SLC26A1 is a major determinant of sulfate homeostasis in humans

Abstract

Sulfate plays a pivotal role in numerous physiological processes in the human body, including bone and cartilage health. A role of the anion transporter SLC26A1 (Sat1) for sulfate reabsorption in the kidney is supported by the observation of hyposulfatemia and hypersulfaturia in Slc26a1 -knockout mice. The impact of SLC26A1 on sulfate homeostasis in humans remains to be defined. By combining clinical genetics, functional expression assays, and population exome analysis, we identify SLC26A1 as a sulfate transporter in humans and experimentally validate several loss-of-function alleles. Whole-exome sequencing from a patient presenting with painful perichondritis, hyposulfatemia, and renal sulfate wasting revealed a homozygous mutation in SLC26A1 , which has not been previously described to the best of our knowledge. Whole-exome data analysis of more than 5,000 individuals confirmed that rare, putatively damaging SCL26A1 variants were significantly associated with lower plasma sulfate at the population level. Functional expression assays confirmed a substantial reduction in sulfate transport for the SLC26A1 mutation of our patient, which we consider to be novel, as well as for the additional variants detected in the population study. In conclusion, combined evidence from 3 complementary approaches supports SLC26A1 activity as a major determinant of sulfate homeostasis in humans. In view of recent evidence linking sulfate homeostasis with back pain and intervertebral disc disorder, our study identifies SLC26A1 as a potential target for modulation of musculoskeletal health.

Coupling of metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and resulting traits and diseases

“…The observed association is well supported by experimental studies establishing that the encoded Na + -sulfate cotransporter NaS1 (SLC13A1) reabsorbs filtered sulfate at the apical membrane of kidney tubular epithelial cells 37 . Second, we had previously confirmed experimentally that plasma sulfate-associated QVs in SLC26A1 reduced sulfate transport capacity 25 and confirmed a lowest possible P-value of 2e-11 for the aggregate effect of driver variants in SLC26A1 ( Supplementary Figure 8 ). The encoded sulfate transporter SAT1 localizes to basolateral membranes of tubular epithelial cells and works in series with NaS1 to mediate transcellular sulfate reabsorption ( Figure 5a ) 38,39 .…”

“…Interestingly, the missense variant p.Thr185Met in SAT1 exhibited the largest effect on sulfate. We have previously shown experimentally a dominant negative mechanism of this variant 25 , providing another mechanism how heterozygous variants may promote insights into an effectively full loss-of-gene-function. Moreover, our findings for the p.Arg272Cys variant in NaS1 show that even very few, heterozygous copies of a metabolite-prioritized QV can give rise to the detection of homozygous individuals and hitherto unreported disease associations in subsequent larger studies.…”

“…Moreover, we had previously confirmed experimentally heterozygous sulfate-associated QVs in SLC26A1 as loss-of-function alleles and designated the encoded protein as an important player in human sulfate homeostasis. 25 However, experimental studies of each of the detected 2,077 QVs and 73 genes are infeasible, and IEMs are so rare that no homozygous person for a given gene may have been observed yet. We therefore used three orthogonal approaches, examination of hemizygosity, in silico knockout modeling, and investigation of variants prioritized through allelic series, to evaluate whether the observed metabolite-associated heterozygous variants captured similar information about a gene’s function as might be derived from homozygous damaging variants in the respective gene.…”

“…Rare loss-of-function variants in SLC13A1 and SLC26A1 have been linked to individual musculoskeletal phenotypes through IEMs and GWAS 25,41,44,45 . We further investigated the association between the same six functional, sulfate-associated QVs in SLC13A1 and SLC26A1 and musculoskeletal disorders, fractures, and injuries in the UKB (Methods).…”

“…Among these, the stop gained variant p.Arg12*, for which a complete loss-of-function has experimentally been validated 43 , the stop gained substitution p.Trp48*, for which associations with decreased serum sulfate levels 44 and skeletal phenotypes 41 were reported, and the missense variant encoding p.Arg272Cys, located in a splice region, were available in the UKB. For SLC26A1, we selected QVs for which reduced sulfate transport activity had previously been shown 25 , of which p.Leu384Pro, p.Ser358Leu, and p.Thr185Met were available in the UKB. All 6 QVs passed the "90pct10dp" QC filter, defined as at least 90% of all genotypes for a given variant, independent of variant allele zygosity, had a read depth of at least 10 (https://biobank.ndph.ox.ac.uk/ukb/ukb/docs/UKB_WES_AnalysisBestPractices.pdf).…”