including solitary kidney and urinary tract obstruction) could be detected during the antenatal period. Congenital heart defect (OR 4.93, 95% CI 1.59-15.34), limbs (OR 9.77, 95% CI 1.53-62.44), and sacral abnormalities (OR 5.06, 95% CI 1.25-20.55) were associated with CAKUT. Six (2.1%) developed UTIs during the study period, with the majority below two years old. The presence of CAKUT was associated with the development of UTI after adjustment (adjusted HR 10.28, 95% CI 1.86-56.83). Conclusions The overall prevalence of CAKUT was 7.0% in patients with SUA, and the majority of significant CAKUT was identified during the antenatal period. Congenital heart defects, limbs, and sacral abnormalities were associated with CAKUT. UTI occurred in 2.1% of patients.

Practical Approach to Congenital Anomalies of the Kidneys: Focus on Anomalies With Insufficient or Abnormal Nephron Development: Renal Dysplasia, Renal Hypoplasia, and Renal Tubular Dysgenesis

Congenital anomalies of the kidney and urinary tract (CAKUT) accounts for up to 30% of antenatal congenital anomalies and is the main cause of kidney failure in children worldwide. This review focuses on practical approaches to CAKUT, particularly those with insufficient or abnormal nephron development, such as renal dysplasia, renal hypoplasia, and renal tubular dysgenesis. The review provides insights into the histological features, pathogenesis, mechanisms, etiologies, antenatal and postnatal presentation, management, and prognosis of these anomalies. Differential diagnoses are discussed as several syndromes may include CAKUT as a phenotypic component and renal dysplasia may occur in some ciliopathies, tumor predisposition syndromes, and inborn errors of metabolism. Diagnosis and genetic counseling for CAKUT are challenging, due to the extensive variability in presentation, genetic and phenotypic heterogeneity, and difficulties to assess postnatal lung and renal function on prenatal imaging. The review highlights the importance of perinatal autopsy and pathological findings in surgical specimens to establish the diagnosis and prognosis of CAKUT. The indications and the type of genetic testing are discussed. The aim is to provide essential insights into the practical approaches, diagnostic processes, and genetic considerations offering valuable guidance for pediatric and perinatal pathologists.

Frameshift Mutation in PAX2 Related to Focal Segmental Glomerular Sclerosis: A Case Report and Literature Review

BACKGROUND

Paired box gene 2 (PAX2) heterozygous mutations can cause renal coloboma syndrome, but its role in patients with focal segmental glomerular sclerosis (FSGS) has been rarely reported.

METHODS

Based on the clinical manifestations and renal pathological characteristics of the patient, as well as familial whole exome sequencing, the diagnosis of FSGS related to PAX2 mutation was confirmed. Treatment such as lowering urinary protein and blood pressure was given, and the patient was followed up and observed.

RESULTS

There is a familial heterozygous case presented with chronic kidney disease secondary to FSGS, which was related to PAX2 frameshift mutation due to the deletion of G at the position 76 (c.76delG). To our knowledge, this is the first report of PAX2 c.76delG variant related to adult-onset FSGS.

CONCLUSION

Here, we further expand the phenotypic spectrum of FSGS. Genetic screening especially PAX2 mutation is recommended in patients with adult-onset FSGS of unknown etiology.

SALL4 deletion and kidney and cardiac defects associated with VACTERL association

Congenital anomalies of the kidney and urinary tract (CAKUT) can be a part of the VACTERL association, which represents the non-random combination of the following congenital anomalies: vertebral anomalies, anal anomalies, cardiac anomalies, tracheal-esophageal anomalies, kidney anomalies, and limb anomalies. VACTERL association is generally considered to be a non-genetic condition. Exceptions include a patient with a heterozygous nonsense SALL4 variant and anal stenosis, tetralogy of Fallot, sacro-vertebral fusion, and radial and thumb anomalies. SALL4 encodes a transcription factor that plays a critical role in kidney morphogenesis. Here, we report a patient with VACTERL association and a heterozygous 128-kb deletion spanning SALL4 who presented with renal hypoplasia, radial and atrio-septal defects, and patent ductus arteriosus. The present report of SALL4 deletion, in addition to a previously reported patient with VACTERL association phenotype and SALL4 nonsense mutation, further supports the notion that SALL4 haploinsufficiency can lead to VACTERL association.

Congenital anomalies of the kidney and urinary tract

Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) refer to a range of conditions that affect the kidney and urinary tract. These anomalies can be severe, such as kidney agenesis, or milder, such as vesicoureteral reflux. CAKUT affects over 1% of live births and accounts for 40-50% of cases of chronic kidney failure in children. The pathogenesis of CAKUT is caused by various environmental, genetic, and epigenetic factors that disrupt normal nephrogenesis. Environmental factors that can lead to CAKUT include maternal diabetes, obesity, malnutrition, alcohol consumption, or medications affecting kidneys development. Genetic factors can cause an imbalance in the metanephros and the ureteric bud interaction. Defects in specific genes such as PAX2, TBX18, NRIP1, REX, SIX2, BMP4, and chromosome 17 cause CAKUT. Over 50 genes have been identified as the root cause of this condition, with monogenetic variants causing up to 20% of all cases. CAKUTs can be diagnosed through fetal ultrasonography, but some anomalies may remain undetected. GWASs, Next Generation Sequencing for targeted and whole exome DNA sequencing may provide additional diagnostic methods. This review article highlights some the leading factors that cause CAKUT, which adversely affects kidney development and urinary tract function.

Tips for Testing Adults With Suspected Genetic Kidney Disease

Genetic kidney disease is common but often unrecognized. It accounts for most cystic kidney diseases and tubulopathies, many forms of congenital abnormalities of the kidney and urinary tract (CAKUT), and some glomerulopathies. Genetic kidney disease is typically suspected where the disease usually has a genetic basis or there is another affected family member, a young age at onset, or extrarenal involvement, but there are also many exceptions to these "rules". Genetic testing requires the patient's written informed consent. When a patient declines testing, another later conversation may be worthwhile. Genetic testing not only indicates the diagnosis but also the inheritance pattern, likely at-risk family members, disease in other organs, clinical course, and possibly effective treatments. Sometimes genetic testing does not identify a pathogenic variant even where other evidence is strong. A variant of uncertain significance (VUS) may be reported but should not be used for clinical decision making. It may be reclassified after more information becomes available without necessarily retesting the patient. Patients should be provided with a copy of their genetic test report, the results explained, and at-risk family members offered "cascade" testing. A referral to a clinical geneticist or genetic counselor helps identify affected family members and in providing advice to assist with reproductive decisions.

Risk of birth defects in children of mothers with defects

BACKGROUND

There is evidence that women with congenital anomalies are at risk of having an infant with the same defect. However, the risk of having an infant with a different type of defect is less well described.

AIMS

We evaluated the extent to which offspring of women with congenital anomalies were at risk of having a birth defect, including defects that were similar to or different from their mother's.

METHODS

We analyzed a retrospective cohort of 1,311,532 infants born in Canada between 2006 and 2022. The exposure was a maternal congenital anomaly, and the outcome included birth defects in the newborn. We estimated risk ratios (RR) and confidence intervals (CI) for the association of specific maternal anomalies with the risk of having an infant with a similar or different defect using log-binomial regression models adjusted for patient characteristics.

RESULTS

While mothers with anomalies were at risk of having an infant with the same defect, associations with other types of defects were not as strong. For example, compared with no maternal anomaly, maternal urogenital defects were associated with up to 45 times the risk of having an infant with a similar urogenital defect (RR 45.33, 95 % CI 31.92-64.36), but <2 times the risk of having an infant with orofacial clefts (RR 1.89, 95 % CI 1.07-3.34) and clubfoot (RR 1.36, 95 % CI 1.02-1.81).

CONCLUSION

The findings suggest that maternal congenital anomalies are only weakly associated with occurrence of a different type of defect in offspring.

GEN1 as a risk factor for human congenital anomalies of the kidney and urinary tract

BACKGROUND

Congenital anomalies of the kidney and urinary tract (CAKUT) are prevalent birth defects. Although pathogenic CAKUT genes are known, they are insufficient to reveal the causes for all patients. Our previous studies indicated GEN1 as a pathogenic gene of CAKUT in mice, and this study further investigated the correlation between GEN1 and human CAKUT.

METHODS

In this study, DNA from 910 individuals with CAKUT was collected; 26 GEN1 rare variants were identified, and two GEN1 (missense) variants in a non-CAKUT group were found. Mainly due to the stability results of the predicted mutant on the website, in vitro, 10 variants (eight CAKUT, two non-CAKUT) were selected to verify mutant protein stability. In addition, mainly based on the division of the mutation site located in the functional region of the GEN1 protein, 8 variants (six CAKUT, two non-CAKUT) were selected to verify enzymatic hydrolysis, and the splice variant GEN1 (c.1071 + 3(IVS10) A > G) was selected to verify shear ability. Based on the results of in vitro experiments and higher frequency, three sites with the most significant functional change were selected to build mouse models.

RESULTS

Protein stability changed in six variants in the CAKUT group. Based on electrophoretic mobility shift assay of eight variants (six CAKUT, two non-CAKUT), the enzymatic hydrolysis and DNA-binding abilities of mutant proteins were impaired in the CAKUT group. The most serious functional damage was observed in the Gen1 variant that produced a truncated protein. A mini-gene splicing assay showed that the variant GEN1 (c.1071 + 3(IVS10) A > G) in the CAKUT group significantly affected splicing function. An abnormal exon10 was detected in the mini-gene splicing assay. Point-mutant mouse strains were constructed (Gen1: c.1068 + 3 A > G, p.R400X, and p.T105R) based on the variant frequency in the CAKUT group and functional impairment in vitro study and CAKUT phenotypes were replicated in each.

CONCLUSION

Overall, our findings indicated GEN1 as a risk factor for human CAKUT.

(Zebra)fishing for nephrogenesis genes

Kidney disease is a devastating condition affecting millions of people worldwide, where over 100,000 patients in the United States alone remain waiting for a lifesaving organ transplant. Concomitant with a surge in personalized medicine, single-gene mutations, and polygenic risk alleles have been brought to the forefront as core causes of a spectrum of renal disorders. With the increasing prevalence of kidney disease, it is imperative to make substantial strides in the field of kidney genetics. Nephrons, the core functional units of the kidney, are epithelial tubules that act as gatekeepers of body homeostasis by absorbing and secreting ions, water, and small molecules to filter the blood. Each nephron contains a series of proximal and distal segments with explicit metabolic functions. The embryonic zebrafish provides an ideal platform to systematically dissect the genetic cues governing kidney development. Here, we review the use of zebrafish to discover nephrogenesis genes.

Genetics of kidney disorders in Phelan-McDermid syndrome: evidence from 357 registry participants

BACKGROUND

Phelan-McDermid syndrome (PMS) is a rare genetic disorder caused by SHANK3 pathogenic variants or chromosomal rearrangements affecting the chromosome 22q13 region. Previous research found that kidney disorders, primarily congenital anomalies of the kidney and urinary tract, are common in people with PMS, yet research into candidate genes has been hampered by small study sizes and lack of attention to these problems.

METHODS

We used a cohort of 357 people from the Phelan-McDermid Syndrome Foundation International Registry to investigate the prevalence of kidney disorders in PMS using a cross-sectional design and to identify 22q13 genes contributing to these disorders.

RESULTS

Kidney disorders reported included vesicoureteral reflux (n = 37), hydronephrosis (n = 36), dysplastic kidneys (n = 19), increased kidney size (n = 19), polycystic kidneys (15 cases), and kidney stones (n = 4). Out of 315 subjects with a 22q13 deletion, 101 (32%) had at least one kidney disorder, while only one out of 42 (2%) individuals with a SHANK3 pathogenic variant had a kidney disorder (increased kidney size). We identified two genomic regions that were significantly associated with having a kidney disorder with the peak associations observed near positions approximately 5 Mb and 400 Kb from the telomere.

CONCLUSIONS

The candidate genes for kidney disorders include FBLN1, WNT7B, UPK3A, CELSR1, and PLXNB2. This study demonstrates the utility of patient registries for uncovering genetic contributions to rare diseases. Future work should focus on functional studies for these genes to assess their potential pathogenic contribution to the different subsets of kidney disorders.

Ocular manifestations of congenital anomalies of the kidney and urinary tract (CAKUT)

Congenital anomalies of the kidney and urinary tract (CAKUT) are among the most common birth defects worldwide and a major cause of kidney failure in children. Extra-renal manifestations are also common. This study reviewed diseases associated with the Genomics England CAKUT-associated gene panel for ocular anomalies. In addition, each gene was examined for expression in the human retina and an ocular phenotype in mouse models using the Human Protein Atlas and Mouse Genome Informatics databases, respectively. Thirty-four (54%) of the 63 CAKUT-associated genes (55 'green' and 8 'amber') had a reported ocular phenotype. Five of the 6 most common CAKUT-associated genes (PAX2, EYA1, SALL1, GATA3, PBX1) that represent 30% of all diagnoses had ocular features. The ocular abnormalities found with most CAKUT-associated genes and with five of the six commonest were coloboma, microphthalmia, optic disc anomalies, refraction errors (astigmatism, myopia, and hypermetropia), and cataract. Seven of the CAKUT-associated genes studied (11%) had no reported ocular features but were expressed in the human retina or had an ocular phenotype in a mouse model, which suggested further possibly-unrecognised abnormalities. About one third of CAKUT-associated genes (18, 29%) had no ocular associations and were not expressed in the retina, and the corresponding mouse models had no ocular phenotype. Ocular abnormalities in individuals with CAKUT suggest a genetic basis for the disease and sometimes indicate the affected gene. Individuals with CAKUT often have ocular abnormalities and may require an ophthalmic review, monitoring, and treatment to preserve vision.

Diagnostic Yield and Benefits of Whole Exome Sequencing in CAKUT Patients Diagnosed in the First Thousand Days of Life

Introduction

Congenital anomalies of the kidney and urinary tract (CAKUT) are the predominant cause of chronic kidney disease (CKD) and the need for kidney replacement therapy (KRT) in children. Although more than 60 genes are known to cause CAKUT if mutated, genetic etiology is detected, on average, in only 16% of unselected CAKUT cases, making genetic testing unproductive.

Methods

Whole exome sequencing (WES) was performed in 100 patients with CAKUT diagnosed in the first 1000 days of life with CKD stages 1 to 5D/T. Variants in 58 established CAKUT-associated genes were extracted, classified according to the American College of Medical Genetics and Genomics guidelines, and their translational value was assessed.

Results

In 25% of these mostly sporadic patients with CAKUT, a rare likely pathogenic or pathogenic variant was identified in 1 or 2 of 15 CAKUT-associated genes, including GATA3, HNF1B, LIFR, PAX2, SALL1, and TBC1D1. Of the 27 variants detected, 52% were loss-of-function and 18.5% de novo variants. The diagnostic yield was significantly higher in patients requiring KRT before 3 years of age (43%, odds ratio 2.95) and in patients with extrarenal features (41%, odds ratio 3.5) compared with patients lacking these criteria. Considering that all affected genes were previously associated with extrarenal complications, including treatable conditions, such as diabetes, hyperuricemia, hypomagnesemia, and hypoparathyroidism, the genetic diagnosis allowed preventive measures and/or early treatment in 25% of patients.

Conclusion

WES offers significant advantages for the diagnosis and management of patients with CAKUT diagnosed before 3 years of age, especially in patients who require KRT or have extrarenal anomalies.

The genetics and pathogenesis of CAKUT

Congenital anomalies of the kidney and urinary tract (CAKUT) comprise a large variety of malformations that arise from defective kidney or urinary tract development and frequently lead to kidney failure. The clinical spectrum ranges from severe malformations, such as renal agenesis, to potentially milder manifestations, such as vesicoureteral reflux. Almost 50% of cases of chronic kidney disease that manifest within the first three decades of life are caused by CAKUT. Evidence suggests that a large number of CAKUT are genetic in origin. To date, mutations in ~54 genes have been identified as monogenic causes of CAKUT, contributing to 12-20% of the aetiology of the disease. Pathogenic copy number variants have also been shown to cause CAKUT and can be detected in 4-11% of patients. Furthermore, environmental and epigenetic factors can increase the risk of CAKUT. The discovery of novel CAKUT-causing genes is challenging owing to variable expressivity, incomplete penetrance and variable genotype-phenotype correlation. However, such a discovery could ultimately lead to improvements in the accurate molecular genetic diagnosis, assessment of prognosis and multidisciplinary clinical management of patients with CAKUT, potentially including personalized therapeutic approaches.

Congenital Anomalies of the Kidney and Urinary Tract: A Continuum of Care

Congenital anomalies of the kidney and urinary tract (CAKUT) are the leading cause of kidney failure in children and adolescents. CAKUT describes a wide spectrum of structural disorders with a prenatal origin. The etiology of CAKUT is multifactorial, including environmental, nongenetic, and genetic causes that impact kidney development as well as upper and lower urinary tract development. Adult nephrologists who treat patients with CAKUT may be challenged by the underlying diseases they are not familiar with and the accumulation of chronic kidney disease complications in childhood. This article discusses CAKUT etiology and presentation, the course during childhood and adolescence, as well as adult issues in CAKUT patients including CKD complications, urologic interventions, and genetic counseling. A smooth transition of CAKUT patients from pediatric to adult care can be challenging. Semin Nephrol 43:x-xx © 2023 Elsevier Inc. All rights reserved.

Maternal risk factors in offspring with congenital anomalies of the kidney and urinary tract in Asian women

BACKGROUND

Congenital anomalies of the kidney and urinary tract (CAKUT) are the primary cause of pediatric chronic kidney disease. Maternal body mass index (BMI) before pregnancy, pregestational diabetic mellitus (DM), and gestational diabetic mellitus (GDM) are potential modifiable risk factors for CAKUT in offspring.

METHODS

In this case control study, 4619 neonates were enrolled during 2012-2020 from Kaohsiung Veterans General Hospital in Taiwan. Maternal risk factors before and during pregnancy were compared in children with and without CAKUT. The yearly incidence of CAKUT in offspring and maternal overweight were recorded.

RESULTS

In total, 73 (1.6%) cases of CAKUT in offspring were identified. Maternal overweight before pregnancy (BMI ≥ 24 kg/m2) was an independent risk factor for CAKUT in offspring. No associations of pregestational DM and GDM with CAKUT in offspring were observed. The incidence rates of CAKUT and maternal obesity have increased in the past 10 years.

CONCLUSIONS

Maternal obesity before pregnancy is associated with CAKUT in offspring and should be addressed to ensure better outcomes. A higher resolution version of the Graphical abstract is available as Supplementary information.

PAX2 Gene Mutation in Pediatric Renal Disorders-A Narrative Review

The PAX2 gene is a transcription factor that is essential for the development of the urinary system among other transcription factors. The role of PAX2 is highlighted from the seventh week of gestation, when it is involved in development processes and the emergence of nephrons and collecting tubes. Being an important factor in renal development, mutations of this gene can produce severe alterations in the development of the urinary tract, namely congenital anomalies of the kidneys and urinary tract. The first reported cases described with the PAX2 mutation included both renal anomalies and the involvement of other organs, such as the eyes, producing renal coloboma syndrome. Over the years, numerous cases have been reported, including those with only renal and urinary tract anomalies. The aim of this review is to present a summary of pediatric patients described to have mutations in the PAX2 gene to contribute to a better understanding of the genetic mechanism causing anomalies of the kidneys and urinary tract. In this review, we have included only pediatric cases with renal and urinary tract disorders, without the involvement of other organs. From what we know so far from the literature, this is the first review gathering pediatric patients presenting the PAX2 mutation who have been diagnosed exclusively with renal and urinary tract disorders.

Whole Genome Sequencing Revealed Inherited Rare Oligogenic Variants Contributing to Schizophrenia and Major Depressive Disorder in Two Families

Schizophrenia and affective disorder are two major complex mental disorders with high heritability. Evidence shows that rare variants with significant clinical impacts contribute to the genetic liability of these two disorders. Also, rare variants associated with schizophrenia and affective disorders are highly personalized; each patient may carry different variants. We used whole genome sequencing analysis to study the genetic basis of two families with schizophrenia and major depressive disorder. We did not detect de novo, autosomal dominant, or recessive pathogenic or likely pathogenic variants associated with psychiatric disorders in these two families. Nevertheless, we identified multiple rare inherited variants with unknown significance in the probands. In family 1, with singleton schizophrenia, we detected four rare variants in genes implicated in schizophrenia, including p.Arg1627Trp of LAMA2, p.Pro1338Ser of CSMD1, p.Arg691Gly of TLR4, and Arg182X of AGTR2. The p.Arg691Gly of TLR4 was inherited from the father, while the other three were inherited from the mother. In family 2, with two affected sisters diagnosed with major depressive disorder, we detected three rare variants shared by the two sisters in three genes implicated in affective disorders, including p.Ala4551Gly of FAT1, p.Val231Leu of HOMER3, and p.Ile185Met of GPM6B. These three rare variants were assumed to be inherited from their parents. Prompted by these findings, we suggest that these rare inherited variants may interact with each other and lead to psychiatric conditions in these two families. Our observations support the conclusion that inherited rare variants may contribute to the heritability of psychiatric disorders.

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.

Inhibition of MAPK/ERK pathway activation rescues congenital anomalies of the kidney and urinary tract (CAKUT) in Robo2PB/+ Gen1PB/+ mice

Congenital anomalies of the kidney and urinary tract (CAKUT) have been attributed to genetic and environmental factors. However, monogenic and copy number variations cannot sufficiently explain the cause of the majority of CAKUT cases. Multiple genes through various modes of inheritance may lead to CAKUT pathogenesis. We previously showed that Robo2 and Gen1 coregulated the germination of ureteral buds (UB), significantly increasing CAKUT incidence. Furthermore, MAPK/ERK pathway activation is the central mechanism of these two genes. Thus, we explored the effect of the MAPK/ERK inhibitor U0126 in the CAKUT phenotype in Robo2^PB/+Gen1^PB/+ mice. Intraperitoneal injection of U0126 during pregnancy prevented the development of the CAKUT phenotype in Robo2^PB/+Gen1^PB/+ mice. Additionally, a single dose of 30 mg/kg U0126 on day 10.5 embryos (E10.5) was most effective for reducing CAKUT incidence and ectopic UB outgrowth in Robo2^PB/+Gen1^PB/+ mice. Furthermore, embryonic kidney mesenchymal levels of p-ERK were significantly decreased on day E11.5 after U0126 treatment, along with decreased cell proliferation index PHH3 and ETV5 expression. Collectively, Gen1 and Robo2 exacerbated the CAKUT phenotype in Robo2^PB/+Gen1^PB/+ mice through the MAPK/ERK pathway, increasing proliferation and ectopic UB outgrowth.

The role of genetic testing in the diagnostic workflow of pediatric patients with kidney diseases: the experience of a single institution

PURPOSE

Inherited kidney diseases are among the leading causes of kidney failure in children, resulting in increased mortality, high healthcare costs and need for organ transplantation. Next-generation sequencing technologies can help in the diagnosis of rare monogenic conditions, allowing for optimized medical management and therapeutic choices.

METHODS

Clinical exome sequencing (CES) was performed on a cohort of 191 pediatric patients from a single institution, followed by Sanger sequencing to confirm identified variants and for family segregation studies.

RESULTS

All patients had a clinical diagnosis of kidney disease: the main disease categories were glomerular diseases (32.5%), ciliopathies (20.4%), CAKUT (17.8%), nephrolithiasis (11.5%) and tubular disease (10.5%). 7.3% of patients presented with other conditions. A conclusive genetic test, based on CES and Sanger validation, was obtained in 37.1% of patients. The highest detection rate was obtained for ciliopathies (74.4%), followed by nephrolithiasis (45.5%), tubular diseases (45%), while most glomerular diseases and CAKUT remained undiagnosed.

CONCLUSIONS

Results indicate that genetic testing consistently used in the diagnostic workflow of children with chronic kidney disease can (i) confirm clinical diagnosis, (ii) provide early diagnosis in the case of inherited conditions, (iii) find the genetic cause of previously unrecognized diseases and (iv) tailor transplantation programs.

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.