Human Genetics

, Volume 131, Issue 11, pp 1725–1738

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

  • Rajshekhar Chatterjee
  • Enrique Ramos
  • Mary Hoffman
  • Jessica VanWinkle
  • Daniel R. Martin
  • Thomas K. Davis
  • Masato Hoshi
  • Stanley P. Hmiel
  • Anne Beck
  • Keith Hruska
  • Doug Coplen
  • Helen Liapis
  • Robi Mitra
  • Todd Druley
  • Paul Austin
  • Sanjay Jain
Original Investigation

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 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.

Supplementary material

439_2012_1181_MOESM1_ESM.ppt (2.2 mb)
Supplementary Figure 1 Malformations in patients with GDNF/RET mutations are also seen in mutant mice with aberrant signaling of the RET pathway. (A-E) Representative images from Gdnf, Ret, or Spry1 mutant mice showing similar phenotypes as observed in patients with GDNF or RET mutations. A, duplicated collecting system in a Ret hypomorph Ret9/Y1015F mutant mice (the bright signal highlight E-cadherin positive urinary tract). B, unilateral agenesis in a Gdnf haploinsufficient mouse showing only one kidney (blue staining represents LacZ signal from a reporter knocked-in Gdnf locus). C, hematoxylin-eosin stained section shows cystic dysplasia highlighted by disorganized architecture and cysts (*asterisks) in a new born Ret-signaling mutant mice. D, Vesicoureteral reflux (blue dye refluxing in the ureters) in Spry1 mutant mice. Urinary tract from wild-type (WT) mice with no reflux is shown for comparison (E) Supplementary material 1 (PPT 2218 kb)
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Supplemental Table S1 (XLS 38 kb)
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Supplemental Table S2 (XLS 27 kb)
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Supplemental Table S3 (XLS 19 kb)
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Supplemental Table S4 (XLS 31 kb)
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Supplementary material 6 (DOC 35 kb)

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Rajshekhar Chatterjee
    • 1
  • Enrique Ramos
    • 2
  • Mary Hoffman
    • 1
  • Jessica VanWinkle
    • 1
  • Daniel R. Martin
    • 1
  • Thomas K. Davis
    • 3
  • Masato Hoshi
    • 1
  • Stanley P. Hmiel
    • 3
  • Anne Beck
    • 3
  • Keith Hruska
    • 3
  • Doug Coplen
    • 4
  • Helen Liapis
    • 1
    • 5
  • Robi Mitra
    • 2
  • Todd Druley
    • 3
  • Paul Austin
    • 4
  • Sanjay Jain
    • 1
    • 5
  1. 1.Department of Internal Medicine (Renal Division)Washington University School of MedicineSt. LouisUSA
  2. 2.Department of GeneticsWashington University School of MedicineSt. LouisUSA
  3. 3.Department of PediatricsWashington University School of MedicineSt. LouisUSA
  4. 4.Department of Surgery (Urology)Washington University School of MedicineSt. LouisUSA
  5. 5.Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUSA

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