Genetic variants in the LAMA5 gene in pediatric nephrotic syndrome

Abstract

Background: Nephrotic syndrome (NS), a chronic kidney disease, is characterized by significant loss of protein in the urine causing hypoalbuminemia and edema. In general, ∼15% of childhood-onset cases do not respond to steroid therapy and are classified as steroid-resistant NS (SRNS). In ∼30% of cases with SRNS, a causative mutation can be detected in one of 44 monogenic SRNS genes. The gene LAMA5 encodes laminin-α5, an essential component of the glomerular basement membrane. Mice with a hypomorphic mutation in the orthologous gene Lama5 develop proteinuria and hematuria.

Methods: To identify additional monogenic causes of NS, we performed whole exome sequencing in 300 families with pediatric NS. In consanguineous families we applied homozygosity mapping to identify genomic candidate loci for the underlying recessive mutation.

Results: In three families, in whom mutations in known NS genes were excluded, but in whom a recessive, monogenic cause of NS was strongly suspected based on pedigree information, we identified homozygous variants of unknown significance (VUS) in the gene LAMA5. While all affected individuals had nonsyndromic NS with an early onset of disease, their clinical outcome and response to immunosuppressive therapy differed notably.

Conclusion: We here identify recessive VUS in the gene LAMA5 in patients with partially treatment-responsive NS. More data will be needed to determine the impact of these VUS in disease management. However, familial occurrence of disease, data from genetic mapping and a mouse model that recapitulates the NS phenotypes suggest that these genetic variants may be inherited factors that contribute to the development of NS in pediatric patients.

Keywords: genetic variants; inherited diseases; nephrotic syndrome; treatment response in pediatric nephrotic syndrome; whole exome sequencing.

FIGURE 1

Homozygosity mapping in families with NS identifies recessive candidate loci. Homozygosity mapping was calculated from WES data using HomozygosityMapper. A homozygous peak on chromosome 20q13 (arrow head) that includes the LAMA5 locus was present in all three families. (A, B) Homozygosity mapping for the two affected siblings (-21 and -22) of family A4389. (C, D) The two affected siblings (-21 and -22) of family B150. (E) Homozygosity mapping data of patient B1284-21.

FIGURE 2

WES identifies recessive variants in the gene LAMA5 in three families with nephrotic syndrome. (A) Exon structure of LAMA5 cDNA (NM_005560.4). The positions of start codons, stop codons and mutated nucleotides are indicated. (B) Domain structure of the encoded protein laminin-α5. Arrows indicate the positions of the altered amino acid residues in families A4389, B150 and B1284. (C) Evolutionary conservation among orthologous proteins of laminin-α5. Altered amino acid residues in families A4389, B150 and B1284 are indicated with arrowheads and a yellow box. (D) Sanger sequencing of the respective regions of LAMA5 in genomic DNA of affected patients, parental DNA and control samples as indicated. aa, amino acid; bp, base pairs; C. elegans, Caenorhabditis elegans; D. melanogaster, Drosophila melanogaster; EGF, laminin EGF-like domain; het, heterozygous; Hom, homozygous; LAM G, laminin G-like domain; LAM IV-A, laminin IV type A; LAM NT, laminin N-terminal domain.