Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy
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-specifi...
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doaj-f927285d7e104cbc8d6e45b143eb55022020-12-08T05:13:45ZengNature Publishing GroupScientific Reports2045-23222018-10-01811910.1038/s41598-018-33612-7Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous NephropathyKhun Zaw Latt0Kenjiro Honda1Myo Thiri2Yuki Hitomi3Yosuke Omae4Hiromi Sawai5Yosuke Kawai6Shunsuke Teraguchi7Kazuko Ueno8Masao Nagasaki9Akihiko Mabuchi10Hajime Kaga11Atsushi Komatsuda12Katsushi Tokunaga13Eisei Noiri14Department of Human Genetics, Graduate School of Medicine, The University of TokyoDepartment of Nephrology and Endocrinology, The University of Tokyo HospitalDepartment of Human Genetics, Graduate School of Medicine, The University of TokyoDepartment of Human Genetics, Graduate School of Medicine, The University of TokyoDepartment of Human Genetics, Graduate School of Medicine, The University of TokyoDepartment of Human Genetics, Graduate School of Medicine, The University of TokyoDepartment of Human Genetics, Graduate School of Medicine, The University of TokyoDepartment of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku UniversityDepartment of Human Genetics, Graduate School of Medicine, The University of TokyoDepartment of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku UniversityDepartment of Human Genetics, Graduate School of Medicine, The University of TokyoDepartment of Hematology, Nephrology, and Rheumatology, Graduate School of Medicine, Akita UniversityDepartment of Hematology, Nephrology, and Rheumatology, Graduate School of Medicine, Akita UniversityDepartment of Human Genetics, Graduate School of Medicine, The University of TokyoDepartment of Nephrology and Endocrinology, The University of Tokyo HospitalAbstract 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.https://doi.org/10.1038/s41598-018-33612-7Idiopathic Membranous NephropathyPhospholipase A2 Receptor (PLA2R)Missense SNPsSingle Nucleotide Polymorphisms (SNPs)Additional Risk Allele |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
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 |
spellingShingle |
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 Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy Scientific Reports Idiopathic Membranous Nephropathy Phospholipase A2 Receptor (PLA2R) Missense SNPs Single Nucleotide Polymorphisms (SNPs) Additional Risk Allele |
author_facet |
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 |
author_sort |
Khun Zaw Latt |
title |
Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy |
title_short |
Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy |
title_full |
Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy |
title_fullStr |
Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy |
title_full_unstemmed |
Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy |
title_sort |
identification of a two-snp pla2r1 haplotype and hla-drb1 alleles as primary risk associations in idiopathic membranous nephropathy |
publisher |
Nature Publishing Group |
series |
Scientific Reports |
issn |
2045-2322 |
publishDate |
2018-10-01 |
description |
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. |
topic |
Idiopathic Membranous Nephropathy Phospholipase A2 Receptor (PLA2R) Missense SNPs Single Nucleotide Polymorphisms (SNPs) Additional Risk Allele |
url |
https://doi.org/10.1038/s41598-018-33612-7 |
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