Detection of Association of Long Noncoding RNA ATP6V0E2-AS1 Single Nucleotide Polymorphism with Susceptibility to Myeloperoxidase-ANCA Associated Vasculitis Based on Transcriptome Analysis

Yuka Iwahashi^1,2, Aya Kawasaki^1,2, Takayo Tsuchiura³, Ken-ei Sada⁴, Fumio Hirano^5,6, Daisuke Tsukui⁷, Shigeto Kobayashi⁸, Hidehiro Yamada⁹, Hiroshi Furukawa^1,2,10, Kenji Nagasaka¹¹, Takahiko Sugihara¹², Nao Nishida³, Kunihiro Yamagata¹³, Takayuki Sumida¹⁴, Shigeto Tohma^10,15, Shoichi Ozaki⁹, Hiroshi Hashimoto¹⁶, Hirofumi Makino¹⁷, Yoshihiro Arimura¹⁸, Hajime Kono¹⁹, Masayoshi Harigai²⁰ and Naoyuki Tsuchiya^1,2, ¹University of Tsukuba, Graduate School of Comprehensive Human Sciences, Masters' Program in Medical Sciences, Tsukuba, Japan, ²University of Tsukuba, Faculty of Medicine, Molecular and Genetic Epidemiology Laboratory, Tsukuba, Japan, ³Genome Medical Science Project, National Center for Global Health and Medicine, Research Center for Hepatitis and Immunology, Ichikawa, Japan, ⁴Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan, ⁵Tokyo Medical and Dental University, Graduate School of Medical and Dental Sciences, Department of Rheumatology, Tokyo, Japan, ⁶Tokyo Medical and Dental UniversityGraduate School of Medical and Dental Sciences, Department of Lifetime Clinical Immunology, Tokyo, Japan, ⁷Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan, ⁸Department of Internal Medicine, Juntendo University Koshigaya Hospital, Koshigaya, Japan, ⁹St. Marianna University, School of Medicine, Department of Internal Medicine, Kawasaki, Japan, ¹⁰National Hospital Organization Sagamihara l Hospital, Clinical Research Center for Allergy and Rheumatology, Sagamihara, Japan, ¹¹Department of Rheumatology, Ome Municipal General Hospital, Ome, Japan, ¹²Department of Medicine and Rheumatology, Tokyo Metropolitan Geriatric Hospital, Tokyo, Japan, ¹³University of Tsukuba, Faculty of Medicine, Department of Nephrology, Tsukuba, Japan, ¹⁴Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan, ¹⁵National Hospital Organization Tokyo National Hospital, Kiyose, Japan, ¹⁶Juntendo University School of Medicine, Tokyo, Japan, ¹⁷Okayama University Hospital, Okayama, Japan, ¹⁸Kyorin University School of Medicine, First Department of Internal Medicine, Tokyo, Japan, ¹⁹Teikyo University School of Medicine, Department of Internal Medicine, Tokyo, Japan, ²⁰Tokyo Women's Medical University, Division of Epidemiology and Pharmacoepidemiology of Rheumatic Diseases, Institute of Rheumatology, Tokyo, Japan

Meeting: 2018 ACR/ARHP Annual Meeting

Keywords: ANCA, genetics and polymorphism, RNA

Session Information

Date: Tuesday, October 23, 2018

Title: Genetics, Genomics and Proteomics Poster

Session Type: ACR Poster Session C

Session Time: 9:00AM-11:00AM

Background/Purpose:

Because of the low prevalence, only three genome-wide association studies, all from the Caucasian populations, have been reported on ANCA-associated vasculitis (AAV) thus far; therefore, efficient candidate gene studies play an important role. In complex diseases, the majority of single nucleotide polymorphisms (SNPs) associated with disease susceptibility are located in the noncoding region and are suggested to affect gene expression. Recently, long noncoding RNAs (lncRNAs) are strongly implicated in the regulation of gene expression. In this study, we made an attempt to detect SNPs associated with susceptibility to AAV by focusing on candidate lncRNAs selected based on the transcriptome analysis.

Methods:

Whole blood transcriptome analysis was conducted on eight patients with AAV and 14 healthy controls (HC). All subjects are Japanese. From the transcriptome data, we selected candidate lncRNAs using two approaches. The first approach took advantage of eQTL (expression quantitative trait loci) SNPs. LncRNAs significantly over- or underexpressed as compared with HC were selected. Then eQTL SNPs associated with expression levels of these lncRNAs were selected as candidate SNPs using GTEx database. In the second approach, in order to more comprehensively capture SNPs with potential relevance, we focused on the SNPs closely located to the candidate lncRNAs. Top 10 lncRNAs were selected based on the fold change (FC) in the expression levels compared with HC. Then SNPs located in the chromosomal regions encompassing the candidate lncRNAs (from 50kb upstream to 50kb downstream) were selected. The candidate SNPs were filtered based on minor allele frequency (>0.1), linkage disequilibrium (r²<0.6) and regulome score(<2). Finally, 96 candidate SNPs associated with 25 lncRNAs were selected for association analysis. Then these SNPs were genotyped in 525 Japanese AAV patients (315 MPA, 108 GPA, 412 MPO-ANCA positive, 70 PR3-ANCA positive) using DigiTag2 or TaqMan SNP genotyping assays, and allele frequencies were compared with 4,394 healthy Japanese controls from our laboratory and Tohoku Medical Megabank Organization (ToMMo).

Results:

After quality control, association with AAV were analyzed on 74 SNPs. The SNP rs6958235, located in the upstream region of ATP6V0E2-AS1, showed a significant association with MPO-ANCA positive AAV (P=5.72×10^-4, odd ratio 1.38, 95% confidence interval 1.15-1.65)(Table). The association remained significant after Bonferroni correction (P_Bonferroni=0.042). The expression level of ATP6V0E2-AS1 was downregulated in AAV as compared with HC (FC -4.4).

Conclusion:

A SNP rs6958235C located in the upstream region of lncRNA ATP6V0E2-AS1 was found to be associated with MPO-AAV for the first time. ATP6V0E2 encodes an isoform of an essential proton pump component that may play a role in the acidification of endosome and lysosome. The functional significance of this SNP requires further study.

Table. Allelic association of rs6958235T>C with AAV subsets in a Japanese population
	n	C allele frequency (%)	P_uncorrected	P_Bonferroni	OR	95%CI
MPA	315	18.3	1.88E-02	>1	1.29	1.04-1.59
GPA	108	19.4	5.79E-02	>1	1.39	0.99-1.96
MPO-ANCA positive	412	19.3	5.72E-04	0.042	1.38	1.15-1.65
PR3-ANCA positive	70	16.4	5.89E-01	>1	1.13	0.72-1.78
healthy controls	4394	14.8
OR: odds ratio, CI: confidence interval

Disclosure: Y. Iwahashi, None; A. Kawasaki, None; T. Tsuchiura, None; K. E. Sada, None; F. Hirano, Chugai Pharmaceutical Co., Ltd.; Ono Pharmaceuticals; Mitsubishi Tanabe Pharma Co.; UCB Japan; CSL Behring; Towa Pharmaceutical Co., Ltd.; Abbvie Japan Co., Ltd.; Japan Blood Products Organization; Ayumi Pharmaceutical Co.; and Nippon Kayaku Co., Ltd.., 5,Sumitomo Dainippon Pharma Chugai Pharmaceutical Co., Ltd., 8; D. Tsukui, None; S. Kobayashi, None; H. Yamada, None; H. Furukawa, None; K. Nagasaka, None; T. Sugihara, Chugai Pharmaceutical Co., Ltd., Takeda Pharmaceutical Co. Ltd., Mitsubishi-Tanabe Pharma Co., Astellas Pharma Inc., Bristol Myers Squibb K.K. and Abbvie Japan Co., Ltd., 5; N. Nishida, None; K. Yamagata, None; T. Sumida, None; S. Tohma, None; S. Ozaki, None; H. Hashimoto, None; H. Makino, None; Y. Arimura, None; H. Kono, Celgene Corporation, 2; M. Harigai, None; N. Tsuchiya, Japan Rheumatism Foundation, 2.

To cite this abstract in AMA style:

Iwahashi Y, Kawasaki A, Tsuchiura T, Sada KE, Hirano F, Tsukui D, Kobayashi S, Yamada H, Furukawa H, Nagasaka K, Sugihara T, Nishida N, Yamagata K, Sumida T, Tohma S, Ozaki S, Hashimoto H, Makino H, Arimura Y, Kono H, Harigai M, Tsuchiya N. Detection of Association of Long Noncoding RNA ATP6V0E2-AS1 Single Nucleotide Polymorphism with Susceptibility to Myeloperoxidase-ANCA Associated Vasculitis Based on Transcriptome Analysis [abstract]. Arthritis Rheumatol. 2018; 70 (suppl 9). https://acrabstracts.org/abstract/detection-of-association-of-long-noncoding-rna-atp6v0e2-as1-single-nucleotide-polymorphism-with-susceptibility-to-myeloperoxidase-anca-associated-vasculitis-based-on-transcriptome-analysis/. Accessed .

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