Characterization of patients with heterozygous cystinuria

Prevalence and characteristics of genetic disease in adult kidney stone formers

BACKGROUND

Molecular mechanisms of kidney stone formation remain unknown in most patients. Previous studies have shown a high heritability of nephrolithiasis, but data on the prevalence and characteristics of genetic disease in unselected adults with nephrolithiasis are lacking. This study was conducted to fill this important knowledge gap.

METHODS

We performed whole exome sequencing in 787 participants in the Bern Kidney Stone Registry, an unselected cohort of adults with one or more past kidney stone episodes [kidney stone formers (KSFs)] and 114 non-kidney stone formers (NKSFs). An exome-based panel of 34 established nephrolithiasis genes was analysed and variants assessed according to American College of Medical Genetics and Genomics criteria. Pathogenic (P) or likely pathogenic (LP) variants were considered diagnostic.

RESULTS

The mean age of KSFs was 47 ± 15 years and 18% were first-time KSFs. A Mendelian kidney stone disease was present in 2.9% (23/787) of KSFs. The most common genetic diagnoses were cystinuria (SLC3A1, SLC7A9; n = 13), vitamin D-24 hydroxylase deficiency (CYP24A1; n = 5) and primary hyperoxaluria (AGXT, GRHPR, HOGA1; n = 3). Of the KSFs, 8.1% (64/787) were monoallelic for LP/P variants predisposing to nephrolithiasis, most frequently in SLC34A1/A3 or SLC9A3R1 (n = 37), CLDN16 (n = 8) and CYP24A1 (n = 8). KSFs with Mendelian disease had a lower age at the first stone event (30 ± 14 versus 36 ± 14 years; P = .003), were more likely to have cystine stones (23.4% versus 1.4%) and less likely to have calcium oxalate monohydrates stones (31.9% versus 52.5%) compared with KSFs without a genetic diagnosis. The phenotype of KSFs with variants predisposing to nephrolithiasis was subtle and showed significant overlap with KSFs without diagnostic variants. In NKSFs, no Mendelian disease was detected and LP/P variants were significantly less prevalent compared with KSFs (1.8% versus 8.1%).

CONCLUSION

Mendelian disease is uncommon in unselected adult KSFs, yet variants predisposing to nephrolithiasis are significantly enriched in adult KSFs.

Declaration: Novel SLC3A1 mutation in a cystinuria patient with xanthine stones: a case report

BACKGROUND

Cystinuria and xanthinuria are both rare genetic diseases involving urinary calculi. However, cases combining these two disorders have not yet been reported.

CASE PRESENTATION

In this study, we report a case of cystinuria with xanthine stones and hyperuricemia. The 23-year-old male patient was diagnosed with kidney and ureteral stones, solitary functioning kidney and hyperuricemia after admission to the hospital. The stones were removed by surgery and found to be composed of xanthine.

CONCLUSION

Genetic testing by next-generation sequencing technology showed that the patient carried the homozygous nonsense mutation c.1113 C> A (p.Tyr371*) in the SLC3A1 gene, which was judged to be a functionally pathogenic variant. Sanger sequencing revealed that the patient's parents carried this heterozygous mutation, which is a pathogenic variant that can cause cystinuria. The 24-h urine metabolism analysis showed that the cystine content was 644 mg (<320 mg/24 h), indicating that the patient had cystinuria, consistent with the genetic test results. This case shows that cystinuria and xanthine stones can occur simultaneously, and provides evidence of a possible connection between the two conditions. Furthermore, our findings demonstrate the potential value of genetic testing using next-generation sequencing to effectively assist in the clinical diagnosis and treatment of patients with urinary calculi.

Metabolic and Genetic Evaluation in Children with Nephrolithiasis

OBJECTIVE

To evaluate metabolic and genetic abnormalities in children with nephrolithiasis attending a referral center in North India.

METHODS

The patients aged 1-18 y old with nephrolithiasis underwent biochemical evaluation and whole-exome sequencing. The authors evaluated for monogenic variants in 56 genes and compared allele frequency of 39 reported polymorphisms between patients and 1739 controls from the GenomeAsia 100 K database.

RESULTS

Fifty-four patients, aged 9.1 ± 3.7 y were included. Stones were bilateral in 42.6%, familial in 33.3%, and recurrent in 25.9%. The most common metabolic abnormalities were hypercalciuria (35.2%), hyperoxaluria (24.1%), or both (11.1%), while xanthinuria (n = 3), cystinuria (n = 1), and hyperuricosuria (n = 1) were rare. Exome sequencing identified an etiology in 6 (11.1%) patients with pathogenic/likely pathogenic causative variants. Three variants in MOCOS and one in ATP7B were pathogenic; likely pathogenic variants included MOCOS (n = 2), AGXT, and SLC7A9 (n = 1, each). Causality was not attributed to two SLC34A1 likely pathogenic variants, due to lack of matching phenotype and dominant family history. Compared to controls, allele frequency of the polymorphism TRPV5 rs4252402 was significantly higher in familial stone disease (allele frequency 0.47 versus 0.53; OR 3.2, p = 0.0001).

CONCLUSION

The chief metabolic abnormalities were hypercalciuria and hyperoxaluria. A monogenic etiology was identified in 11% with pathogenic or likely pathogenic variants using a gene panel for nephrolithiasis. Heterozygous missense variants in the sodium-phosphate cotransporter SLC34A1 were common and required evaluation for attributing pathogenicity. Rare polymorphisms in TRPV5 might increase the risk of familial stones. These findings suggest that a combination of metabolic and genetic evaluation is useful for determining the etiology of nephrolithiasis.

The Long-Term Follow-Up of Patients with Cystine Stones: A Single-Center Experience for 13 Years

Introduction: Cystine stone development is relatively uncommon among patients with urolithiasis, and most studies have reported only on small sample sizes and short follow-up periods. We evaluated clinical courses and treatment outcomes of patients with cystine stones with long-term follow-up at our center. Methods: We retrospectively analyzed 22 patients diagnosed with cystine stones between January 1989 and May 2019. Results: The median follow-up was 160 (range 6–340) months, and the median patient age at diagnosis was 46 (range 12–82) years. All patients underwent surgical interventions at the first visit (4 extracorporeal shockwave lithotripsy, 5 ureteroscopy, and 13 percutaneous nephrolithotripsy). The median number of stone events and surgical interventions per year was 0.45 (range 0–2.6) and 0.19 (range 0–1.3) after initial surgical intervention. The median time to stone events and surgical intervention was 2 years and 3.25 years, respectively. There was a significant difference in time to stone events and second surgical intervention when patients were divided at 50 years of age at diagnosis (p = 0.02, 0.04, respectively). Conclusions: Only age at a diagnosis under 50 was significantly associated with recurrent stone events and intervention. Adequate follow-up and treatment are needed to manage patients with cystine stones safely.

Cystinuria: urine sediment as a diagnostic test

Objectives

To demonstrate the importance of carrying out the urinary sediment study with the correct interpretation and crystals typification as a clinical laboratory diagnostic tool, as well as the elaboration of protocols that determine the need to realize this type of microscopic urinary sediment examination routinely.

Case presentation

Elderly male patient with no personal or family history of interest that presented with left iliac fossa fixed and non-irradiated pain lasting three days. This is the first time that he suffered pain episodes of this type. The urine analysis reveals proteinuria, hematuria and the sediment shows abundant flat and hexagonal crystals, typical of cystine. Amino acid analysis confirms the finding, showing high dibasic amino acids and cystine concentrations.

Conclusions

The study of the urinary sediment by the clinical laboratory reveals the presence of a case of cystinuria due to the appearance of their pathognomonic crystals at an advanced age and without a previous history. The case reported in this paper is of interest for clinical laboratory practice, as it demonstrates the utility of urine sediment examination in the diagnosis of a genetic disease that manifests as a simple renal colic.

The impact of surgical intervention on renal function in cystinuria

Introduction:

Cystinuria is an autosomal recessive disorder due to intestinal and renal transport defects in cystine and dibasic amino acids, which result in recurrent urolithiasis and surgical interventions. This study aimed to assess the impact of surgical interventions on renal function by analyzing estimated glomerular filtration rates.

Methods:

Thirteen pediatric patients with cystinuria, who were followed-up in a single tertiary institution between 2004 and 2016, were included in the study. Medical records were reviewed to collect data on clinical presentation of patients, urine parameters, stone formation, medical treatment, surgical intervention, stone recurrence after surgical procedure, stone analysis, ultrasonography, 99m-technetium dimercaptosuccinic acid (99mTc-DMSA) radionuclide imaging results, and follow-up time. Creatinine clearances estimated by modified Schwartz (eGFR) formula before and after surgery were used to assess renal function and compared statistically.

Results:

Nine patients (69.2%) had renal scarring which were detected with 99mTc-DMSA radionuclide imaging. In ten patients (76.9%), open surgical intervention for stones were needed during follow-up. Significant difference was not detected between eGFR before and after surgical intervention (mean 92 versus 106, p = 0.36). Nine of the patients (69.2%) were stone free in the last ultrasonographic examination. Relapses of stone after surgery were seen in 66.6% of patients who underwent surgical intervention.

Conclusions:

Surgical interventions for urinary stones are commonly required in patients with cystinuria. Renal scarring is a prevalent finding in cystinuric patients. Surgical interventions have no negative impact on eGFR in patients with cystinuria according to the present study.

Cystinuria in a patient with 19q12q13.1 deletion

Cystinuria is a genetic cause of kidney stones with a prevalence of 1 in 7000 births. So far, two genes have been described responsible for this disorder (SLC3A1 and SLC7A9). We report a patient with an SLC7A9 gene mutation located in 19q13.1 on one allele and with a 19q12q13 region deletion on the other allele. The characteristic clinical features of the 19q13.1 microdeletion syndrome include facial dysmorphism, signs of ectodermal dysplasia, growth retardation, neurologic features and genitourinary anomalies. Cystinuria has not yet been described as part of this syndrome, although one of its responsible genes (SLC7A9) is in the same genomic location. The index case is a 6-year-old male presented with distinctive facial features, cutis aplasia of the scalp, rudimentary teeth, microcephaly, intrauterine and postnatal growth retardation, psychomotor developmental delay, speech delay, epilepsy, inguinal hernias and cystinuria. An array-CGH analysis was performed, finding a large deletion of the 19q12q13.11 cytobands, which affects 19 genes. Two of them are involved in the 19q13.11 deletion syndrome and another affected gene is SLC7A9, responsible for type B cystinuria. Sanger sequencing was performed as well, detecting a heterozygous mutation of the SLC7A9 gene, located in 19q13.1. As far as we know, this is the first described case of cystinuria in a patient with SLC7A9 gene mutation located in 19q13.1 on one allele and with 19q12q13 region deletion on the other allele. Although this patient can be classified as a type B heterozygote and, therefore, his renal prognosis is not severe, the occasional nephrolithiasis found in such patients justifies a close follow-up with regular testing of urinary cystine excretion. We suggest that the recessive behavior of this case, explains the clinical features regarding cystinuria. We propose that in the face of patients affected of a phenotype matchable with 19q13.11 syndrome and cystinuria, a mutational or sequencing study of the SLC7A9 gene should be performed to allow an early onset of diagnosis and treatment.

Epidemiology of stone disease across the world

Nephrolithiasis is a highly prevalent disease worldwide with rates ranging from 7 to 13% in North America, 5-9% in Europe, and 1-5% in Asia. Due to high rates of new and recurrent stones, management of stones is expensive and the disease has a high level of acute and chronic morbidity. The goal of this study is to review the epidemiology of stone disease in order to improve patient care. A review of the literature was conducted through a search on Pubmed^®, Medline^®, and Google Scholar^®. This review was presented and peer-reviewed at the 3rd International Consultation on Stone Disease during the 2014 Société Internationale d'Urologie Congress in Glasgow. It represents an update of the 2008 consensus document based on expert opinion of the most relevant studies. There has been a rising incidence in stone disease throughout the world with a narrowing of the gender gap. Increased stone prevalence has been attributed to population growth and increases in obesity and diabetes. General dietary recommendations of increased fluid, decreased salt, and moderate intake of protein have not changed. However, specific recommended values have either changed or are more frequently reported. Geography and environment influenced the likelihood of stone disease and more information is needed regarding stone disease in a large portion of the world including Asia and Africa. Randomized controlled studies are lacking but are necessary to improve recommendations regarding diet and fluid intake. Understanding the impact of associated conditions that are rapidly increasing will improve the prevention of stone disease.

Fourteen monogenic genes account for 15% of nephrolithiasis/nephrocalcinosis

Nephrolithiasis is a prevalent condition with a high morbidity. Although dozens of monogenic causes have been identified, the fraction of single-gene disease has not been well studied. To determine the percentage of cases that can be molecularly explained by mutations in 1 of 30 known kidney stone genes, we conducted a high-throughput mutation analysis in a cohort of consecutively recruited patients from typical kidney stone clinics. The cohort comprised 272 genetically unresolved individuals (106 children and 166 adults) from 268 families with nephrolithiasis (n=256) or isolated nephrocalcinosis (n=16). We detected 50 likely causative mutations in 14 of 30 analyzed genes, leading to a molecular diagnosis in 14.9% (40 of 268) of all cases; 20 of 50 detected mutations were novel (40%). The cystinuria gene SLC7A9 (n=19) was most frequently mutated. The percentage of monogenic cases was notably high in both the adult (11.4%) and pediatric cohorts (20.8%). Recessive causes were more frequent among children, whereas dominant disease occurred more abundantly in adults. Our study provides an in-depth analysis of monogenic causes of kidney stone disease. We suggest that knowledge of the molecular cause of nephrolithiasis and nephrocalcinosis may have practical implications and might facilitate personalized treatment.