Traditional and targeted exome sequencing reveals common, rare and novel functional deleterious variants in RET-signaling complex in a cohort of living US patients with urinary tract malformations

Abstract

Signaling by the glial cell line-derived neurotrophic factor (GDNF)-RET receptor tyrosine kinase and SPRY1, a RET repressor, is essential for early urinary tract development. Individual or a combination of GDNF, RET and SPRY1 mutant alleles in mice cause renal malformations reminiscent of congenital anomalies of the kidney or urinary tract (CAKUT) in humans and distinct from renal agenesis phenotype in complete GDNF or RET null mice. We sequenced GDNF, SPRY1 and RET in 122 unrelated living CAKUT patients to discover deleterious mutations that cause CAKUT. Novel or rare deleterious mutations in GDNF or RET were found in 6 unrelated patients. A family with duplicated collecting system had a novel mutation, RETR831Q, which showed markedly decreased GDNF dependent MAPK activity. Two patients with RET-G691S polymorphism harbored additional rare non-synonymous variants GDNF-R93W and RET-R982C. The patient with double RET-G691S/R982C genotype had multiple defects including renal dysplasia, megaureters and cryptorchidism. Presence of both mutations were necessary to affect RET activity. Targeted whole exome and next-generation sequencing revealed a novel deleterious mutation G443D in GFRα1, the co-receptor for RET, in this patient. Pedigree analysis indicated that the GFRα1 mutation was inherited from the unaffected mother and the RET mutations from the unaffected father. Our studies indicate that 5% of living CAKUT patients harbor deleterious rare variants or novel mutations in GDNF-GFRα1-RET pathway. We provide evidence for the coexistence of deleterious rare and common variants in genes in the same pathway as a cause of CAKUT and discovered novel phenotypes associated with the RET pathway.

Congenital Anomalies of the Kidney and Urinary Tract: An Overview

“…Patients with CAKUT have mutations in the RET/GDNF signaling pathway [ 13 -16 ]. A study of 122 patients with CAKUT identifi ed heterozygous deleterious sequence variants in GDNF or RET in 6/122 patients, 5 %, while another group screened 749 families from all over the world and identifi ed three families with heterozygous mutations in RET [ 13 ]. Similar fi ndings have been reported in studies of fetuses with bilateral or unilateral renal agenesis [ 14 , 16 ].…”

Genetic, environmental, and epigenetic factors involved in CAKUT

“…Analysis of multiple genes in parallel using NGS in patients with CAKUT has demonstrated that <10% patients with isolated CAKUT carry variants in previously implicated genes, such as HNF1B, PAX2, EYA1, SIX5, and RET. 23,24,37 This finding implies that the majority of causes of CAKUT are still unknown. Meanwhile, the list of novel variants requiring functional charac terization to determine whether they are true risk factors or harmless polymorphisms has expanded.…”

Identification of 8 Novel Mutations in Nephrogenesis-Related Genes in Chinese Han Patients with Unilateral Renal Agenesis

“…Since then, mutations in several genes, including GDNF [7], RET [8], HNF1B [9], SALL1 [10], SIX5 [11], BMP4 [12], GREM1 [13], FRAS1 , and FREM2 [13,14], have been identified as causing URA. All of these genes are involved in crucial signaling during nephrogenesis, and the majority show an autosomal dominant (AD) mode of inheritance.…”