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

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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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Authors and Affiliations

  1. Laboratory for Diabetic Nephropathy, SNP Research Centre, Institute of Physical and Chemical Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

    Masumi Kamiyama, Masaaki Kobayashi & Shiro Maeda

  2. Department of Medicine, Shiga University of Medical Science, Otsu, 520-2192, Japan

    Shin-ichi Araki & Atsunori Kashiwagi

  3. Laboratory for Pharmacogenetics, SNP Research Centre, Institute of Physical and Chemical Research, Yokohama, 230-0045, Japan

    Aritoshi Iida

  4. Laboratory for Medical Informatics, SNP Research Centre, Institute of Physical and Chemical Research, Yokohama, 230-0045, Japan

    Tatsuhiko Tsunoda

  5. Kawai Clinic, Tsukuba, 305-0812, Japan

    Koichi Kawai

  6. Department of Internal Medicine, Osaka City General Hospital, Osaka, 534-0021, Japan

    Masahito Imanishi

  7. Department of Internal Medicine, Osaka Rosai Hospital, Sakai, 591-8025, Japan

    Makoto Nomura

  8. Diabetes Center, Tokyo Women’s Medical University, Tokyo, 162-8666, Japan

    Tetsuya Babazono & Yasuhiko Iwamoto

  9. Division of Endocrinology and Metabolism, Department of Internal Medicine, Kawasaki Medical School, Kurashiki, 701-0192, Japan

    Kohei Kaku

  10. Department of Medicine, Metabolism and Endocrinology, School of Medicine, Juntendo University, Tokyo, 113-8421, Japan

    Ryuzou Kawamori

  11. Department of Community, Occupational and Family Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore, 117597

    Daniel P. K. Ng

  12. Steno Diabetes Center, 2820, Gentofte, Denmark

    Torben Hansen, Peter Gaede & Oluf Pedersen

  13. Faculty of Health Science, University of Aarhus, Aarhus, Denmark

    Oluf Pedersen

  14. Laboratory of Molecular Medicine, Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan

    Yusuke Nakamura

Authors
  1. Masumi Kamiyama
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  2. Masaaki Kobayashi
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  3. Shin-ichi Araki
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Correspondence to Shiro Maeda.

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Kamiyama, M., Kobayashi, M., Araki, Si. 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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