Evidence map›Paper›PMID 18219441›Full record

ArticleJournal of human genetics2008

A functional SNP in the NKX2.5-binding site of ITPR3 promoter is associated with susceptibility to systemic lupus erythematosus in Japanese population.

Tetsuya Oishi, Aritoshi Iida, Shigeru Otsubo, Yoichiro Kamatani, Masayuki Usami, Takashi Takei, Keiko Uchida, Ken Tsuchiya, Susumu Saito, Yozo Ohnisi and 10 more

Open access · bronzeAbstract readComparative Study
PubMed Publisher
In one paragraph

Article in Journal of human genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed, 1 pooled it
1.3field-weighted citation impact, top 20% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

16 citing papers in PubMed, 1 synthesis or guideline pooled it, 31 citations in OpenAlex.

  1. Pooled it
  2. Article
  3. Article
  4. Review
  5. Article
  6. Article
  7. Article
  8. Immunogenetics of Kawasaki disease.Clinical reviews in allergy & immunology · 2020
    Review
  9. Review
  10. Review
  11. Cardiac inositol 1,4,5-trisphosphate receptors.Biochimica et biophysica acta. Molecular cell research · 2017
    Review
  12. Article
  13. Review
  14. Article
  15. Article
  16. Recent advances in the genetics of systemic lupus erythematosus.Expert review of clinical immunology · 2010
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

20 authors at 4 institutions in 1 country.

Tetsuya OishiLaboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo, 108-8639, Japan.
Aritoshi IidaLaboratory for Genotyping, SNP Research Center, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, 230-0045, Japan.
Shigeru OtsuboLaboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo, 108-8639, Japan.
Yoichiro KamataniLaboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo, 108-8639, Japan.
Masayuki UsamiLaboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo, 108-8639, Japan.
Takashi TakeiDepartment of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
Keiko UchidaDepartment of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
Ken TsuchiyaDepartment of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
Susumu SaitoLaboratory for Genotyping, SNP Research Center, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, 230-0045, Japan.
Yozo OhnisiLaboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo, 108-8639, Japan.
Katsushi TokunagaDepartment of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, 108-8639, Japan.
Kosaku NittaDepartment of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
Yasushi KawaguchiInstitute of Rheumatology, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
Naoyuki KamataniInstitute of Rheumatology, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
Yuta KochiLaboratory for Rheumatic Diseases, SNP Research Center, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, 230-0045, Japan.
Kenichi ShimaneLaboratory for Rheumatic Diseases, SNP Research Center, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, 230-0045, Japan.
Kazuhiko YamamotoLaboratory for Rheumatic Diseases, SNP Research Center, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, 230-0045, Japan.
Yusuke NakamuraLaboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo, 108-8639, Japan.
Wako YumuraDepartment of Medicine, Kidney Center, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.
Koichi MatsudaLaboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo, 108-8639, Japan. koichima@ims.u-tokyo.ac.jp.
Tokyo Women's Medical University · JPThe University of Tokyo · JPRIKEN · JPInstitute for Rheumatic Diseases (Japan) · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Systemic lupus erythematosus (SLE) is one of the common autoimmune diseases with complex genetic components. To identify a gene(s) susceptible to SLE, we performed a case-control association study using genome-wide gene-based single nucleotide polymorphisms (SNPs) in Japanese population. Here we report that an SNP (rs3748079) located in a promoter region of the inositol 1,4,5-triphosphate receptor type 3 (ITPR3) gene on chromosome 6p21 was significantly associated with SLE in two independent Japanese case-control samples [P=0.0000000178 with odds ratio of 1.88, 95% confidence interval (CI) of 1.51-2.35]. This particular SNP also revealed associations with rheumatoid arthritis (RA) (P=0.0084 with odds ratio of 1.23, 95% CI of 1.05-1.43) and with Graves' disease (GD) (P=0.00036 with odds ratio of 1.57, 95% CI of 1.22-2.02). We found the binding of NKX2.5 specific to the non-susceptible T allele in the region including this SNP. Furthermore, an SNP in NKX2.5 also revealed an association with SLE (P=0.0037 with odds ratio of 1.74, 95% CI of 1.19-2.55). Individuals with risk genotype of both ITPR3 and NKX2.5 loci have higher risk for SLE (odds ratio=5.77). Our data demonstrate that genetic and functional interactions of ITPR3 and NKX2.5 play a crucial role in the pathogenesis of SLE.

Indexed as

Genetic Predisposition to DiseaseAdultArthritis, RheumatoidBinding SitesCase-Control StudiesChromatin ImmunoprecipitationCohort StudiesFemaleGenotypeGraves DiseaseHomeobox Protein Nkx-2.5Homeodomain ProteinsHumansInositol 1,4,5-Trisphosphate ReceptorsJapanLuciferasesHomeobox Protein Nkx-2.5Homeodomain ProteinsInositol 1,4,5-Trisphosphate ReceptorsITPR3 protein, humanLuciferasesNKX2-5 protein, humanRNA, MessengerTranscription Factors

Identifiers

PMID18219441
OpenAlexW2110274269

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.