Next-Generation Sequencing (NGS) Analysis Illustrates the Phenotypic Variability of Collagen Type IV Nephropathies

Abstract

Mutations in COL4A3-A5 cause a spectrum of glomerular disorders, including thin basement membrane nephropathy (TBMN) and Alport syndrome (AS). The wide application of next-generation sequencing (NGS) in the last few years has revealed that mutations in these genes are not limited to these clinical entities. In this study, 176 individuals with a clinical diagnosis of inherited kidney disorders underwent an NGS-based analysis to address the underlying cause; those who changed or perfected the clinical diagnosis after molecular analysis were selected. In 5 out of 83 individuals reaching a molecular diagnosis, the genetic result was unexpected: three individuals showed mutations in collagen type IV genes. These patients showed the following clinical pictures: (1) familial focal segmental glomerulosclerosis; (2) end-stage renal disease (ESRD) diagnosed incidentally in a 49-year-old man, with diffuse cortical calcifications on renal imaging; and (3) dysmorphic and asymmetric kidneys with multiple cysts and signs of tubule-interstitial defects. Genetic analysis revealed rare heterozygote/compound heterozygote COL4A4-A5 variants. Our study highlights the key role of NGS in the diagnosis of inherited renal disorders and shows the phenotype variability in patients carrying mutations in collagen type IV genes.

Keywords: COL4; NGS; basal membrane; kidney disease.

Figure 1

The cohort of patients undergoing NGS analysis, including patients that underwent confirmation and change/perfection of diagnosis after molecular screening.

Figure 2

NGS analysis results of the patient cohort, consisting of 176 individuals with inherited kidney disorders. Percentage of genetic diagnoses reached for each category of kidney disease.

Figure 3

Genealogical trees of COL4 patients. The arrows indicate the index cases.

Figure 4

Case 1 kidney biopsy. Light microscopy and immunohistochemistry revealed a classic FSGS with IgM and C3 mesangial deposits, a picture shared with his mother; immunohistochemistry revealed increased deposition of extracellular matrix.

Figure 5

(A) Case 2 computed tomography (CT), in axial (upper) and coronal (low) planes, showing cortical and circumferential calcifications. The image on the right shows that the renal cortex has a density similar to the bone, further indicating the diagnosis of cortical nephrocalcinosis. (B) Case 3 abdomen CT showing subcentimetric cysts on the right and larger cysts on the left kidney.

Figure 6

DNA variants of COL4 patients and resulting protein change.