Genetics of kidney stone disease-Polygenic meets monogenic

Role of Genetic Testing in Kidney Stone Disease: A Narrative Review

PURPOSE OF REVIEW

Kidney stone disease (KSD) is a common and potentially life-threatening condition, and half of patients experience a repeat kidney stone episode within 5-10 years. Despite the ~50% estimate heritability of KSD, international guidelines have not kept up with the pace of discovery of genetic causes of KSD. The European Association of Urology guidelines lists 7 genetic causes of KSD as 'high risk'.

RECENT FINDINGS

There are currently 46 known monogenic (single gene) causes of kidney stone disease, with evidence of association in a further 23 genes. There is also evidence for polygenic risk of developing KSD. Evidence is lacking for recurrent disease, and only one genome wide association study has investigated this phenomenon, identifying two associated genes (SLC34A1 and TRPV5). However, in the absence of other evidence, patients with genetic predisposition to KSD should be treated as 'high risk'. Further studies are needed to characterize both monogenic and polygenic associations with recurrent disease, to allow for appropriate risk stratification. Durability of test result must be balanced against cost. This would enable retrospective analysis if no genetic cause was found initially. We recommend genetic testing using a gene panel for all children, adults < 25 years, and older patients who have factors associated with high risk disease within the context of a wider metabolic evaluation. Those with a genetic predisposition should be managed via a multi-disciplinary team approach including urologists, radiologists, nephrologists, clinical geneticists and chemical pathologists. This will enable appropriate follow-up, counselling and potentially prophylaxis.

Association of single nucleotide genetic polymorphisms of vitamin D receptor and calcium-sensitive receptor with calcium-containing kidney stones in Chinese Dai populations: a prospective multi-center study

PURPOSE

To evaluate the association between vitamin D receptor (VDRs) and calcium-sensitive receptor (CaSR) gene polymorphisms and calcium-containing kidney stones (CCKS) in Dai populations.

METHODS

A total of 160 CCKS patients and 87 healthy controls were included in this study. CCKS was confirmed using urological computed tomography (CT), plain abdominal radiograph, or surgical lithotomy. Stone samples obtained during surgery were analyzed using infrared spectroscopy. Venous blood and 24-h urine samples were collected and analyzed using Sanger sequencing and high-performance liquid chromatography, respectively. Genetic variants in the VDR gene (rs7975232, rs2228570, rs731236, and rs1544410) and CaSR gene (rs7652589, rs1801725, and rs1042636) were identified through sequence analysis.

RESULTS

Analysis of genotype and allele frequencies revealed that the rs7975232 polymorphism in the VDR gene and the rs7652589 allele in the CaSR gene were significantly associated with CCKS. Furthermore, patients carrying the AC and AA genotypes of rs7975232 showed a higher incidence of hypocitraturia compared to those with other genotypes (p < 0.05). The AA and GG genotypes of rs1042636 and the AA genotype of rs7652589 were significantly associated with hypercalciuria (p < 0.05).

CONCLUSION

CCKS in this study population may be closely related to hypocitraturia caused by the VDR locus rs7975232 polymorphism and hypercalciuria caused by the CaSR locus rs1042636 and rs7652589 polymorphism.

Metabolomic Changes Associated with AGXT2 Genotype Variants and Stone Formation in a Colony of Cats

OBJECTIVE

The objective of this study was to assess serum chemistries and metabolomic parameters in cats with genetic variants of the alanine-glyoxylate aminotransferase 2 (AGXT2) gene to determine abnormalities associated with urolith formation and better understand effective approaches for the treatment of cats with uroliths.

METHODS

AGXT2 genotypes of 445 cats in the colony at Hill's Pet Nutrition, Inc. (Topeka, KS, USA) were assessed in a genome-wide association study. Additionally, the serum chemistries and metabolic profiles of each cat were determined, along with their lifetime history of stone incidence. Factor analysis was used as a data-reduction method for metabolites in order to perform statistical hypothesis testing and to select significant metabolites from the more than 600 serum metabolites identified.

RESULTS

Of the 82 cats forming stones in the colony (18.4%), the majority were calcium oxalate. Results showed that approximately one third of the cats with the AA variant of the AGXT2 gene have stones, that chronic kidney disease (CKD) is more common in cats with stones, and that having stones results in a shorter lifespan. A discriminant variable selection process was performed to determine the complete blood count, serum biochemistries, and serum metabolomic factors that best discriminated among the three genotypes (AA, AG, GG) and between cats forming stones and non-stone formers. Several of the highly ranked discriminating factors included metabolites related to decreased aminotransferase activity in cats with the AA variant of the AGXT2 gene. Another factor that ranked highly for discriminating between stone formers and non-stone formers contained lipid metabolites, consisting of multiple sphingomyelin species and cholesterol.

CONCLUSIONS

These findings support the results of feeding studies in cats, whereby CKD cats fed food supplemented with betaine and prebiotics have experienced an increase in total body mass, reduced uremic toxins, and altered sphingomyelin concentrations.

Association of serum soluble α‑klotho with risk of kidney stone disease: a population-based cross-sectional study

BACKGROUND

The aim of the study was to explore the association of serum soluble klotho with kidney stone disease (KSD) in the general population over the age of 40 years in the United States.

METHODS

We integrated the data in National Health and Nutrition Examination Survey from 2007 to 2016 years. The relationship between serum soluble α‑klotho and prevalence of KSD was analyzed by constructing weighted multivariable logistic regression model, restricted cubic spline (RCS) curve, and subgroup analyses.

RESULTS

In the study, a total of 13,722 individuals were included in our study. A U-shaped association between serum soluble klotho and the risk of KSD was shown by the RCS curve (P value for nonlinear < 0.05). In the full adjusted model, compared with the lowest quartile of serum soluble α‑klotho, the adjusted odd ratios (95% confidence intervals) for KSD across the quartiles were (0.999 (0.859, 1.164), 1.005 (0.858, 1.176), and 1.061 (0.911, 1.235)). Subgroup analyses also showed that the U-shaped association of serum soluble α‑klotho with KSD was found among subjects who were age < 60 years, female or male, with or without hypertension, and BMI ≥ 30 kg/m2.

CONCLUSIONS

Our findings suggested that serum klotho levels had a U-shaped correlation with risk of KSD. When the Klotho level is at 818.66 pg/mL, prevalence of KSD is lowest. Therefore, maintaining a certain level of serum soluble α‑klotho could prevent the occurrence of KSD.

Urinary stone disease: closing the heritability gap by challenging conventional Mendelian inheritance

Urinary stone disease is based on gene-environment interaction with an almost 50% heritability. Despite all efforts from exome-sequencing and genome-wide association studies, the genetic factors making up for observed heritability have been incompletely characterized. The study by Sadeghi-Alavijeh et al. leverages the invaluable resources of the 100,000 Genomes Project and the UK Biobank to identify heterozygous rare variants in the phosphate transporter SLC34A3 as a significant factor of urinary stone disease, challenging the traditional concept of Mendelian inheritance.

Identification of mutations in 15 nephrolithiasis-related genes leading to a molecular diagnosis in 85 Chinese pediatric patients

BACKGROUND

The aim of this study was to describe the genotypic and phenotypic characteristics of Chinese pediatric patients with hereditary nephrolithiasis.

METHODS

Whole-exome sequencing (WES) was performed on 218 Chinese pediatric patients with kidney stones, and genetic and clinical data were collected and analyzed retrospectively.

RESULTS

The median age at onset in our cohort was 2.5 years (age range, 0.3-13 years). We detected 79 causative mutations in 15 genes, leading to a molecular diagnosis in 38.99% (85/218) of all cases. Monogenic mutations were present in 80 cases, and digenic mutations were present in 5 cases; 34.18% (27/79) of mutations were not included in the databases. Six common mutant genes, i.e., HOGA1, AGXT, GRHPR, SLC3A1, SLC7A9, and SLC4A1, were found in 84.71% of the patients overall. Furthermore, three mutations (A278A, c.834_834 + 1GG > TT, and C257G) in HOGA1, two mutations (K12QfX156 and S275RfX28) in AGXT, and one mutation (C289DfX22) in GRHPR represented hotspot mutations. The patients with HOGA1 mutations had the earliest onset age (0.8 years), followed by those with SLC7A9 (1.8 years), SLC4A1 (2.7 years), AGXT (4.3 years), SLC3A1 (4.8 years), and GRHPR (8 years) mutations (p = 0.002). Nephrocalcinosis was most commonly observed in patients with AGXT gene mutations.

CONCLUSIONS

Fifteen causative genes were detected in 85 Chinese pediatric patients with kidney stone diseases. The most common mutant genes, novel mutations, hotspot mutations, and genotype-phenotype correlations were also found. This study contributes to the understanding of genetic profiles and clinical courses in pediatric patients with hereditary nephrolithiasis. A higher resolution version of the Graphical abstract is available as Supplementary information.

Relationship between Serum Selenium Level and Self-Reported History of Kidney Stone

A relationship may exist between selenium and kidney calculi, but there is a lack of research in this field at present. Our study explored the relationship between the serum selenium level and a medical history of adult kidney calculi. We utilized data from the National Health and Nutrition Examination Survey conducted between 2011 and 2016. Participants self-reported their history of kidney stones, while serum selenium levels were measured using inductively coupled plasma dynamic reaction cell mass spectrometry. Our findings indicate a negative correlation between serum selenium levels and the risk of kidney stone history. In the multiple-adjusted model, the lowest serum selenium level group had a higher risk than the other groups. The odds ratio (95% confidence interval) of ever having kidney stones for the highest serum selenium level group was 0.54 (0.33-0.88). In the results of stratified analysis, this relationship was still significant in the groups of women and those 40-59 years. We also found that as a nonlinear dose-response relationship between serum selenium levels and the history of kidney stones disease. In our research, we found that people with higher serum selenium levels had a lower risk of having a history of kidney stones. We concluded that selenium may have a protective effect on kidney stones. In the future, more population studies are needed to explore the relationship between selenium and kidney stones.

Past, present and future of genomics for kidney stone disease

PURPOSE OF REVIEW

To summarize the latest findings and developments in genomics for kidney stone disease (KSD) that help to understand hereditary pathomechanisms, identify high risk stone formers, provide early treatment and prevent recurrent kidney stone formation.

RECENT FINDINGS

Several gene loci associated to KSD have presently been discovered in large Genome-wide association studies. Monogenic causes are rare, but are thought to have higher penetrance, while polygenic causes are more frequent with less penetrance. Although there is a great effort identifying genetic causes of KSD, targeted therapies are scarce.

SUMMARY

There have been great advancements in genetic research in identifying genetic variants associated with KSD. Identifying these variants and understanding the underlying pathophysiology will not only provide individual risk assessment but open the way for new treatment targets and preventive care strategies.

Perioperative Fast-Track Surgery Nursing Intervention for Patients with Kidney Stone Disease under Computed Tomography Imaging

This research aims to analyze the clinical intervention effect of perioperative fast-track surgery (FTS) nursing on patients with kidney stone disease (KSD) under computed tomography (CT) imaging. One-hundred KSD patients were selected as research objects and grouped after CT examination. These objects were randomly divided into a research group (FTS nursing intervention, n = 50) and a control group (general routine nursing intervention, n = 50). The preoperative psychological status of patients was compared between the two groups, using Self-rating Anxiety Scale and Self-rating Depression Scale. The hunger and thirst situations were compared using Numerical Rating Scale; postoperative recovery time, incidence of complications, and nursing satisfaction were also compared. The high-density shadow could be clearly observed in the right kidney of the patients in the CT imaging examination. The nursing outcomes suggested that there was no notable difference in hunger between the two groups, and anxiety, depression, and thirst in the research group were highly better than those in the control group (P < 0.01). The time of the first exhaust, the time of body temperature returning to normal, the time of getting out of bed, and the length of hospital stay in the research group were all shorter than those in the control group (P < 0.05). The total postoperative satisfaction of the research group (98.00%) was greatly better than the 88.00% in the control group (P < 0.05). As the FTS concept was applied in the perioperative nursing of KSD patients under CT imaging, the preoperative and postoperative negative emotions of patients could be improved. Thereby, the postoperative recovery rate of patients was promoted, postoperative complications and patients' pain were reduced, and the postoperative quality of life of patients was also improved.

Construction of a ternary component chip with enhanced desorption efficiency for laser desorption/ionization mass spectrometry based metabolic fingerprinting

Introduction: In vitro metabolic fingerprinting encodes diverse diseases for clinical practice, while tedious sample pretreatment in bio-samples has largely hindered its universal application. Designed materials are highly demanded to construct diagnostic tools for high-throughput metabolic information extraction. Results: Herein, a ternary component chip composed of mesoporous silica substrate, plasmonic matrix, and perfluoroalkyl initiator is constructed for direct metabolic fingerprinting of biofluids by laser desorption/ionization mass spectrometry. Method: The performance of the designed chip is optimized in terms of silica pore size, gold sputtering time, and initiator loading parameter. The optimized chip can be coupled with microarrays to realize fast, high-throughput (∼second/sample), and microscaled (∼1 μL) sample analysis in human urine without any enrichment or purification. On-chip urine fingerprints further allow for differentiation between kidney stone patients and healthy controls. Discussion: Given the fast, high throughput, and easy operation, our approach brings a new dimension to designing nano-material-based chips for high-performance metabolic analysis and large-scale diagnostic use.

Use of whole-exome sequencing to identify novel monogenic gene mutations and genotype-phenotype correlations in Chinese Han children with urolithiasis

The incidence of urolithiasis (UL) in children has been increasing. Although the pathogenesis of pediatric UL is controversial and remains unclear, multiple monogenic causes of UL have been identified. We aim to investigate the prevalence of inherited UL causes and explore the genotype-phenotype correlation in a Chinese pediatric group. In this study, we analyzed the DNA of 82 pediatric UL patients using exome sequencing (ES). The data of metabolic evaluation and genomic sequencing were subsequently analyzed together. We detected 54 genetic mutations in 12 of 30 UL-related genes. A total of 15 detected variants were described as pathogenic mutations, and 12 mutations were considered likely pathogenic. Molecular diagnoses were made in 21 patients with pathogenic or likely pathogenic variants. Six novel mutations that were not previously reported were identified in this cohort. Calcium oxalate stones were detected in 88.9% cases (8/9) with hyperoxaluria-related mutations, while 80% of individuals (4/5) with cystinuria-causing defects were diagnosed with cystine stones. Our study highlights the significant genetic abnormalities in pediatric UL and demonstrates the diagnostic power of ES for screening patients with UL.