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Polymorphisms in the 3′ UTR in the neurocalcin δ gene affect mRNA stability, and confer susceptibility to diabetic nephropathy

Abstract

Using a large-scale genotyping analysis of gene-based single nucleotide polymorphisms (SNPs) in Japanese type 2 diabetic patients, we have identified a gene encoding neurocalcin δ (NCALD) as a candidate for a susceptibility gene to diabetic nephropathy; the landmark SNP was found in the 3′ UTR of NCALD (rs1131863: exon 4 +1340 A vs. G, P = 0.00004, odds ratio = 1.59, 95% CI 1.27–1.98). We also discovered two other SNPs in exon 4 of this gene (+999 T/A, +1307 A/G) that showed absolute linkage disequilibrium to the landmark SNP. Subsequent in vitro functional analysis revealed that synthetic mRNA corresponding to the disease susceptible haplotype (exon 4 +1340 G, +1307 G, +999 A) was degraded faster than mRNA corresponding to the major haplotype (exon 4 +1340 A, +1307 A, +999 T), and allelic mRNA expression of the disease susceptibility allele was significantly lower than that of the major allele in normal kidney tissues. In an experiment using a short interfering RNA targeting NCALD, we found that silencing of the NCALD led to a considerable enhancement of cell migration, accompanied by a significant reduction in E-cadherin expression, and by an elevation of α smooth muscle actin expression in cultured renal proximal tubular epithelial cells. We also identified the association of the landmark SNP with the progression of diabetic nephropathy in a 8-year prospective study (A vs. G, P = 0.03, odds ratio = 1.91, 95% CI 1.07–3.42). These results suggest that the NCALD gene is a likely candidate for conferring susceptibility to diabetic nephropathy.

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Abbreviations

SNP:

Single nucleotide polymorphism

LD:

Linkage disequilibrium

HWE:

Hardy–Weinberg equilibrium

TEMT:

Tubular epithelial mesenchymal-transdifferentiation

UTR:

Untranslated region

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Acknowledgments

We thank A. Kanazawa, S. Tsukada and the technical staff of the Laboratory for Diabetic Nephropathy at the SNP Research Center. This work was partly supported by a grant from the Japanese Millennium Project. Support for Ng DPK was provided by the National Medical Research Council (Singapore) (NMRC/1018/2005). All authors have no conflict of interest, and nothing to declare.

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Correspondence to Shiro Maeda.

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Kamiyama, M., Kobayashi, M., Araki, S. et al. Polymorphisms in the 3′ UTR in the neurocalcin δ gene affect mRNA stability, and confer susceptibility to diabetic nephropathy. Hum Genet 122, 397–407 (2007). https://doi.org/10.1007/s00439-007-0414-3

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Keywords

  • Diabetic Nephropathy
  • Major Haplotype
  • Overt Nephropathy
  • Normal Kidney Tissue
  • Entire Human Genome