Rumsby, Gill

ABSTRACT Background Primary hyperoxaluria (PH), a rare autosomal recessive disease of oxalate accumulation in the kidneys, is caused by biallelic pathogenic changes in three known genes: AGXT (PH1), GRHPR (PH2) and HOGA1 (PH3). Methods To better understand the overall risk of developing clinical PH, we manually curated and classified PH genetic variants and calculated the estimated genetic prevalence overall and in five ethnic subpopulations using allelic frequencies from the population Genome Aggregation Database (gnomAD version 2.1.1). Results Of the 651 identified PH variants, 273 were found in gnomAD 2.1.1 on the day of download and after reclassification, 208 were determined pathogenic (P) or likely pathogenic (LP) (AGXT, n = 94; GRHPR, n = 46; and HOGA1, n = 68) and a further 65 were classified as rare variants of uncertain significance (VUS). Using P and LP only, estimated carrier frequency was 1:229 for PH1, 1:465 for PH2 and 1:151 for PH3, while genetic prevalence was 1:209 357 for PH1, 1:863 028 for PH2 and 1:90 834 for PH3 (i.e. nearly 5, 1 and 11 per 1 million individuals, respectively). The highest carrier frequencies for AGXT pathogenic variants were in East Asians (1 in 146) and the European non-Finnish population (1 in 187); for GRHPR, South Asians (1 in 313) and the European non-Finnish population (1 in 413); and for HOGA1, Ashkenazi Jewish (1 in 38) and East Asians (1 in 100). The estimated risk of developing PH was ≈1:59 017. Conclusions This careful benchmarking exercise indicates that a significant number of individuals at risk for PH symptoms remain undiagnosed. Since these numbers exceed known diagnosed cases of PH, improved screening and diagnosis of this underestimated disease is necessary.

ABSTRACT Human alanine:glyoxylate aminotransferase (AGT) is a liver peroxisomal enzyme that metabolizes glyoxylate, the oxalate precursor, to glycine. AGT deficiency, due to recessive pathogenic changes in the AGXT gene, results in calcium oxalate accumulation and kidney stones, a condition known as primary hyperoxaluria type 1 (PH1). Most missense variants lead to PH1 by causing AGT misfolding, but their effects manifest differently based on the presence of two polymorphic variants, p.Pro11Leu (p.P11L) and p.Ile340Met (p.I340M), which are usually present in linkage disequilibrium and generate the minor haplotype. While the p.P11L substitution reduces AGT global stability and worsens the effects of pathogenic changes, the p.I340M exerts a stabilizing effect whose role on PH1 pathogenesis has never been elucidated. The p.Ile279Thr (p.I279T) variant is frequent in healthy populations (0.29%), mainly on the major allele, but we present data from six PH1 families (eight patients) suggesting p.I279T as a PH1 pathogenic allele. Interestingly, in these families, p.Thr279 is always associated with p.Leu11 and p.Ile340, thus with a split AGXT haplotype. Analysis of the effects of the p.I279T mutation by in silico predictions, biochemical analyses on purified proteins, and expression in two cellular models of disease ( AGXT1 ‐KO HepG2 and CHO cells) shows that it causes a folding defect that is exacerbated by p.P11L but mitigated by p.I340M, thus explaining why p.Thr279 is pathogenic just on the p.Leu11–p.Ile340 haplotype. These data indicate that genetic screenings for PH1 should document the AGXT haplotype, including its components, to obtain an accurate diagnosis and possible prognostic information.

Patients with primary hyperoxaluria experience kidney stones from a young age and can develop progressive oxalate nephropathy. Progression to kidney failure often develops over a number of years, and is associated with systemic oxalosis, intensive dialysis, and often combined kidney and liver transplantation. There are no therapies approved by the Food and Drug Association. Thus, the Kidney Health Initiative, in partnership with the Oxalosis and Hyperoxaluria Foundation, initiated a project to identify end points for clinical trials. A workgroup of physicians, scientists, patients with primary hyperoxaluria, industry, and United States regulators critically examined the published literature for clinical outcomes and potential surrogate end points that could be used to evaluate new treatments. Kidney stones, change in eGFR, urine oxalate, and plasma oxalate were the strongest candidate end points. Kidney stones affect how patients with primary hyperoxaluria feel and function, but standards for measurement and monitoring are lacking. Primary hyperoxaluria registry data suggest that eGFR decline in most patients is gradual, but can be unpredictable. Epidemiologic data show a strong relationship between urine oxalate and long-term kidney function loss. Urine oxalate is reasonably likely to predict clinical benefit, due to its causal role in stone formation and kidney damage in CKD stages 1–3a, and plasma oxalate is likely associated with risk of systemic oxalosis in CKD 3b–5. Change in slope of eGFR could be considered the equivalent of a clinically meaningful end point in support of traditional approval. A substantial change in urine oxalate as a surrogate end point could support traditional approval in patients with primary hyperoxaluria type 1 and CKD stages 1–3a. A substantial change in markedly elevated plasma oxalate could support accelerated approval in patients with primary hyperoxaluria and CKD stages 3b–5. Primary hyperoxaluria type 1 accounts for the preponderance of available data, thus heavily influences the conclusions. Addressing gaps in data will further facilitate testing of promising new treatments, accelerating improved outcomes for patients with primary hyperoxaluria.