SLC17 transporters mediate renal excretion of Lac-Phe in mice and humans

N-lactoyl-phenylalanine (Lac-Phe) is a lactate-derived metabolite that suppresses food intake and body weight. Little is known about the mechanisms that mediate Lac-Phe transport across cell membranes. Here we identify SLC17A1 and SLC17A3, two kidney-restricted plasma membrane-localized solute carriers, as physiologic urine Lac-Phe transporters. In cell culture, SLC17A1/3 exhibit high Lac-Phe efflux activity. In humans, levels of Lac-Phe in urine exhibit a strong genetic association with the SLC17A1-4 locus. Urine Lac-Phe levels are also increased following a Wingate sprint test. In mice, genetic ablation of either SLC17A1 or SLC17A3 reduces urine Lac-Phe levels. Despite these differences, both knockout strains have normal blood Lac-Phe and body weights, demonstrating that urine and plasma Lac-Phe pools are functionally and biochemically de-coupled. Together, these data establish SLC17 family members as the physiologic urine transporters for Lac-Phe and uncover a biochemical pathway for the renal excretion of this signaling metabolite.

Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine

The kidneys operate at the interface of plasma and urine by clearing molecular waste products while retaining valuable solutes. Genetic studies of paired plasma and urine metabolomes may identify underlying processes. We conducted genome-wide studies of 1,916 plasma and urine metabolites and detected 1,299 significant associations. Associations with 40% of implicated metabolites would have been missed by studying plasma alone. We detected urine-specific findings that provide information about metabolite reabsorption in the kidney, such as aquaporin (AQP)-7-mediated glycerol transport, and different metabolomic footprints of kidney-expressed proteins in plasma and urine that are consistent with their localization and function, including the transporters NaDC3 (SLC13A3) and ASBT (SLC10A2). Shared genetic determinants of 7,073 metabolite-disease combinations represent a resource to better understand metabolic diseases and revealed connections of dipeptidase 1 with circulating digestive enzymes and with hypertension. Extending genetic studies of the metabolome beyond plasma yields unique insights into processes at the interface of body compartments.

SLC26A1 is a major determinant of sulfate homeostasis in humans

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.

Genome-wide studies reveal factors associated with circulating uromodulin and its relationships to complex diseases

Uromodulin (UMOD) is a major risk gene for monogenic and complex forms of kidney disease. The encoded kidney-specific protein uromodulin is highly abundant in urine and related to chronic kidney disease, hypertension, and pathogen defense. To gain insights into potential systemic roles, we performed genome-wide screens of circulating uromodulin using complementary antibody-based and aptamer-based assays. We detected 3 and 10 distinct significant loci, respectively. Integration of antibody-based results at the UMOD locus with functional genomics data (RNA-Seq, ATAC-Seq, Hi-C) of primary human kidney tissue highlighted an upstream variant with differential accessibility and transcription in uromodulin-synthesizing kidney cells as underlying the observed cis effect. Shared association patterns with complex traits, including chronic kidney disease and blood pressure, placed the PRKAG2 locus in the same pathway as UMOD. Experimental validation of the third antibody-based locus, B4GALNT2, showed that the p.Cys466Arg variant of the encoded N-acetylgalactosaminyltransferase had a loss-of-function effect leading to higher serum uromodulin levels. Aptamer-based results pointed to enzymes writing glycan marks present on uromodulin and to their receptors in the circulation, suggesting that this assay permits investigating uromodulin's complex glycosylation rather than its quantitative levels. Overall, our study provides insights into circulating uromodulin and its emerging functions.

MO048: Genome-wide studies reveal factors associated with circulating uromodulin and its relations with complex diseases

BACKGROUND AND AIMS

UMOD is a major risk gene for monogenic and complex forms of kidney disease. The encoded kidney-specific protein uromodulin is the most abundant protein in urine and related to chronic kidney disease, hypertension and pathogen defense. Through basolateral release from kidney epithelial cells, uromodulin also reaches the blood, where its function is largely unknown. To gain insights into potential systemic roles, we performed genome-wide screens of circulating uromodulin in seven cohorts using two complementary assays.

METHOD

Separate genome-wide association study meta-analyses for circulating uromodulin were conducted for the antibody-based assay (five cohorts, N = 13 985) and the aptamer-based SOMAscan assay (two cohorts, N = 18 070). Genome-wide significant loci were placed into their functional genomic context using RNA-seq, ATAC-seq and Hi-C data generated from primary human kidney tissue. An array of downstream genetic analyses was then performed for significant loci, including fine-mapping, colocalization analyses and gene-by-gene interaction analyses. The B4GALNT2 p.Cys466Arg allele was expressed in MDCK cells and studied by immunofluorescence and Western blotting analyses.

RESULTS

We detected and replicated 13 genome-wide significant loci (P <5e−8; 12 novel). At the UMOD locus, functional genomics data of primary human kidney tissue highlighted an upstream regulatory variant with differential accessibility and UMOD transcription in uromodulin-synthesizing kidney cells. Shared association patterns with complex traits, including chronic kidney disease and blood pressure, placed the PRKAG2 locus in the same context as UMOD. Experimental validation of another locus, B4GALNT2, showed that the detected p.Cys466Arg variant of the encoded N-acetylgalactosaminyltransferase has a loss-of-function effect leading to higher serum uromodulin levels. Lastly, our results point to enzymes writing glycan marks present on uromodulin and to their receptors in the circulation.

CONCLUSION

This study provides human genetic evidence of new pathway members of uromodulin and delivers novel insights into its determinants and systemic role in the circulation.

Genetics of osteopontin in patients with chronic kidney disease: The German Chronic Kidney Disease study

Osteopontin (OPN), encoded by SPP1, is a phosphorylated glycoprotein predominantly synthesized in kidney tissue. Increased OPN mRNA and protein expression correlates with proteinuria, reduced creatinine clearance, and kidney fibrosis in animal models of kidney disease. But its genetic underpinnings are incompletely understood. We therefore conducted a genome-wide association study (GWAS) of OPN in a European chronic kidney disease (CKD) population. Using data from participants of the German Chronic Kidney Disease (GCKD) study (N = 4,897), a GWAS (minor allele frequency [MAF]≥1%) and aggregated variant testing (AVT, MAF<1%) of ELISA-quantified serum OPN, adjusted for age, sex, estimated glomerular filtration rate (eGFR), and urinary albumin-to-creatinine ratio (UACR) was conducted. In the project, GCKD participants had a mean age of 60 years (SD 12), median eGFR of 46 mL/min/1.73m2 (p25: 37, p75: 57) and median UACR of 50 mg/g (p25: 9, p75: 383). GWAS revealed 3 loci (p<5.0E-08), two of which replicated in the population-based Young Finns Study (YFS) cohort (p<1.67E-03): rs10011284, upstream of SPP1 encoding the OPN protein and related to OPN production, and rs4253311, mapping into KLKB1 encoding prekallikrein (PK), which is processed to kallikrein (KAL) implicated through the kinin-kallikrein system (KKS) in blood pressure control, inflammation, blood coagulation, cancer, and cardiovascular disease. The SPP1 gene was also identified by AVT (p = 2.5E-8), comprising 7 splice-site and missense variants. Among others, downstream analyses revealed colocalization of the OPN association signal at SPP1 with expression in pancreas tissue, and at KLKB1 with various plasma proteins in trans, and with phenotypes (bone disorder, deep venous thrombosis) in human tissue. In summary, this GWAS of OPN levels revealed two replicated associations. The KLKB1 locus connects the function of OPN with PK, suggestive of possible further post-translation processing of OPN. Further studies are needed to elucidate the complex role of OPN within human (patho)physiology.

pgainsim: an R-package to assess the mode of inheritance for quantitative trait loci in GWAS

MOTIVATION

When performing genome-wide association studies conventionally the additive genetic model is used to explore whether a single nucleotide polymorphism (SNP) is associated with a quantitative trait. But for variants, which do not follow an intermediate mode of inheritance (MOI), the recessive or the dominant genetic model can have more power to detect associations and furthermore the MOI is important for downstream analyses and clinical interpretation. When multiple MOIs are modelled the question arises, which describes the true underlying MOI best.

RESULTS

We developed an R-package allowing for the first time to determine study specific critical values when one of the three models is more informative than the other ones for a quantitative trait locus. The package allows for user-friendly simulations to determine these critical values with predefined minor allele frequencies and study sizes. For application scenarios with extensive multiple testing we integrated an interpolation functionality to determine critical values already based on a moderate number of random draws.

AVAILABILITY AND IMPLEMENTATION

The R-package pgainsim is freely available for download on Github at https://github.com/genepi-freiburg/pgainsim.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Prevalence of common mental disorders among Syrian refugee children and adolescents in Sultanbeyli district, Istanbul: results of a population-based survey

AIMS

Research demonstrates elevated levels of common mental disorders among Syrian refugees, but the majority of studies have, to date, focused on adult populations. This study aims to estimate the prevalence of depression, anxiety and post-traumatic stress disorder (PTSD) among Syrian children and adolescents living in Sultanbeyli district of Istanbul, Turkey.

METHODS

A population-based survey among Syrian children and adolescents aged 8-17 years living in Sultanbeyli district was conducted in 2019, as part of an all-age survey of disability. 80 clusters of 50 participants (all-ages) were selected from the local municipality's refugee registration database using probability proportionate to size sampling. Children aged 8-17 years were assessed for symptoms of common mental disorders using the Child Revised Impact of Event Scale (CRIES-8) and abbreviated versions of the Center for Epidemiologic Studies Depression Scale for Children (CES-DC) and the Screen for Child Anxiety Related Disorders (SCARED).

RESULTS

Of the 852 participants, 23.7% (95% CI 19.9-27.2) screened positive for symptomatic depression, PTSD and anxiety. The prevalence estimates for depression, PTSD and anxiety were 12.5% (95% CI 9.8-15.6), 11.5% (95% CI 9.1-14.4) and 9.2% (95% CI 6.8-12.1), respectively. Depression and PTSD were significantly more common in older adolescents, whilst anxiety and PTSD were significantly more common in girls. Depression was more common in children from poorer households and those who had received no education. Children coming from larger households were less likely to show symptoms of PTSD.

CONCLUSIONS

Syrian refugee children and adolescents are vulnerable to common mental disorders, and culturally appropriate prevention and intervention support are needed for this population.

Arterial properties of the carotid and femoral artery in endurance-trained and paraplegic subjects

In humans, the relationships of blood flow changes to structure, function, and shear rate of conducting arteries have not been thoroughly examined. Therefore, the purpose of this study was to investigate these parameters of the elastic-type, common carotid artery (CCA) and the muscular-type, common femoral artery (CFA) in long-term highly active and extremely inactive individuals, assuming that the impact of activity-induced blood flow changes on conduit arteries, if any, should be seen in these subjects. We examined 21 highly endurance-trained athletes (A), 10 paraplegic subjects (P), and 20 sedentary subjects (S) by means of noninvasive ultrasound. As a result, the CFA diameter and compliance were highest in A (9.7+/-0.81 mm; 1.84 +/-0.54 mm(2)/kPa) and lowest in P (5.9+/-0.7 mm; 0.54+/-0.27 mm(2)/kPa) compared with S (8.3+/-1.0 mm; 0.92+/-0.48 mm(2)/kPa) with P <0.01 among the groups. Both parameters correlated with each other (r = 0.62; P<0.01). Compared with A (378+/-84 s(-1); 37+/-15 s(-1)) and S (356+/-113 s(-1); 36+/-20 s(-1)), the peak and mean shear rates of the CFA were almost or more than doubled in P (588+/-120 s(-1); 89+/-26 s(-1)). In the CCA, only the compliance and peak shear rate showed significant differences among the groups (A: 1.28+/-0.47 mm(2)/kPa, 660+/-138 s(-1); S: 1.04+/-0.27 mm(2)/kPa, 588+/-109 s(-1); P: 0.65+/- 0.22 mm(2)/kPa, 490+/-149 s(-1); P<0.05). In conclusion, the results suggest a structural and functional adaptation in the CFA and a predominantly functional adaptation of the arterial wall properties to differences in the physical activity level and associated exercise-induced blood flow changes in the CCA. The results for humans confirm those from animal experiments. Similar shear rate values of S and P in the CFA support the hypothesis of constant shear stress regulation due to local blood flow changes in humans. On the other hand, the increased shear rate in the CFA in P indicates an at least partially nonphysiological response of the arterial wall in long-term chronic sympathectomy due to a change in local blood flow.