Identification of novel cystinuria mutations and polymorphisms in SLC3A1 and SLC7A9 genes: absence of SLC7A10 gene mutations in cystinuric patients

Analysis of SLC7A9 gene mutations among Jordanian patients with cystinuria

Background

Cystinuria is known as a heritable disorder affecting the cysteine reabsorption by renal system as well as the reabsorption of dibasic amino acids. The main objectives of the present study were to identify genetic mutations in SLC7A9 gene associated with cystinuria.

Methods

A cross sectional study design was conducted. A total of 28 patients diagnosed with cystinuria were included. Molecular techniques were applied to identify genetic mutations in SLC7A9 gene.

Results

The mean age of study participants was 31.57 ± 2.88 years, and slightly more than two thirds of participants were males. Mutations of SLC 7A9 gene showed that the majority of cases (57.1%) were homogeneous, (7.1%) heterogeneous, and slightly more than one third of patients had no mutations. There was no statistically significant relationship between mutations for the SLC7A9 gene and gender (p = 0.249).

Conclusion

Mutations in the SLC7A9 gene are prevalent and can be used as molecular tools to diagnose cystinuria.

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Cystinuria is an inherited disorder of dibasic amino acid as cystine transport in kidney.

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SLC7A9 Cystinuria gene was recently isolated in many cystinuria patient from different racial populations.

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Mutations in the SLC7A9 gene are prevalent in Jordanian (Arab) populations.

No evidence for point mutations in the novel renal cystine transporter AGT1/SLC7A13 contributing to the etiology of cystinuria

BACKGROUND

Cystinuria is caused by the defective renal reabsorption of cystine and dibasic amino acids, and results in cystine stone formation. So far, mutations in two genes have been identified as causative. The SLC3A1/rBAT gene encodes the heavy subunit of the heterodimeric rBAT-b0,+AT transporter, whereas the light chain is encoded by the SLC7A9/ b0,+AT gene. In nearly 85% of patients mutations in both genes are detectable, but a significant number of patients currently remains without a molecular diagnosis. Thus, the existence of a further cystinuria gene had been suggested, and the recently identified AGT1/SLC7A13 represents the long-postulated partner of rBAT and third cystinuria candidate gene.

METHODS

We screened a cohort of 17 cystinuria patients for SLC7A13 variants which were negative for SLC3A1 and SLC7A9 mutations.

RESULTS

Despite strong evidences for an involvement of SLC7A13 mutations in cystinuria, we could not confirm a relevant role of SLC7A13 for the disease.

CONCLUSION

With the exclusion of SLC7A13/AGT1 as the third cystinuria gene accounting for the SLC3A1 and SLC7A9 mutation negative cases, it becomes obvious that other genetic factors should be responsible for the cystinuria phenotype in nearly 15% of patients.

Clinical and genetic characterization of Chinese pediatric cystine stone patients

INTRODUCTION

Cystine stone is the only clinical manifestation in patients with cystinuria, which is an autosomal recessive inheritable disease. However, clinical and genetic data vary among patients in different countries.

OBJECTIVE

To investigate the characteristics of Chinese pediatric cystine stone patients.

PATIENTS AND METHODS

Thirteen pediatric patients with cystine stones were evaluated in our clinic between 2012 and 2015. Gene mutations in SLC3A1 and SLC7A9 were investigated. Metabolic evaluation was also performed. Thirteen pediatric patients with calcium oxalate stones were selected as controls.

RESULTS

Of these patients, eight were males and five were females. Average age at detection of the first stone was 6.8 ± 5.2 years. Urinary stones in three of the 13 cystine patients were composed of cystine and calcium oxalate. The 63.6% of patients with upper urinary stones had bilateral stones. A total of 17 different missense mutations were identified, and 12 of these mutations were first reported in this study. Metabolic abnormalities could be detected in 77% of cystine stone patients. The most common metabolic abnormality was hyperoxaluria, followed by hypercalciuria and hypocitraturia. Compared with calcium stone patients, our cystine stone patients had a higher rate of bilateral stones, larger stone size, higher levels of serum BUN and Cr, urine citrate excretion (Table), and higher mean value of surgeries per patient. By contrast, the opposite was true for urine oxalate excretion and AP (CaOx) index EQ. The urine excretion of cystine was not correlated with other urinary constituents.

DISCUSSION

Patients with cystinuria frequently suffer recurrent renal stones and may subsequently need a series of stone removal procedures during their lifetime. This condition is likely to affect their overall renal function. SLC3A1 and SLC7A9 have been extensively investigated, but a detection rate of 100% in cystinuric patients has yet to be obtained. In our study, we found 14 missense mutations in 18 of 26 alleles except four mutation polymorphisms. Most of the gene mutations found in our study were their first reports. Metabolic abnormalities were frequently found in cystine stone patients, but their risk of calcium oxalate stone formation was relatively lower than that of patients with calcium oxalate stones.

CONCLUSIONS

Cystine stone patients are at risk of impaired renal function and the formation of calcium oxalate stones. Most of the gene mutations identified in our patients were first reported in this study. Therefore, cystinuria possibly exhibits genetic and allelic heterogeneity in Chinese pediatric cystine stone patients.

Cystinuria Associated with Different SLC7A9 Gene Variants in the Cat

Cystinuria is a classical inborn error of metabolism characterized by a selective proximal renal tubular defect affecting cystine, ornithine, lysine, and arginine (COLA) reabsorption, which can lead to uroliths and urinary obstruction. In humans, dogs and mice, cystinuria is caused by variants in one of two genes, SLC3A1 and SLC7A9, which encode the rBAT and bo,+AT subunits of the bo,+ basic amino acid transporter system, respectively. In this study, exons and flanking regions of the SLC3A1 and SLC7A9 genes were sequenced from genomic DNA of cats (Felis catus) with COLAuria and cystine calculi. Relative to the Felis catus-6.2 reference genome sequence, DNA sequences from these affected cats revealed 3 unique homozygous SLC7A9 missense variants: one in exon 5 (p.Asp236Asn) from a non-purpose-bred medium-haired cat, one in exon 7 (p.Val294Glu) in a Maine Coon and a Sphinx cat, and one in exon 10 (p.Thr392Met) from a non-purpose-bred long-haired cat. A genotyping assay subsequently identified another cystinuric domestic medium-haired cat that was homozygous for the variant originally identified in the purebred cats. These missense variants result in deleterious amino acid substitutions of highly conserved residues in the bo,+AT protein. A limited population survey supported that the variants found were likely causative. The remaining 2 sequenced domestic short-haired cats had a heterozygous variant at a splice donor site in intron 10 and a homozygous single nucleotide variant at a branchpoint in intron 11 of SLC7A9, respectively. This study identifies the first SLC7A9 variants causing feline cystinuria and reveals that, as in humans and dogs, this disease is genetically heterogeneous in cats.

Molecular and Clinical Investigation of Cystinuria in the Greek-Cypriot Population

BACKGROUND AND AIMS

Cystinuria represents 3% of nephrolithiasis in humans. Two genes have been identified as the main genetic causes of cystinuria, SLC3A1 and SLC7A9, with an autosomal recessive mode of inheritance. In the present study, we studied for the first time, genetically and clinically, all the cystinuric families identified so far in the Greek-Cypriot population.

METHODS

Discovery of mutations was performed through polymerase chain reaction (PCR)-single analysis and DNA resequencing. New families were investigated through PCR-RFLPs. Clinical data were collected through the hospital patients' records and analytical follow-up of the families.

RESULTS AND DISCUSSION

We found a total of five mutations in 28 Greek-Cypriot cystinuric patients belonging in 12 families. The most frequent mutation among the 28 Greek-Cypriot patients is the SLC3A1-p.T216M, which is also the second most frequent mutation in Europe, representing a genetic founder effect. Sixteen of the 28 patients are homozygous for this mutation. Even though a consanguinity loop was obvious in only one family, other patients were from families in small villages where endogamy was practiced for many centuries. Timely clinical and genetic diagnosis, accompanied by early treatment, is significant for the good health of most of our patients. Only ∼14% of them developed chronic renal failure, and only one reached end-stage renal disease (ESRD).

CONCLUSION

Five SLC3A1 and SLC7A9 mutations appear to be responsible for the genetic basis of cystinuria in the Greek-Cypriot patients; having such a limited number of causative mutations will simplify diagnostics for this population.

Mutation analysis of SLC3A1 and SLC7A9 genes in patients with cystinuria

Cystinuria is an autosomal inherited disorder of renal reabsorption of cystine, arginine, lysine, and ornithine. Increased urinary excretion of cystine results in the formation of kidney stones. Considering the few studies on the genetic basis of the cystinuria in the Middle East and the population-specific distribution of mutations in the SLC3A1 and SLC7A9 genes, in the present study, mutation analysis of these two genes was performed in a cohort of Iranian patients with cystinuria. Thirty unrelated cystinuria patients were analyzed for four of the most common mutations using ARMS-PCR (M467T, T216M) and RFLP-PCR (G105R, R333W) methods. For negative sample, two exons of both genes, which harbor many mutations, were subject to DNA sequencing. Eight variants were identified including missense, polymorphism, intron variant, and a novel variant. The most frequent mutations were not detected in our patients and only G105R was found. Since the molecular genetic testing results may influence the therapy and prognosis of cystinuria, this paper contributes to understanding of the molecular basis of cystinuria in the Iranian patients.

Cystinuria: an inborn cause of urolithiasis

Cystinuria (OMIM 220100) is an inborn congenital disorder characterised by a defective cystine metabolism resulting in the formation of cystine stones. Among the heterogeneous group of kidney stone diseases, cystinuria is the only disorder which is exclusively caused by gene mutations. So far, two genes responsible for cystinuria have been identified: SLC3A1 (chromosome 2p21) encodes the heavy subunit rBAT of a renal b^0,+ transporter while SLC7A9 (chromosome 19q12) encodes its interacting light subunit b^0,+AT. Mutations in SLC3A1 are generally associated with an autosomal-recessive mode of inheritance whereas SLC7A9 variants result in a broad clinical variability even within the same family. The detection rate for mutations in these genes is larger than 85%, but it is influenced by the ethnic origin of a patient and the pathophysiological significance of the mutations. In addition to isolated cystinuria, patients suffering from the hypotonia-cystinuria syndrome have been reported carrying deletions including at least the SLC3A1 and the PREPL genes in 2p21. By extensive molecular screening studies in large cohort of patients a broad spectrum of mutations could be identified, several of these variants were functionally analysed and thereby allowed insights in the pathology of the disease as well as in the renal trafficking of cystine and the dibasic amino acids. In our review we will summarize the current knowledge on the physiological and the genetic basis of cystinuria as an inborn cause of kidney stones, and the application of this knowledge in genetic testing strategies.

Management of Cystinuria

Cystinuria is a monogenic disorder in which there is a transepithelial transport defect of di-basic amino acids, including cystine, ornithine, lysine, and arginine (COLA). This results in diminished reabsorption of these amino acids in both the intestine and renal proximal tubule. This article describes the disorder, reviews the mechanisms of normal COLA renal transport, and summarizes issues related to the disorder, such as the role of mutations, associated diseases, clinical manifestations, therapies, the renal impact, and handling of pediatric patients.

Evidence for association of SLC7A9 gene haplotypes with cystinuria manifestation in SLC7A9 mutation carriers

Cystinuria is a complex genetic disorder. In the present study, we report on the strict linkage disequilibrium of SLC7A9 mutations with the wild type SLC7A9 haplotype of 15 single nucleotide polymorphisms (SNPs) and their effect on cystinuria manifestation and classification. Specifically, screening for mutations and polymorphisms was performed in the family members of ten cystinuric patients with SLC7A9 gene mutations. The molecular genetic and clinical data of cystinuric patients and their relatives were combined to construct the SLC7A9 SNP haplotypes and evaluate the manifestation of the disorder in carriers for a SLC7A9 gene mutation. It was found that all carriers of a SLC7A9 mutation manifested cystinuria if their normal allele had non-wild type nucleotides in two or more of the identified polymorphic sites. Subsequently, the polymorphic background of the SLC7A9 gene probably affects the expression of the disorder in SLC7A9 mutation carriers and points to a revised genetic classification of cystinuric patients.