Familial clustering of medullary sponge kidney is autosomal dominant with reduced penetrance and variable expressivity

Medullary Sponge Kidney and Its Relationship with Primary Distal Renal Tubular Acidosis: Case Reports and a Comprehensive Genetics-First Approach

Medullary sponge kidney (MSK) is a description of radiographic features. However, the pathogenesis of MSK remains unclear. MSK is supposed to be the cause of secondary distal renal tubular acidosis (dRTA), although there are case reports suggesting that MSK is a complication of primary dRTA. In addition to these reports, we report 3 patients with metabolic acidosis and MSK, in whom primary dRTA is confirmed by molecular genetic analyses of SLC4A1 and ATP6V1B1 genes. With a comprehensive genetics-first approach using the 100,000 Genomes Rare Diseases Project dataset, the association between MSK and primary dRTA is examined. We showed that many patients with MSK phenotypes are genetically tested with a gene panel which does not contain dRTA-associated genes, revealing opportunities for missed genetic diagnosis. Our cases highlight that the radiological description of MSK is not a straightforward disease or clinical phenotype. Therefore, when an MSK appearance is noted, a broader set of causes should be considered including genetic causes of primary dRTA as the underlying reason for medullary imaging abnormalities.

Ultrasound Patterns and Disease Progression in Medullary Sponge Kidney in Adults

Our paper presents the ultrasound (US) patterns of a rare kidney disease-medullary sponge kidney (MSK)-that have not been described before in comparison with other causes of medullary hyperechogenicity and correlates them with the severity of the disease and prognosis. This is a clinical observational study of all US examinations in the Nephrology Department over a period of 6 years. The abdominal US focused on the kidneys was recorded. US characteristics of the medulla and cortex were analyzed. We found 10 patients with characteristic daisy flower (DF) kidneys. Positive diagnosis in association with other renal risk factors, prognosis, and evolution were evaluated. Two patterns of medullary hyperechogenicity were found and were correlated with disease severity and kidney function. The first pattern is a homogenous echogenicity of the medulla described as a "daisy-like" appearance. The second pattern: calcifications associated with medullar echogenicity, stone production, nephrocalcinosis, and impaired kidney function: "atypical daisy-like." Medullary hyperechogenicity can have more US patterns. In MSK, if the medullary echogenicity is homogenous the evolution is benign, whereas the second, inhomogeneous pattern, has a variable clinical presentation with nephrocalcinosis and the outcome is more severe, leading to chronic kidney disease and impairing the quality of life.

Single-Cell Gene Expression Analysis in Patients with Medullary Sponge Kidney and a Retrospective Study

OBJECTIVE

To establish better diagnosis thinking and provide advanced understanding of MSK, the CT imaging features, clinical characteristics, and the expression of suspected genes in the kidney spatiotemporal immune zonation and fetal renal development were investigated.

METHODS

17 patients with MSK hospitalized in our hospital were selected as our research subjects. Human Phenotype Ontology, MalaCards: The Human Disease Database, GeneCards: The Human Gene Database, Human Protein Atlas, and Single Cell Expression Atlas were used to analyze this disease.

RESULTS

In our 17 patients, the incidence of MSK tended to be the same in male and female, and the onset age of MSK was probably 31-50 years old. The top one related disease of MSK was nephrocalcinosis and the most frequent phenotype related to MSK was nephrolithiasis. In addition, the expression of HNF1B, CLCN5, GDNF, ATP6V0A4, ATP6V1B1, LAMA2, RET, ACAN, and ABCC8 has been implicated in both human kidney immune zonation and fetal kidney development.

CONCLUSIONS

HNF1B, CLCN5, GDNF, ATP6V0A4, ATP6V1B1, LAMA2, RET, ACAN, and ABCC8 could be independent indicators for the diagnosis and preventive intervention of MSK patients, and abnormal kidney development due to mutations in key genes was the underlying cause of MSK.

Sphingomyelin and Medullary Sponge Kidney Disease: A Biological Link Identified by Omics Approach

Background: Molecular biology has recently added new insights into the comprehension of the physiopathology of the medullary sponge kidney disease (MSK), a rare kidney malformation featuring nephrocalcinosis and recurrent renal stones. Pathogenesis and metabolic alterations associated to this disorder have been only partially elucidated.

Methods: Plasma and urine samples were collected from 15 MSK patients and 15 controls affected by idiopathic calcium nephrolithiasis (ICN). Plasma metabolomic profile of 7 MSK and 8 ICN patients was performed by liquid chromatography combined with electrospray ionization tandem mass spectrometry (UHPLC–ESI-MS/MS). Subsequently, we reinterrogated proteomic raw data previously obtained from urinary microvesicles of MSK and ICN focusing on proteins associated with sphingomyelin metabolism. Omics results were validated by ELISA in the entire patients' cohort.

Results: Thirteen metabolites were able to discriminate MSK from ICN (7 increased and 6 decreased in MSK vs. ICN). Sphingomyelin reached the top level of discrimination between the two study groups (FC: −1.8, p < 0.001). Ectonucleotide pyrophophatase phosphodiesterase 6 (ENPP6) and osteopontin (SPP1) resulted the most significant deregulated urinary proteins in MSK vs. ICN (p < 0.001). ENPP6 resulted up-regulated also in plasma of MSK by ELISA.

Conclusion: Our data revealed a specific high-throughput metabolomics signature of MSK and indicated a pivotal biological role of sphingomyelin in this disease.

Analysis of urinary exosomes applications for rare kidney disorders

Introduction: Exosomes are nanovesicles that play important functions in a variety of physiological and pathological conditions. They are powerful cell-to-cell communication tool thanks to the protein, mRNA, miRNA, and lipid cargoes they carry. They are also emerging as valuable diagnostic and prognostic biomarker sources. Urinary exosomes carry information from all the cells of the urinary tract, downstream of the podocyte. Rare kidney diseases are a subset of an inherited diseases whose genetic diagnosis can be unclear, and presentation can vary due to genetic, epigenetic, and environmental factors. Areas covered: In this review, we focus on a group of rare and often neglected kidney diseases, for which we have sufficient available literature data on urinary exosomes. The analysis of their content can help to comprehend pathological mechanisms and to identify biomarkers for diagnosis, prognosis, and therapeutic targets. Expert opinion: The foreseeable large-scale application of system biology approach to the profiling of exosomal proteins as a source of renal disease biomarkers will be also useful to stratify patients with rare kidney diseases whose penetrance, phenotypic presentation, and age of onset vary sensibly. This can ameliorate the clinical management.

Ultrasound to address medullary sponge kidney: a retrospective study

Background

Medullary sponge kidney (MSK) is a rare disease characterized by cystic dilatation of papillary collecting ducts. Intravenous urography is still considered the gold standard for diagnosis. We identified a cohort of patients from our outpatient clinic with established diagnosis of MSK to outline some ultrasonographic characteristics that may help establish a diagnosis.

Methods

We conducted a retrospective study of patients seen between January 1st 2009 and January 1st 2019 in our clinic. Out of 4321 patients, 18 had a diagnosis of MSK. We reviewed their clinical and family history, laboratory data and imaging studies. Specifically, we focused on ultrasound imaging.

Results

Patients were referred to our outpatient clinic because of renal impairment (44%), family history of nephropathy (17%), nephrolithiasis or an established diagnosis of MSK (39%). Seventy-two percent of patients presented with chronic kidney disease, 22% required hemodialysis. Urinary tract infections (44%), nephrolithiasis (33%), microscopic hematuria (50%) and proteinuria (44%) were reported. Seven patients underwent computed tomography; all of them received ultrasound. Ultrasound examination showed bilateral renal cysts, usually small and located in the renal medulla, and microcalcifications located in the medulla or within the cysts.

Conclusion

We identified a peculiar tetrad associated with MSK: 1) hypoechoic medullary areas, 2) hyperechoic spots, 3) microcystic dilatation of papillary zone, 4) multiple calcifications (linear, small stones or calcified intracystic sediment) in each papilla. The presence of this diagnostic tetrad, added to laboratory data and clinical history, could be helpful in the differential diagnosis to identify patients with MSK.

Medullary Sponge Kidney: Current Perspectives

Medullary Sponge Kidney (MSK) disease is a rare congenital malformation of the distal nephron where cystic dilatation is appreciable in the collecting ducts and renal papillae. Most cases of the malformation are thought to arise from a malfunction within neurotrophic factor and tyrosine kinase interactions. Presentation and prognosis are usually indolent; however, they include urinary tract infections (UTI), nephrolithiasis and nephrocalcinosis, distal renal tubular acidosis (dRTA) and hypocitraturia. With an insidious and asymptomatic onset, MSK is a difficult renal manifestation to both diagnose and treat. Difficulty diagnosing MSK today arises from clinical settings deviating from the usage of contrast methods when assessing the urogenital tract. Many healthcare standards for kidney disorders center diagnosis around imaging techniques rather than contrast methods. This ultimately leads to a decrease in the total number of confirmed cases of MSK. Though intra-venous urogram (IVU) remains as the current gold standard to diagnose MSK, other methods such as endoscopy and Multi-detector computed tomography (MDCT) are being put into place. Endoscopic examination and renal biopsy may allow definitive diagnosis; however, such invasive methods may be considered excessive. Moving forward, differential diagnoses for MSK can be made more precisely when patients present with other renal manifestations, especially in groups at risk. These groups include patients between the age of 20 and 30, patients with other renal malformations, high sodium diet patients, hyperparathyroid patients, and patients with family history of MSK. Basic treatment is aimed at controlling stone formation by stabilizing urinary pH. Treatment for patients, especially those prone to forming stones, includes the application of potassium citrate compounds, prophylactic water and diet control, surgical intervention or lithotripsy for removal of symptomatic kidney stones.

Proteomic Analysis of Urinary Microvesicles and Exosomes in Medullary Sponge Kidney Disease and Autosomal Dominant Polycystic Kidney Disease

BACKGROUND AND OBJECTIVES

Microvesicles and exosomes are involved in the pathogenesis of autosomal dominant polycystic kidney disease. However, it is unclear whether they also contribute to medullary sponge kidney, a sporadic kidney malformation featuring cysts, nephrocalcinosis, and recurrent kidney stones. We addressed this knowledge gap by comparative proteomic analysis.

DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS

The protein content of microvesicles and exosomes isolated from the urine of 15 patients with medullary sponge kidney and 15 patients with autosomal dominant polycystic kidney disease was determined by mass spectrometry followed by weighted gene coexpression network analysis, support vector machine learning, and partial least squares discriminant analysis to compare the profiles and select the most discriminative proteins. The proteomic data were verified by ELISA.

RESULTS

A total of 2950 proteins were isolated from microvesicles and exosomes, including 1579 (54%) identified in all samples but only 178 (6%) and 88 (3%) specific for medullary sponge kidney microvesicles and exosomes, and 183 (6%) and 98 (3%) specific for autosomal dominant polycystic kidney disease microvesicles and exosomes, respectively. The weighted gene coexpression network analysis revealed ten modules comprising proteins with similar expression profiles. Support vector machine learning and partial least squares discriminant analysis identified 34 proteins that were highly discriminative between the diseases. Among these, CD133 was upregulated in exosomes from autosomal dominant polycystic kidney disease and validated by ELISA.

CONCLUSIONS

Our data indicate a different proteomic profile of urinary microvesicles and exosomes in patients with medullary sponge kidney compared with patients with autosomal dominant polycystic kidney disease. The urine proteomic profile of patients with autosomal dominant polycystic kidney disease was enriched of proteins involved in cell proliferation and matrix remodeling. Instead, proteins identified in patients with medullary sponge kidney were associated with parenchymal calcium deposition/nephrolithiasis and systemic metabolic derangements associated with stones formation and bone mineralization defects.

PODCAST

This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2019_04_24_CJASNPodcast_19_06_.mp3.

Renal Tubular Acidosis

Renal tubular acidosis should be suspected in poorly thriving young children with hyperchloremic and hypokalemic normal anion gap metabolic acidosis, with/without syndromic features. Further workup is needed to determine the type of renal tubular acidosis and the presumed etiopathogenesis, which informs treatment choices and prognosis. The risk of nephrolithiasis and calcinosis is linked to the presence (proximal renal tubular acidosis, negligible stone risk) or absence (distal renal tubular acidosis, high stone risk) of urine citrate excretion. New formulations of slow-release alkali and potassium combination supplements are being tested that are expected to simplify treatment and lead to sustained acidosis correction.

Living kidney donation from people at risk of nephrolithiasis, with a focus on the genetic forms

Deciding whether to accept a donor with nephrolithiasis is a multifaceted task because of the challenge of finding enough suitable donors while at the same time ensuring the safety of both donors and recipients. Until not long ago, donors with a history of renal stones or with stones emerging during screening on imaging were not considered ideal, but recent guidelines have adopted less stringent criteria for potential donors at risk of stones. This review goes through the problems that need to be approached to arrive at a wise clinical decision, balancing the safety of donors and recipients with the need to expand the organ pool. The risk of declining renal function and worsening stone formation is examined. Documents (consensus statements, guidelines, etc.) on this issue released by the most important medical societies and organizations are discussed and compared. Specific problems of living kidney donation associated with certain systemic (chronic hypercalcemia due to CYP24A1 gene mutations, primary hyperoxaluria, APRT deficiency) and renal (medullary sponge kidney, cystinuria, distal renal tubular acidosis, Dent's disease, Bartter syndrome, familial hypomagnesemia with hypercalciuria and nephrocalcinosis) Mendelian disorders that cause nephrolithiasis are also addressed.

Association of medullary sponge kidney and hyperparathyroidism with RET G691S/S904S polymorphism: a case report

Background

Medullary sponge kidney is a rare renal malformation, which usually manifests as nephrocalcinosis, renal tubular acidosis, and recurrent urinary tract infections. Medullary sponge kidney is often associated with renal developmental anomalies and tumors, and its exact pathogenesis is not yet clearly explained. Given the key role of the interaction of glial cell line-derived neurotrophic factor gene, GDNF, and the “rearranged during transfection” proto-oncogene, RET, in kidney and urinary tract development, variations in these genes are proposed to be candidates for medullary sponge kidney. Hyperparathyroidism is observed in a few patients with medullary sponge kidney, but the exact pathogenesis of this association is unknown. This case report highlights the coexistence of these two conditions associated with RET polymorphism, which contributes toward the understanding of the pathogenesis of medullary sponge kidney.

Case presentation

A 52-year-old Chinese woman with recurrent renal stones presented to our hospital. Subsequently she was diagnosed as having medullary sponge kidney and tertiary hyperparathyroidism and underwent parathyroidectomy. Genomic DNA was isolated from lymphocytes and the GDNF and RET genes were determined by Sanger sequencing. Two RET polymorphisms were found in our patient, one was nonsynonymous c.2071G>A (G691S; rs1799939) located in exon 11, the other was synonymous c.2712C>G. (p.S904S; rs1800863) located in exon 15.

Conclusions

We demonstrated a case of medullary sponge kidney combined with tertiary hyperparathyroidism, which contributes to further understanding of the pathogenesis of this disease. Besides, we also found RET G691S/S904S polymorphism in this patient, but additional studies are required to explore the role of the RET gene in medullary sponge kidney with hyperparathyroidism.

Efficacy of Multi-Detector Computed Tomography for the Diagnosis of Medullary Sponge Kidney

Objective

To expand the diagnostic armamentarium for medullary sponge kidney (MSK), we evaluate the use of high-resolution multidetector computed tomography (MDCT) for MSK diagnosis and compare to the standard intravenous urography (IVU). Despite a significant prevalence amongst stone formers, diagnosis of this well described condition has declined. IVU, the gold standard in MSK diagnosis, has largely been replaced by CT, which has previously been shown unable to demonstrate signs of MSK.

Methods and Materials

Patients with known history of MSK based on IVU underwent limited MDCT urogram. Control group patients, without MSK, also had MDCT urograms performed for other clinically indicated conditions. Studies were scored by board-certified radiologists on a 0-2 scale based on the likelihood of MSK. IVU studies, when available, were similarly graded.

Results

MDCT was diagnostic of MSK in 9 out of the 10 patients with known history of MSK. No false positives were present in our series. The one case of MSK not detected on MDCT was graded as a "1" on its respective IVU. Sensitivity and specificity were 90 and 100%, respectively, when compared with IVU.

Conclusion

Concordance with IVU findings, despite a small reduction in sensitivity, indicates MDCT to be a suitable, and more readily available replacement for IVU in the diagnosis of MSK.

Genetic, pathophysiological, and clinical aspects of nephrocalcinosis

Nephrocalcinosis describes the ectopic deposition of calcium salts in the kidney parenchyma. Nephrocalcinosis can result from a number of acquired causes but also an even greater number of genetic diseases, predominantly renal but also extrarenal. Here we provide a review of the genetic causes of nephrocalcinosis, along with putative mechanisms, illustrated by human and animal data.

[Unilateral renal agenesis. New arguments about the genetic relationship between kidney malformations and urolithiasis]

BACKGROUND

In few previous works, it has been reported that hypercalciuria is associated with some types of CAKUT, namely ureteropelvic junction obstruction, vesicoureteral reflux or simple renal cysts. In addition, one higher prevalence of hypercalciuria and/or urolithiasis has been described in their family members compared to the general population. This study was carried out to find out whether children with unilateral renal agenesis (URA) have these features previously described in other CAKUT types.

METHODS

In a descriptive and multicenter study we studied the prevalence of hypercalciuria, hypocitraturia and urolithiasis in 67 children (43 males and 24 females) with URA and their families.

RESULTS

The two metabolic anomalies that promote stone formation were observed in 26 children (38.8%), distributed as follows: hypercalciuria in 16, hypocitraturia in 9, and both hypercalciuria and hypocitraturia in 1. Eight children (11.9%) suffered renal colic during follow-up. Familial history of urolithiasis was found in 42/67 children (62.7%): in 12 of the first-degree relatives, in 15 of the second degree relatives and in 15 patients both in the first-degree as in their second degree relatives. In contrast, in historic control group, only in 28.1% of families at least one member had urolithiasis.

CONCLUSION

Our results show that the prevalence of hypercalciuria and/or hypocitraturia is greater in pediatric patients with URA than in the general population. Likewise, the prevalence of urolithiasis in the families of these children is also higher than that in the general population.

Recent advances in managing and understanding nephrolithiasis/nephrocalcinosis

Urinary stone disease is a very common disease whose prevalence is still increasing. Stone formation is frequently associated with other diseases of affluence such as hypertension, osteoporosis, cardiovascular disease, metabolic syndrome, and insulin resistance. The increasing concentration of lithogenic solutes along the different segments of the nephron involves supersaturation conditions leading to the formation, growth, and aggregation of crystals. Crystalline aggregates can grow free in the tubular lumen or coated on the wall of the renal tubule. Plugs of crystalline material have been highlighted in the tubular lumen in some patients, but crystalline growth starting from plaques of calcium phosphate within the renal papillae has been demonstrated in others. Urinary supersaturation is the result of a complex interaction between predisposing genetic features and environmental factors. Dietary intake is certainly the most important environmental risk factor. In particular, an insufficient intake of dietary calcium (<600 mg/day) can increase the intestinal absorption of oxalate and the risk of calcium oxalate stone formation. Other possible risk factors that have been identified include excessive intake of salt and proteins. The potential role of dietary acid load seems to play an important role in causing a state of subclinical chronic acidosis; therefore, the intake of vegetables is encouraged in stone-forming patients. Consumption of sugar-sweetened soda and punch is associated with a higher risk of stone formation, whereas consumption of coffee, tea, beer, wine, and orange juice is associated with a lower risk. A high fluid intake is widely recognized as the cornerstone of prevention of all forms of stones. The effectiveness of protein and salt restriction has been evaluated in some studies that still do not allow definitive conclusions to be made. Calcium stone formation can be prevented by the use of different drugs with different mechanisms of action (thiazide diuretics, allopurinol, and potassium citrate), but there is no ideal drug that is both risk free and well tolerated.

Medullary sponge kidney: A treatment conundrum

Medullary sponge kidney (MSK) is a congenital kidney malformation that is characterized by dilatation of the collecting tubules in the medullary pyramids. Cyst-like areas then form which predispose to nephrocalcinosis, stone formation and recurrent urinary tract infection (UTI). There is an association with defective distal renal tubular acidification and concentration abnormalities such as hypocitraturia. MSK is generally believed to be a sporadic disorder, but an autosomal dominant inheritance is also reported. More recently genetic mutations have been recognised as a possible contributor to the aetiology of the condition. In this article we summarize the available English language literature on the subject of MSK, including its pathogenesis, diagnosis, prognosis and treatment.

What is nephrocalcinosis?

The available publications on nephrocalcinosis are wide-ranging and have documented multiple causes and associations of macroscopic or radiological nephrocalcinosis, most often located in the renal medulla, with various metabolic and genetic disorders; in fact, so many and various are these that it is difficult to define a common underlying mechanism. We have reviewed nephrocalcinosis in relation to its definition, genetic associations, animal models, and putative mechanisms. We have concluded, and hypothesized, that nephrocalcinosis is primarily a renal interstitial process, resembling metastatic calcification, and that it may have some features in common with, and pathogenic links to, vascular calcification.

From genes to health - challenges and opportunities

In genome science, the advancement in high-throughput sequencing technologies and bioinformatics analysis is facilitating the better understanding of Mendelian and complex trait inheritance. Charting the genetic basis of complex diseases - including pediatric cancer, and interpreting huge amount of next-generation sequencing data are among the major technical challenges to be overcome in order to understand the molecular basis of various diseases and genetic disorders. In this review, we provide insights into some major challenges currently hindering a better understanding of Mendelian and complex trait inheritance, and thus impeding medical benefits to patients.

CT urography for the diagnosis of medullary sponge kidney

BACKGROUND

Medullary sponge kidney (MSK) is characterized by malformation of the terminal collecting ducts and is associated with an increased risk of nephrolithiasis, nephrocalcinosis, urinary tract infections, renal acidification defects, and reduced bone density. It has been historically diagnosed with intravenous pyelography (IVP), which is falling out of favor as an imaging modality. CT urography (CTU) performed with multidetector CT (MDCT) has been shown to create images of the renal collecting system with similar detail as IVP; however, its utility in diagnosing MSK has not been defined.

CASE REPORT

We present the first 15 patients with recurrent symptomatic nephrolithiasis who were evaluated in our renal stone clinic with CTU. Four patients were diagnosed with MSK after visualization of the characteristic radiologic findings.

DISCUSSION

CTU effectively demonstrates the characteristic radiologic findings of MSK including collecting tubule dilatation, medullary nephrocalcinosis, nephrolithiasis, and medullary cysts. Dose reduction protocols can reduce radiation exposure below that associated with conventional IVP. We propose CTU be considered for the diagnosis of MSK.

Evidence for inheritance of medullary sponge kidney

Medullary sponge kidney (MSK) is associated with recurrent calcium stones. Gambaro's group evaluated the relatives of probands with MSK. When prior imaging was not available, they performed renal ultrasounds. They demonstrated familial clustering, providing the best evidence yet that MSK is a heritable disorder. Although a small proportion of MSK cases are associated with variants of glial cell-derived neurotrophic factor (GDNF), the genetic basis for most instances of MSK is not known.