A functional variant in NEPH3 gene confers high risk of renal failure in primary hematuric glomerulopathies. Evidence for predisposition to microalbuminuria in the general population.

BACKGROUND: Recent data emphasize that thin basement membrane nephropathy (TBMN) should not be viewed as a form of benign familial hematuria since chronic renal failure (CRF) and even end-stage renal disease (ESRD), is a possible development for a subset of patients on long-term follow-up, through the onset of focal and segmental glomerulosclerosis (FSGS). We hypothesize that genetic modifiers may explain this variability of symptoms. METHODS: We looked in silico for potentially deleterious functional SNPs, using very strict criteria, in all the genes significantly expressed in the slit diaphragm (SD). Two variants were genotyped in a cohort of well-studied adult TBMN patients from 19 Greek-Cypriot families, with a homogeneous genetic background. Patients were categorized as "Severe" or "Mild", based on the presence or not of proteinuria, CRF and ESRD. A larger pooled cohort (HEMATURIA) of 524 patients, including IgA nephropathy patients, was used for verification. Additionally, three large general population cohorts [Framingham Heart Study (FHS), KORAF4 and SAPHIR] were used to investigate if the NEPH3-V353M variant has any renal effect in the general population. RESULTS AND CONCLUSIONS: Genotyping for two high-scored variants in 103 TBMN adult patients with founder mutations who were classified as mildly or severely affected, pointed to an association with variant NEPH3-V353M (filtrin). This promising result prompted testing in the larger pooled cohort (HEMATURIA), indicating an association of the 353M variant with disease severity under the dominant model (p = 3.0x10-3, OR = 6.64 adjusting for gender/age; allelic association: p = 4.2x10-3 adjusting for patients' kinships). Subsequently, genotyping 6,531 subjects of the Framingham Heart Study (FHS) revealed an association of the homozygous 353M/M genotype with microalbuminuria (p = 1.0x10-3). Two further general population cohorts, KORAF4 and SAPHIR confirmed the association, and a meta-analysis of all three cohorts (11,258 individuals) was highly significant (p = 1.3x10-5, OR = 7.46). Functional studies showed that Neph3 homodimerization and Neph3-Nephrin heterodimerization are disturbed by variant 353M. Additionally, 353M was associated with differential activation of the unfolded protein response pathway, when overexpressed in stressed cultured undifferentiated podocyte cells, thus attesting to its functional significance. Genetics and functional studies support a "rare variant-strong effect" role for NEPH3-V353M, by exerting a negative modifier effect on primary glomerular hematuria. Additionally, genetics studies provide evidence for a role in predisposing homozygous subjects of the general population to micro-albuminuria

Clinico-pathological correlations in 127 patients in 11 large pedigrees, segregating one of three heterozygous mutations in the COL4A3/ COL4A4 genes associated with familial haematuria and significant late progression to proteinuria and chronic kidney disease from focal segmental glomerulosclerosis

<p><strong>Background.</strong> Heterozygous mutations in the <i>COL4A3/ COL4A4</i> genes are currently thought to be responsible for familial benign microscopic haematuria and maintenance of normal long-term kidney function.</p><p><strong>Methods.</strong> We report on 11 large Cypriot pedigrees with three such mutations. A total of 236 at-risk family members were genetically studied, and 127 (53.8%) carried a heterozygous mutation. Clinico-pathological correlations were available in all of these patients. Renal biopsies in 21 of these patients all showed various stages of focal, segmental glomerulosclerosis (FSGS). Thirteen of these biopsies were also studied with EM and showed thinning of the glomerular basement membrane.</p><p><strong>Results.</strong> Mutation G1334E (<i>COL4A3</i>) was found in six pedigrees, mutation G871C (<i>COL4A3</i>) in four and mutation 3854delG (<i>COL4A4</i>) in one pedigree. Clinical and laboratory correlations in all 127 mutation carriers (MC) showed that microscopic haematuria was the only urinary finding in patients under age 30. The prevalence of 'haematuria alone' fell to 66% between 31 and 50 years, to 30% between 51 and 70 and to 23% over age 71. Proteinuria with CRF developed on top of haematuria in 8% of all MC between 31 and 50 years, to 25% between 51 and 70 years and to 50% over 71 years. Altogether 18 of these 127 MC (14%) developed ESRD at a mean age of 60 years. Two members with different mutations married, and two of their children inherited both mutations and developed adolescent, autosomal recessive Alport syndrome (ATS), confirming that these mutations are pathogenic.</p><p><strong>Conclusions.</strong> Our data confirm for the first time a definite association of heterozygous <i>COL4A3/COL4A4</i> mutations with familial microscopic haematuria, thin basement membrane nephropathy and the late development of familial proteinuria, CRF, and ESRD, due to FSGS, indicating that the term 'benign familial haematuria' is a misnomer, at least in this cohort. A strong hypothesis for a causal relationship between these mutations and FSGS is also made. Benign familial haematuria may not be so benign as commonly thought.</p&gt

Genotype distribution of the studied <i>MYH9</i> variants, by cohort and by severity.

<p>Genotype distribution of the studied <i>MYH9</i> variants, by cohort and by severity.</p

Frequency of COL4A3/COL4A4 mutations amongst families segregating glomerular microscopic hematuria and evidence for activation of the unfolded protein response. Focal and segmental glomerulosclerosis is a frequent development during ageing.

Familial glomerular hematuria(s) comprise a genetically heterogeneous group of conditions which include Alport Syndrome (AS) and thin basement membrane nephropathy (TBMN). Here we investigated 57 Greek-Cypriot families presenting glomerular microscopic hematuria (GMH), with or without proteinuria or chronic kidney function decline, but excluded classical AS. We specifically searched the COL4A3/A4 genes and identified 8 heterozygous mutations in 16 families (28,1%). Eight non-related families featured the founder mutation COL4A3-p.(G1334E). Renal biopsies from 8 patients showed TBMN and focal segmental glomerulosclerosis (FSGS). Ten patients (11.5%) reached end-stage kidney disease (ESKD) at ages ranging from 37-69-yo (mean 50,1-yo). Next generation sequencing of the patients who progressed to ESKD failed to reveal a second mutation in any of the COL4A3/A4/A5 genes, supporting that true heterozygosity for COL4A3/A4 mutations predisposes to CRF/ESKD. Although this could be viewed as a milder and late-onset form of autosomal dominant AS, we had no evidence of ultrastructural features or extrarenal manifestations that would justify this diagnosis. Functional studies in cultured podocytes transfected with wild type or mutant COL4A3 chains showed retention of mutant collagens and differential activation of the unfolded protein response (UPR) cascade. This signifies the potential role of the UPR cascade in modulating the final phenotype in patients with collagen IV nephropathies

Description of cohorts and patients under study.

<p>Please note that cohort B1 is the male only patients with CFHR5 nephropathy.</p><p>MH: Microscopic Hematuria, ESKD: End Stage Kidney Disease, XLAS: X-linked Alport syndrome.</p>1<p>“Mild” patients born before 01/1963. Gender difference (Mild vs Severe) is not significant (p = 0.141).</p>2<p>“Mild” patients born before 01/1975. Gender difference (Mild vs Severe) is significant (p = 0.001).</p>3<p>“Severe” patients: ESKD≤40 yo.</p>4<p>“Mild” patients born before 01/1979. Gender difference (Mild vs Severe) is significant (p = 0.001).</p

Genotype associations for the three <i>MYH9</i> variants genotyped in this study.

<p>P-values were calculated by Pearson Chi-Square test. The whole CFHR5 cohort (B) was genotyped only for <i>MYH9</i> rs11089788, the only SNP that gave p-value close to 0.1 for the male CFHR5 patients (B1).</p>*<p>P-values calculated by Fisher's Exact Test (2-sided) due to existence of genotypes values less than 10.</p>**<p>Odds ratio (OR) cannot be estimated due to zero genotypic values in the “Severe” category.</p

<i>MYH9</i> rs11089788 statistical analysis for a replicate cohort (D) and for the sum of cohorts B and D, that gave statistical significance.

<p>Patients in cohort D belong to families that segregate microscopic hematuria but no known mutation has been found in any of the genes <i>COL4A3</i>, <i>COL4A4</i>, or <i>CFHR5</i>, so far.</p

Mutant <i>COL4A3</i> chains expressed in AB8/13 cultured podocytes demonstrate a trend for increased intracellular retention.

<p>(a) AB8/13 cells were transiently transfected with expression vectors containing wild-type <i>COL4A3</i>-WT or the mutant <i>COL4A3</i> (p.G1334E, p.G871C, p.G484R, p.A587G) cDNAs that included a HA epitope at C-terminus. Single chain expression was measured via Western blot analysis of the cell lysate, 48 h after transfection. No HA antigen was detected in AB8/13 cells transfected with a construct expressing the empty vectors. Shown is a representative Western blot of proteins in cell lysates. (b) All mutant chains show a trend towards increased intracellular retention as compared to the wild type chain, although not reaching significance at the 48 h time point. Shown is densitometry analysis data normalized to tubulin expression. Data are represented as means ± SEM of n≥3 independent experiments.</p

Mutations detected in <i>COL4A3</i> and <i>COL4A4</i> genes.

<p>*these mutations tested negative in an additional collection of 52 patients with chronic kidney disease.</p><p>**this mutation was detected only in a single patient during screening of 153 patient samples. It was subsequently detected in six of 120 Cypriot controls. It is a suspect founder mutation and is under further investigation.</p>+<p>these mutations tested negative in an additional collection of 40 patients with glomerulonephritis of unknown aetiology CY, Cypriot samples; RO, Romanian sample; ND: Not Done; NA: Not applicable.</p><p>Mutations detected in <i>COL4A3</i> and <i>COL4A4</i> genes.</p

Summary of pathogenic <i>COL4A3/A4</i> mutations found in Greek-Cypriot families studied here.

<p>One additional deletion mutation was detected in a Cypriot of Romanian origin.</p><p>Summary of pathogenic <i>COL4A3/A4</i> mutations found in Greek-Cypriot families studied here.</p