The copy number variation landscape of congenital anomalies of the kidney and urinary tract

Abstract

Congenital anomalies of the kidney and urinary tract (CAKUT) are a major cause of pediatric kidney failure. We performed a genome-wide analysis of copy number variants (CNVs) in 2,824 cases and 21,498 controls. Affected individuals carried a significant burden of rare exonic (that is, affecting coding regions) CNVs and were enriched for known genomic disorders (GD). Kidney anomaly (KA) cases were most enriched for exonic CNVs, encompassing GD-CNVs and novel deletions; obstructive uropathy (OU) had a lower CNV burden and an intermediate prevalence of GD-CNVs; and vesicoureteral reflux (VUR) had the fewest GD-CNVs but was enriched for novel exonic CNVs, particularly duplications. Six loci (1q21, 4p16.1-p16.3, 16p11.2, 16p13.11, 17q12 and 22q11.2) accounted for 65% of patients with GD-CNVs. Deletions at 17q12, 4p16.1-p16.3 and 22q11.2 were specific for KA; the 16p11.2 locus showed extensive pleiotropy. Using a multidisciplinary approach, we identified TBX6 as a driver for the CAKUT subphenotypes in the 16p11.2 microdeletion syndrome.

FIGURE 1.

Burden of rare copy number variations in CAKUT cases compared to controls. A, B. Burden of large, rare, exonic CNVs in all CAKUT cases and controls (A) and in KA and VUR cases and controls (B). C, D. Prevalence of known genomic disorders (C) and novel likely pathogenic copy number variants (D) in CAKUT cases and controls. Deletions are marked in red, duplications are marked in green. KA, OU, PUV and DCS were significantly enriched for genomic disorders. The genomic architecture of KA cases was predominantly devised by deletions, while the genetic basis of PUV and DCS cases mostly constituted of duplications. CAKUT = congenital anomalies of the kidney and urinary tract, DCS = duplex collecting system, EK-HK = ectopic kidney/horseshoe kidney, ERM = extrarenal malformations, KA = kidney anomaly, Mb = megabases, OU = obstructive uropathy, PUV = posterior urethral valves, VUR = vesicoureteral reflux.

FIGURE 2.

Common genomic disorders loci in CAKUT cases and their prevalence in controls. Deletions are marked in red, duplications are marked in green. Among these common genomic loci, the chromosome 16p11.2 locus showed high pleiotropy, whereas the Wolf-Hirschhorn, 17q12 and 22q11.2 loci were mostly identified in KA cases. CAKUT = congenital anomalies of the kidney and urinary tract, Ctrls = controls, DCS = duplex collecting system, EK-HK = ectopic kidney/horseshoe kidney, KA = kidney anomaly, LUTM = other lower urinary tract malformation, OU = obstructive uropathy, PUV = posterior urethral valves, RCAD = renal cysts and diabetes, VUR = vesicoureteral reflux.

FIGURE 3.

Analysis of urinary tract phenotypes in Tbx6^rv/- mutants. A-C. Whole mounts of urogenital tracts isolated from E18.5 wild type (A) and Tbx6^rv/- mutants showing severe bilateral renal hypoplasia (B) and unilateral renal agenesis with contralateral renal hypoplasia (C); K = kidney, U = ureter, B = bladder. D-F. H&E stained sagittal sections from E18.5 wild type (D) and Tbx6^rv/- mutants (E,F). In the wild type it is appreciable the normal developing nephrogenic zone (nz) and kidney medulla (m). The arrows in E point to the dilated renal pelvis (upper arrow) and ureter (lower arrow), which are indicative of hydronephrosis and hydroureter, respectively. In E the kidney parenchyma also appears severely hypoplastic. The arrowhead in F points to the rudimentary kidney, which is embedded in paraspinal musculature. Few dilated tubule and microcysts are present. G-I. H&E stained kidney from and E15.5 wild type embryo (G) and E15.5 Tbx6^rv/- mutant embryos (H, I). The mutants show moderate to severe hypoplasia with reduction of nephrogenic zone (nz) (H); the arrowhead indicated severely underdeveloped kidney tissue with tubule dilation and microcysts (I). J-L. H&E histological analysis of kidneys from E13.5 wild type embryos (J) and Tbx6^rv/- mutants (K,L). The arrowheads point to the rudimentary kidneys that are embedded in the body wall. M,N. Immunostaining of E11.5 wild type and Tbx6^rv/- mutant embryos stained with Pax2 (red) and Cdh1 (green) showing the ureteric bud (ub) nephron progenitors (np), and nephric duct (nd). Note in the wild type embryo, the ureteric bud has invaded the metanephric mesenchyme and branched, while in the mutant, the ureteric bud has not fully invaded the metanephric mesenchyme.

FIGURE 4.

Analysis of urinary tract phenotypes in Tbx6^rv/rv mutants. A-C. H&E stained sagittal sections from a wild type P0 pup (A) and P0 Tbx6^rv/rv pups (B,C). In the wild type can be appreciated the renal cortex (rc) resulting from the development of the nephrogenic zone; the medulla (m) and the renal pelvis (p). The arrows in B point to the duplicated kidneys. The arrows in C point to hypoplastic kidney and the dilated renal pelvis and proximal ureter. D-F. H&E stained sections from E15.5 wild type embryo (D) and Tbx6^rv/rv mutant embryos (E,F). The arrow in E points to the dilated renal pelvis and proximal ureter. The arrows in F points to the hypoplastic kidney and dilated ureter.