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.
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 six unrelated patients. A family with duplicated collecting system had a novel mutation, RET-R831Q, 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 was 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.
Department of Internal Medicine (Renal Division), Washington University School of Medicine, Box 8126, 660 S. Euclid Ave, St. Louis, MO 63110, USA.
Rajshekhar
R
Chatterjee
Enrique
E
Ramos
Mary
M
Hoffman
Jessica
J
VanWinkle
Daniel R
DR
Martin
Thomas K
TK
Davis
Masato
M
Hoshi
Stanley P
SP
Hmiel
Anne
A
Beck
Keith
K
Hruska
Doug
D
Coplen
Helen
H
Liapis
Robi
R
Mitra
Todd
T
Druley
Paul
P
Austin
Sanjay
S
Jain
D000293:Adolescent; D000328:Adult; D000595:Amino Acid Sequence; D015153:Blotting, Western; D002478:Cells, Cultured; D015331:Cohort Studies; D059472:Exome / Q000235:genetics*; D005260:Female; D051097:Glial Cell Line-Derived Neurotrophic Factor Receptors / Q000235:genetics*; D006801:Humans; D008297:Male; D008565:Membrane Proteins / Q000235:genetics; D008875:Middle Aged; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009154:Mutation / Q000235:genetics*; D010375:Pedigree; D010641:Phenotype; D010750:Phosphoproteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D051096:Proto-Oncogene Proteins c-ret / Q000235:genetics*; D017386:Sequence Homology, Amino Acid; D014481:United States / Q000453:epidemiology; D014551:Urinary Tract / Q000002:abnormalities* / Q000378:metabolism / Q000473:pathology*; D014564:Urogenital Abnormalities; D014718:Vesico-Ureteral Reflux / Q000453:epidemiology / Q000235:genetics*; D055815:Young Adult
C494987:GFRA1 protein, human; D051097:Glial Cell Line-Derived Neurotrophic Factor Receptors; D008565:Membrane Proteins; D010750:Phosphoproteins; C486055:SPRY1 protein, human; D051096:Proto-Oncogene Proteins c-ret; C099282:RET protein, human