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. 2020 Nov;98(5):1308-1322.
doi: 10.1016/j.kint.2020.05.029. Epub 2020 Jun 14.

Common risk variants in NPHS1 and TNFSF15 are associated with childhood steroid-sensitive nephrotic syndrome

Collaborators, Affiliations

Common risk variants in NPHS1 and TNFSF15 are associated with childhood steroid-sensitive nephrotic syndrome

Xiaoyuan Jia et al. Kidney Int. 2020 Nov.

Abstract

To understand the genetics of steroid-sensitive nephrotic syndrome (SSNS), we conducted a genome-wide association study in 987 childhood SSNS patients and 3,206 healthy controls with Japanese ancestry. Beyond known associations in the HLA-DR/DQ region, common variants in NPHS1-KIRREL2 (rs56117924, P=4.94E-20, odds ratio (OR) =1.90) and TNFSF15 (rs6478109, P=2.54E-8, OR=0.72) regions achieved genome-wide significance and were replicated in Korean, South Asian and African populations. Trans-ethnic meta-analyses including Japanese, Korean, South Asian, African, European, Hispanic and Maghrebian populations confirmed the significant associations of variants in NPHS1-KIRREL2 (Pmeta=6.71E-28, OR=1.88) and TNFSF15 (Pmeta=5.40E-11, OR=1.33) loci. Analysis of the NPHS1 risk alleles with glomerular NPHS1 mRNA expression from the same person revealed allele specific expression with significantly lower expression of the transcript derived from the risk haplotype (Wilcox test p=9.3E-4). Because rare pathogenic variants in NPHS1 cause congenital nephrotic syndrome of the Finnish type (CNSF), the present study provides further evidence that variation along the allele frequency spectrum in the same gene can cause or contribute to both a rare monogenic disease (CNSF) and a more complex, polygenic disease (SSNS).

Keywords: glomerulus; nephrotic syndrome; pediatric nephrology; podocyte.

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Figures

Figure 1.
Figure 1.. Flowchart.
Main outline of the discovery genome-wide association study (GWAS), replication of candidate SNPs outside HLA with multiple populations and trans-ethnic meta-analysis. GINS-J: The Research Consortium on Genetics of Childhood Nephrotic Syndrome in Japan, KCHRD: Korean Consortium of Hereditary Renal Diseases in Children, MWPNC: Midwest Pediatric Nephrology Consortium, NPHROVIR: Children Cohort Nephrosis and Virus, ItSpa: Italian and Spanish cohort.
Figure 2.
Figure 2.. Manhattan plot in the discovery GWAS.
In the discovery stage, 987 patients with childhood SSNS and 3,206 healthy adult controls with 6,834,340 autosomal SNVs and INDELs after whole-genome imputation were included. P-values were calculated using logistic regression and adjusting for sex and PC1-4.
Figure 3.
Figure 3.. Regional plots of loci with genome-wide significance (P<5E-08) or marginal genome-wide significance in the discovery stage.
(A) Classical HLA region on chromosome 6 exhibited the most significant association (P-value=2.80E-33). (B) Candidate locus with genome-wide significance on chromosome 19 (P-value=4.94E-20). (C) Candidate locus with genome-wide significance on chromosome 9 (P-value=2.54E-08). (D) Candidate locus with marginal genome-wide significance on chromosome 18 (P=7.68E-08).
Figure 3.
Figure 3.. Regional plots of loci with genome-wide significance (P<5E-08) or marginal genome-wide significance in the discovery stage.
(A) Classical HLA region on chromosome 6 exhibited the most significant association (P-value=2.80E-33). (B) Candidate locus with genome-wide significance on chromosome 19 (P-value=4.94E-20). (C) Candidate locus with genome-wide significance on chromosome 9 (P-value=2.54E-08). (D) Candidate locus with marginal genome-wide significance on chromosome 18 (P=7.68E-08).
Figure 3.
Figure 3.. Regional plots of loci with genome-wide significance (P<5E-08) or marginal genome-wide significance in the discovery stage.
(A) Classical HLA region on chromosome 6 exhibited the most significant association (P-value=2.80E-33). (B) Candidate locus with genome-wide significance on chromosome 19 (P-value=4.94E-20). (C) Candidate locus with genome-wide significance on chromosome 9 (P-value=2.54E-08). (D) Candidate locus with marginal genome-wide significance on chromosome 18 (P=7.68E-08).
Figure 3.
Figure 3.. Regional plots of loci with genome-wide significance (P<5E-08) or marginal genome-wide significance in the discovery stage.
(A) Classical HLA region on chromosome 6 exhibited the most significant association (P-value=2.80E-33). (B) Candidate locus with genome-wide significance on chromosome 19 (P-value=4.94E-20). (C) Candidate locus with genome-wide significance on chromosome 9 (P-value=2.54E-08). (D) Candidate locus with marginal genome-wide significance on chromosome 18 (P=7.68E-08).
Figure 4.
Figure 4.. Glomerular NPHS1 mRNA expression in NEPTUNE cohort
(A) NPHS1 fragments per kilobase million (FPKM) expression comparing samples withand without NPHS1 risk haplotype. Samples with the NPHS1 risk haplotype do not show significantly different expression levels (Wilcox test p=0.39). (B) Allele-specific expression (ASE) comparing samples with and without NPHS1 risk haplotype. ASE = |0.5 − (haplotype A / total reads)|. In patients with the risk alleles, haplotype A harbors all five NPHS1 risk variants, in patients without the risk haplotype, haplotype A is randomly selected from one of their two haplotypes. Sample with less than two heterozygous SNPs or in the bottom 10% of total counts are indicated in gray. Samples with the NPHS1 risk haplotype show significant allele specific expression with lower expression of the risk haplotype (Wilcox test p=9.3E-4).
Figure 4.
Figure 4.. Glomerular NPHS1 mRNA expression in NEPTUNE cohort
(A) NPHS1 fragments per kilobase million (FPKM) expression comparing samples withand without NPHS1 risk haplotype. Samples with the NPHS1 risk haplotype do not show significantly different expression levels (Wilcox test p=0.39). (B) Allele-specific expression (ASE) comparing samples with and without NPHS1 risk haplotype. ASE = |0.5 − (haplotype A / total reads)|. In patients with the risk alleles, haplotype A harbors all five NPHS1 risk variants, in patients without the risk haplotype, haplotype A is randomly selected from one of their two haplotypes. Sample with less than two heterozygous SNPs or in the bottom 10% of total counts are indicated in gray. Samples with the NPHS1 risk haplotype show significant allele specific expression with lower expression of the risk haplotype (Wilcox test p=9.3E-4).

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