Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-10-22

AUTHORS

Khun Zaw Latt, Kenjiro Honda, Myo Thiri, Yuki Hitomi, Yosuke Omae, Hiromi Sawai, Yosuke Kawai, Shunsuke Teraguchi, Kazuko Ueno, Masao Nagasaki, Akihiko Mabuchi, Hajime Kaga, Atsushi Komatsuda, Katsushi Tokunaga, Eisei Noiri

ABSTRACT

The associations of single nucleotide polymorphisms (SNPs) in PLA2R1 and HLA-DQA1, as well as HLA-DRB1*15:01-DQB1*06:02 haplotype with idiopathic membranous nephropathy (IMN) is well known. However, the primary associations of these loci still need to be determined. We used Japanese-specific SNP genotyping array and imputation using 2,048 sequenced Japanese samples to fine-map PLA2R1 region in 98 patients and 413 controls. The most significant SNPs were replicated in a separate sample set of 130 patients and 288 controls. A two-SNP haplotype of intronic and missense SNPs showed the strongest association. The intronic SNP is strongly associated with PLA2R1 expression in the Genotype-Tissue Expression (GTEx) database, and the missense SNP is predicted to alter peptide binding with HLA-DRB1*15:01 by the Immune Epitope Database (IEDB). In HLA region, we performed relative predispositional effect (RPE) tests and identified additional risk alleles in both HLA-DRB1 and HLA-DQB1. We collapsed the risk alleles in each of HLA-DRB1 and HLA-DQB1 into single risk alleles. Reciprocal conditioning of these collapsed risk alleles showed more residual significance for HLA-DRB1 collapsed risk than HLA-DQB1 collapsed risk. These results indicate that changes in the expression levels of structurally different PLA2R protein confer risk for IMN in the presence of risk HLA-DRB1 alleles. More... »

PAGES

15576

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41598-018-33612-7

DOI

http://dx.doi.org/10.1038/s41598-018-33612-7

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1107670608

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30349113


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21 schema:description The associations of single nucleotide polymorphisms (SNPs) in PLA2R1 and HLA-DQA1, as well as HLA-DRB1*15:01-DQB1*06:02 haplotype with idiopathic membranous nephropathy (IMN) is well known. However, the primary associations of these loci still need to be determined. We used Japanese-specific SNP genotyping array and imputation using 2,048 sequenced Japanese samples to fine-map PLA2R1 region in 98 patients and 413 controls. The most significant SNPs were replicated in a separate sample set of 130 patients and 288 controls. A two-SNP haplotype of intronic and missense SNPs showed the strongest association. The intronic SNP is strongly associated with PLA2R1 expression in the Genotype-Tissue Expression (GTEx) database, and the missense SNP is predicted to alter peptide binding with HLA-DRB1*15:01 by the Immune Epitope Database (IEDB). In HLA region, we performed relative predispositional effect (RPE) tests and identified additional risk alleles in both HLA-DRB1 and HLA-DQB1. We collapsed the risk alleles in each of HLA-DRB1 and HLA-DQB1 into single risk alleles. Reciprocal conditioning of these collapsed risk alleles showed more residual significance for HLA-DRB1 collapsed risk than HLA-DQB1 collapsed risk. These results indicate that changes in the expression levels of structurally different PLA2R protein confer risk for IMN in the presence of risk HLA-DRB1 alleles.
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28 Genotype-Tissue Expression (GTEx) database
29 HLA
30 HLA region
31 HLA-DQA1
32 HLA-DQB1
33 HLA-DRB1
34 HLA-DRB1 alleles
35 Immune Epitope Database
36 Japanese sample
37 PLA2R1
38 PLA2R1 expression
39 additional risk allele
40 alleles
41 array
42 association
43 changes
44 conditioning
45 confer risk
46 control
47 database
48 effect test
49 expression
50 expression database
51 expression levels
52 haplotypes
53 identification
54 idiopathic membranous nephropathy
55 imputation
56 intronic single nucleotide polymorphism
57 levels
58 loci
59 membranous nephropathy
60 missense single nucleotide polymorphism
61 nephropathy
62 nucleotide polymorphisms
63 patients
64 polymorphism
65 presence
66 primary association
67 reciprocal conditioning
68 region
69 results
70 risk
71 risk alleles
72 risk association
73 sample set
74 samples
75 separate sample sets
76 set
77 significance
78 significant single nucleotide polymorphisms
79 single nucleotide polymorphisms
80 single risk allele
81 strong association
82 test
83 two-SNP haplotype
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