Integration of Genetic Testing and Pathology for the Diagnosis of Adults with FSGS

Abstract

Background and objectives: FSGS and nephrotic syndrome studies have shown that single gene causes are more likely to be found in pediatric cases than adults. Consequently, many studies have examined limited gene panels in largely pediatric cohorts.

Design, setting, participants, & measurements: Whole-exome sequencing was performed in adults with FSGS diagnosed between 1976 and 2017 in the Toronto GN Registry. An expanded panel of 109 genes linked to FSGS, glomerular basement membrane abnormalities, as well as causes of pediatric ESKD including congenital abnormalities of the kidney and urinary tract (CAKUT) and nephronophthisis, were examined.

Results: The cohort was composed of 193 individuals from 179 families. Nearly half (49%) developed ESKD at a mean age of 47±17 years. The genetic diagnostic rate was 11%. Of definitely pathogenic variants, 55% were in COL4A (A3/A4/A5), 40% were in podocyte genes, and 5% were in CAKUT genes. Many, but not all individuals with COL4A definitely pathogenic variants had some evidence of glomerular basement membrane abnormalities. The estimated mean survival/age of kidney failure for individuals with COL4A definitely pathogenic variants was 58 years (95% confidence interval, 49 to 69), far later than what has been reported in the literature. Likely pathogenic variants were identified in an additional 9% of the cohort, with most in COL4A. Correlation with glomerular basement membrane morphology suggested a causal role for at least some of these likely pathogenic variants.

Conclusions: Even with an expanded gene panel, we find that COL4A disorders are the leading monogenic cause in adults diagnosed with FSGS.

Podcast: This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2019_01_15_CJASNPodcast_19_02_.mp3.

Keywords: Cohort Studies; FSGS; Genetic Testing; Glomerular Basement Membrane; Kidney Failure, Chronic; Podocytes; Registries; Renal Insufficiency; Urogenital Abnormalities; Whole Exome Sequencing; glomerulonephritis; human genetics; idiopathic nephrotic syndrome; kidney; nephrotic syndrome; renal development; type 4A collagen; vesico-ureteral reflux.

Graphical abstract

Figure 1.

Distribution of gene groups in definitely and likely pathogenic variants reveal that COL4A is leading single gene cause. The overall genetic diagnostic rate was 11% (20 out of 179) in the case series when only considering definitely pathogenic variants. There were (A) 20 definitely pathogenic, (B) 18 likely pathogenic, and (C) 15 possibly pathogenic variants identified. Of the (A) definitely pathogenic and (B) likely pathogenic variants, the highest percentage was in COL4A3/A4/A5, followed by podocyte then CAKUT genes. A minority of likely pathogenic and (C) possibly pathogenic variants were also found in the NPHP genes. Numbers in graph represent percentage.

Figure 2.

Kaplan-Meier plots demonstrating that patients with pathogenic variants in genes expressed in the podocyte or associated with development defects had a trend toward an earlier age at disease onset and ESKD compared to other subgroups, although none of the pairwise comparisons were significant. The lowest P values achieved were for age at ESKD for podocyte/developmental defects compared with no proven genetic basis subgroup (P=0.06), and COL4A compared with no proven genetic basis subgroup (P=0.06). COL4A, COL4A subgroup; NG, no proven genetic basis subgroup; Podocyte, podocyte and kidney development defect subgroup.

Figure 3.

Kidney pathology in COL4A-associated FSGS often demonstrate glomerular basement membrane abnormalities. Female patient (6062) with COL4A3-associated disease showing (A) segmental scarring (periodic acid–Schiff staining, ×20 magnification), and on (B) ultrastructural examination, diffusely thin glomerular basement membranes, and extensive podocyte foot process effacement, at approximately 80% (×10,000 magnification). Female patient (6251) with NPHS2-associated disease showing (C) enlarged glomeruli (periodic acid–Schiff staining, ×10 magnification) and one glomerulus with a segmental scar (not shown). (D) Ultrastructural examination shows normal thickness glomerular basement membranes and diffuse podocyte foot process effacement, at approximately 90% (×6000 magnification).

Figure 4.

Genetic testing and pathology can be complementary tests to improve interpretation. Kidney pathology in a female (7939) with a likely pathogenic variant in COL4A3. (A) The glomeruli show mildly thickened capillary walls and no segmental scarring (in 53 glomeruli available for light microscopy; periodic acid-Schiff staining, x40 magnification). (B) Ultrastructural examination confirms thickened glomerular basement membranes, at approximately two-fold, and demonstrates extensive podocyte foot process effacement, at approximately 80% (×4000 magnification).