Genetic testing in renal stone disease 15% of stone formers have a molecular genetic cause
nuances of the underlying NGS technologies are not essential knowledge as both provide excellent and comparable diagnostic yields. The clear advantage of genome wide approaches allows the reanalysis of data over time and the ability to incorporate new knowledge regarding gene variants into its interpretation [11, 12]. My personal approach is to, following informed consent, take a single EDTA blood sample for DNA storage from every recurrent kidney stone former to allow genetic investigations to proceed if there are features suggesting a monogenic cause. The yield of a NGS panel approach will be 10-20% but the use of exome or genome sequencing will allow alternative predictive genetic data to be generated and will provide valuable data to allow future understanding of this important disease. Recruiting kidney stone forming patients to research registries (such as ERKNet), databases and biobanks remains an important priority if we are to gain the benefits of the genomic revolution. "Recruiting kidney stone forming patients to research registries, databases and biobanks remains an important priority." Genetic versus environmental factors in kidney stone disease It is clear that there is interplay of both genetic and environmental factors in kidney stone formation. These interact with both urinary inhibitors of stone formation (such as citrate, magnesium, pyrophosphate, and others) as well as urinary promoters of stone formation (such as calcium, phosphate, urate, cystine) [13] which will tip the balance towards calculus formation. A good example of this interplay would be 1,25 dihydroxy Vitamin D levels. These are influenced by diet, lifestyle, ethnicity, exposure to sunlight as well as metabolic processes withing the liver and kidney, which are undertaken by key enzymes, the expression of which are genetically determined. Vitamin D overdose leading to kidney stone disease is unusual, but in the context of a mutation in CYP24A1 encoding CYP24A1, the enzyme which inactivates 1,25 dihydroxy Vitamin D, a phenotype of hypercalcaemia, hypercalciuria and kidney stones is seen [14]. Aside from full blown pathogenic variant in CYP24A1, more subtle variants, known as polymorphisms, (or risk alleles) may play a role in risk of calcium stone formers [15]. We have therefore become good at detecting and defining rare disease variants that account for monogenic kidney stone disease. The variants are defined as causal and have, in most cases, have a defined pathophysiology. At the alternate end of the
Clearly, we are not at a stage where blanket genetic testing can provide all the answers but a reasonable approach to a recurrent kidney stone formed would be to consider the chemical composition of the stone, whether there is a relevant family history of kidney stone disease, the age of onset of stone disease and the biochemical features of serum and urine. These considerations and tests often then point towards an underlying genetic condition. Monogenic disorders such as cystinuria, primary hyperoxaluria, and APRT deficiency, all may lead to frequent and recurrent stones, chronic kidney disease and a risk of kidney failure. Sometimes there may be relevant extra renal manifestations such as deafness (e.g. distal renal tubular acidosis), oxalosis of tissues (e.g. primary hyperoxaluria), and bone disease (e.g. hypophosphatemia rickets with hypercalciuria). Biochemical abnormalities detected on 24-hour urine testing such as hypercalciuria, hyperoxaluria, and hypocitraturia may all have underlying monogenic causes and genetic testing is an effective means of identifying these disorders. Is genetic testing worthwhile and how do I do it? There is a growing list of monogenic causes of stone disease which includes over 35 rare inherited disorders. A previous study identified a molecular generic cause in 15% of stone formers when applying a next generation sequencing panel to a cohort of 268 patients with stones or nephrocalcinosis [8]. This study pointed to the immediate and practical implications of a genetic diagnosis, confirming the clinical diagnosis in 60% of cases but in 40% provided new diagnostic and practical implications which allowed targeted medical therapies and approaches to be used for stone treatment and prevention. The findings were replicated in other studies showing 17% solve rate in paediatric cohorts of stone formers [9] and 30% solve rate in a cohort of young stone forms who manifested phenotypes before 25 years of age [10]. "There is a family history of stones in up to 37% of kidney stone formers and the heritability has been estimated to be up to 60%." The typical approach when genetically investigating a recurrent stone former would be to use next generation sequencing (NGS) to perform a targeted gene panel for known causes of inherited kidney stones. This method is obviously resource dependent, but the cost of such assays are rapidly decreasing to less than 500 Euro. Alternative approaches of whole exome and whole genome sequencing with the application of virtual gene panels are also rapidly entering clinical practice. The
spectrum, we have also become adept at genome wide association studies (GWAS) that are able to examine large populations and identify common genetic variants that have tiny but accumulative effects on risk of kidney stone disease. These genetic variants can be gathered and used to form polygenic risk scores. What remains fascinating, is that many of these common genetic risk alleles are in or nearby genes implicated in the rare monogenic stone diseases. Finally, there is the middle ground between monogenic and GWAS identified variants where genetic sequencing of carefully phenotyped populations, such as those in the UKBiobank, allows genetic variants that are intermediate (i.e. not common or rare) to be examined and this approach has successfully identified coding gene variants with moderate to large effects sizes [16]. A good example of this are variants in SLC34A1 which can be causal for rare monogenic kidney stone disease as well as acting as moderate and minor risk alleles for calcium stone formation. These variants may therefore explain the missing heritability of kidney stones (Figure 1). In conclusion, analogous to sending kidney stones for biochemical analysis, performing a genetic screen for kidney stone formers provides valuable information. A monogenic disorder will be identifiable in over 15% of cases. In cases where a monogenic disorder is excluded, risk alleles may be identified and going forward will contribute enormously to our understanding of the pathogenicity of kidney stone disease. Genetic studies allow a more precise and personalised approach to stone formers. I urge urologists to interact with nephrologists and clinical geneticists interested in kidney stone disease to maximise the gains from these very affordable and increasingly powerful genetic testing approaches. References 1. Connor, H., Medieval uroscopy and its representation on misericords – Part 1: uroscopy. Clinical Medicine, 2001. 1(6): p. 507-509. 2. Nöske, H.D., [The "Pisse-Prophet" or the "English fortune-teller from urine". A critical book on uroscopy bei Thomas Brian]. Urologe A, 2005. 44(9): p. 1062-3. 3. Hill, F. and J.A. Sayer, Precision medicine in renal stone-formers. Urolithiasis, 2019. 47(1): p. 99-105. 4. Scales, C.D., Jr., et al., Prevalence of kidney stones in the United States. Eur Urol, 2012. 62(1): p. 160-5. 5. Goldfarb, D.S., et al., A twin study of genetic and dietary influences on nephrolithiasis: a report from the Vietnam Era Twin (VET) Registry. Kidney Int, 2005. 67(3): p. 1053-61. 6. Sayer, J.A., Progress in Understanding the Genetics of Calcium-Containing Nephrolithiasis. J Am Soc Nephrol, 2017. 28(3): p. 748-759. 7. Stechman, M.J., N.Y. Loh, and R.V. Thakker, Genetics of hypercalciuric nephrolithiasis: renal stone disease. Ann N Y Acad Sci, 2007. 1116: p. 461-84. 8. Halbritter, J., et al., Fourteen monogenic genes account for 15% of nephrolithiasis/nephrocalcinosis. J Am Soc Nephrol, 2015. 26(3): p. 543-51. 9. Braun, D.A., et al., Prevalence of Monogenic Causes in Pediatric Patients with Nephrolithiasis or Nephrocalcinosis. Clin J Am Soc Nephrol, 2016. 11(4): p. 664-72. 10. Daga, A., et al., Whole exome sequencing frequently detects a monogenic cause in early onset nephrolithiasis and nephrocalcinosis. Kidney Int, 2018. 93(1): p. 204-213. 11. Cirino, A.L., et al., A Comparison of Whole Genome Sequencing to Multigene Panel Testing in Hypertrophic Cardiomyopathy Patients. Circ Cardiovasc Genet, 2017. 10(5). 12. Hocking, L.J., et al., Genome sequencing with gene panel-based analysis for rare inherited conditions in a publicly funded healthcare system: implications for future testing. Eur J Hum Genet, 2022. 13. Halbritter, J., Genetics of kidney stone disease-Polygenic meets monogenic. Nephrol Ther, 2021. 17s: p. S88-s94. 14. Willows, J. and J.A. Sayer, CYP24A1 mutations and hypervitaminosis D. Clin Med (Lond), 2019. 19(1): p. 92-93. 15. Howles, S.A., et al., Genetic variants of calcium and vitamin D metabolism in kidney stone disease. Nat Commun, 2019. 10(1): p. 5175. 16. Sun, B.B., et al., Genetic associations of protein-coding variants in human disease. Nature, 2022. 603(7899): p. 95-102.
Prof. John Sayer Professor of Renal Medicine Translational and Clinical Research Institute, Newcastle University (GB)
Urology is an attractive surgical specialty and has moved rapidly with innovation and precision therapies. Sub-specialisation into endourology and kidney stones provides the urologist opportunities to become adept at preventative therapies and personalised approaches for improved patient outcomes. The consideration of the urine’s colour, odour and composition was an ancient art [1, 2] which now has been taken forward into modern day urology, especially kidney stone disease. The application of modern-day genetics and genomics to kidney stone disease provides a robust assessment tool for the diagnosis of genetic diseases and genetic risk factors underlying kidney stone disease. The benefits of a molecular genetic diagnosis There are numerous benefits of undertaking a molecular genetic approach to kidney stones. A precision medicine diagnosis can be made, which allows a tailored plan for patient management, focussing on prevention of recurrent stones [3]. A molecular genetic diagnosis provides insights into disease pathogenesis and allows novel medical therapies to be designed. It also allows targeted screening of at-risk relatives and family members who may also be predisposed to kidney stone disease. When and why perform genetic investigations? Kidney stones are common, with 1 in 11 people having a stone within their lifetime, and over 50% recurrence risk within 5-10 years. Kidney stones predominantly affect working age adults, 10% require hospital admission and 5% require urological surgical intervention. Stone incidence is also increasing, and rates in females are catching up with males [4], pointing to the fact that both environmental and genetic factors are interacting to increase risk. It is well known that kidney stones cluster within families, there is a family history of stones in up to 37% of kidney stone formers and the heritability has been estimated to be up to 60% [5]. 80% of kidney stones are calcium oxalate containing or calcium phosphate containing [6] and up to 70% of people with hypercalciuria who form kidney stones have a relative with kidney stones disease [7].
Sunday 12 March 14:33 - 14:43 Personalised stone approach through innovation Pink Area, Coral 6
Figure 1: Genetic studies in kidney stone formers The combination of identifying rare monogenic stone disease variants as well as intermediate and common risk alleles allows a diagnostic and research pathway to lead towards precision medicine and personalised therapies for patients.
European Urology Today
February/March 2023
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