Exome sequencings were conducted using 59 patients having rheumatoid arthritis (RA) and 93 controls. After stepwise filtering, 107 genes showed less than 0.05 of P-values by gene-burden tests. Among 107 genes, NDUFA7 which is a subunit of the complex I in the mitochondrial respiratory chain was selected for further analysis based on previous reports. A case–control study was performed on the three single-nucleotide variants (SNVs) of NDUFA7 with 432 cases and 432 controls. An association was observed between NDUFA7 and RA with severe erosive arthritis. These results together with previous reports suggested the involvement of reactive oxygen species (ROS) in the pathogenesis of RA. In the next step, four SNVs from three genes related to the mitochondrial respiratory chain were selected, which is a major source of ROS, and conducted a case–control study. An association was observed based on a pathway-burden test comprising NDUFA7, SDHAF2, SCO1 and ATP5O: P=1.56E-04, odds ratio=2.16, 95% confidence interval=1.43–3.28. Previous reports suggested the involvement of ROS in the pathogenesis of RA. The aggregation of SNVs in the mitochondria respiratory chain suggests the pivotal role of those SNVs in the pathogenesis of RA with severe erosive arthritis.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $37.50 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
McInnes, I. B. & Schett, G. The pathogenesis of rheumatoid arthritis. N. Engl. J. Med. 365, 2205–2219 (2011).
MacGregor, A. J., Snieder, H., Rigby, A. S., Koskenvuo, M., Kaprio, J., Aho, K. et al. Characterizing the quantitative genetic contribution to rheumatoid arthritis using data from twins. Arthritis Rheum. 43, 30–37 (2000).
Okada, Y., Wu, D., Trynka, G., Raj, T., Terao, C., Ikari, K. et al (2014) Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506, 376–381 (2014).
Bodmer, W. & Bonilla, C. Common and rare variants in multifactorial susceptibility to common diseases. Nat. Genet. 40, 695–701 (2008).
Cirulli, E. T. & Goldstein, D. B. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat. Rev. Genet. 11, 415–425 (2010).
Evans, D., Arze, J., Aberle, J. & Beil, F. U. Rare variants in the lipoprotein lipase (LPL) gene are common in hypertriglyceridemia but rare in Type III hyperlipidemia. Atherosclerosis 214, 386–390 (2011).
Diogo, D., Kurreeman, F., Stahl, E. A., Liao, K. P., Gupta, N., Greenberg, J. D. et al. Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis. Am. J. Hum. Genet. 92, 15–27 (2013).
Cruchaga, C., Karch, C. M., Jin, S. C., Benitez, B. A., Cai, Y., Guerreiro, R. et al. Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer's disease. Nature 505, 550–554 (2014).
Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., Lee, C. et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272–276 (2009).
Ng, S. B., Buckingham, K. J., Lee, C., Bigham, A. W., Tabor, H. K., Dent, K. M. et al. Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet. 42, 30–35 (2010).
Mitsunaga, S., Hosomichi, K., Okudaira, Y., Nakaoka, H., Kunii, N., Suzuki, Y. et al. Exome sequencing identifies novel rheumatoid arthritis-susceptible variants in the BTNL2. J. Hum. Genet. 58, 210–215 (2013).
Phillips, D. C., Dias, H. K., Kitas, G. D. & Griffiths, H. R. Aberrant reactive oxygen and nitrogen species generation in rheumatoid arthritis (RA): causes and consequences for immune function, cell survival, and therapeutic intervention. Antioxid. Redox Signal. 12, 743–785 (2010).
Veselinovic, M., Barudzic, N., Vuletic, M., Zivkovic, V., Tomic-Lucic, A., Djuric, D. et al. Oxidative stress in rheumatoid arthritis patients: relationship to diseases activity. Mol. Cell. Biochem. 391, 225–232 (2014).
Rall, L. C., Roubenoff, R., Meydani, S. N., Han, S. N. & Meydani, M. Urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG) as a marker of oxidative stress in rheumatoid arthritis and aging: effect of progressive resistance training. J. Nutr. Biochem. 11, 581–584 (2000).
Kageyama, Y., Takahashi, M., Ichikawa, T., Torikai, E. & Nagano, A. Reduction of oxidative stress marker levels by anti-TNF-alpha antibody, infliximab, in patients with rheumatoid arthritis. Clin. Exp. Rheumatol. 26, 73–80 (2008).
Arnett, F. C., Edworthy, S. M., Bloch, D. A., McShane, D. J., Fries, J. F., Cooper, N. S. et al. The American Rheumatism Association 1987 revised criteria for the classification of rheumatoid arthritis. Arthritis Rheum 31, 315–324 (1988).
Ochi, T., Iwase, R., Yonemasu, K., Matsukawa, M., Yoneda, M., Yukioka, M. et al. Natural course of joint destruction and fluctuation of serum C1q levels in patients with rheumatoid arthritis. Arthritis Rheum. 31, 37–43 (1988).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18, 1851–1858 (2008).
Lee, S., Abecasis, G. R., Boehnke, M. & Lin, X. Rare-variant association analysis: study designs and statistical tests. Am. J. Hum. Genet. 95, 5–23 (2014).
Morgenthaler, S. & Thilly, W. G. A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutat Res. 615, 28–56 (2007).
Nakaoka, H., Cui, T., Tajima, A., Oka, A., Mitsunaga, S., Kashiwase, K. et al. A systems genetics approach provides a bridge from discovered genetic variants to biological pathways in rheumatoid arthritis. PLoS One 6, e25389 (2011).
Falconer, D. S. & Mackay, T. F. C. Introduction to Quantitative Genetics4 edn (Longmans Green, Harlow, Essex, UK, 1996).
Balaban, R. S., Nemoto, S. & Finkel, T. Mitochondria, oxidants, and aging. Cell 120, 483–495 (2008).
Siebels, I. & Dröse, S. Q-site inhibitor induced ROS production of mitochondrial complex II is attenuated by TCA cycle dicarboxylates. Biochim. Biophys. Acta 1827, 1156–1164 (2013).
Jayanthi, S., Lewis, B. D. & Cadet, J. L. Fas-induced apoptosis of glioma cells is associated with down-regulation of the hSCO1 protein, a subunit of complex IV. Brain Res. Mol. Brain Res. 91, 131–136 (2001).
Natera-Naranjo, O., Kar, A. N., Aschrafi, A., Gervasi, N. M., Macgibeny, M. A., Gioio, A. E. et al. Local translation of ATP synthase subunit 9 mRNA alters ATP levels and the production of ROS in the axon. Mol. Cell. Neurosci. 49, 263–270 (2012).
Tahara, E. B., Navarete, F. D. & Kowaltowski, A. J. Tissue-, substrate-, and site-specific characteristics of mitochondrial reactive oxygen species generation. Free Radic. Biol. Med. 46, 1283–1297 (2009).
Schellekens, G. A., Visser, H., de Jong, B. A., van den Hoogen, F. H., Hazes, J. M., Breedveld, F. C. et al. The diagnostic properties of rheumatoid arthritis antibodies recognizing a cyclic citrullinated peptide. Arthritis Rheum. 43, 155–163 (2000).
Iwamoto, T., Ikari, K., Nakamura, T., Kuwahara, M., Toyama, Y., Tomatsu, T. et al. Association between PADI4 and rheumatoid arthritis: a meta-analysis. Rheumatology (Oxford) 45, 804–807 (2006).
Chang, X., Yamada, R., Suzuki, A., Sawada, T., Yoshino, S., Tokuhiro, S. et al. Localization of peptidylarginine deiminase 4 (PADI4) and citrullinated protein in synovial tissue of rheumatoid arthritis. Rheumatology (Oxford) 44, 40–50 (2005).
Tanikawa, C., Ueda, K., Nakagawa, H., Yoshida, N., Nakamura, Y. & Matsuda, K. Regulation of protein citrullination through p53/PADI4 network in DNA damage response. Cancer Res. 69, 8761–8769 (2009).
Lan, A., Liao, X., Mo, L., Yang, C., Yang, Z., Wang, X. et al. Hydrogen sulfide protects against chemical hypoxia-induced injury by inhibiting ROS-activated ERK1/2 and p38MAPK signaling pathways in PC12 cells. PLoS One 6, e25921 (2011).
Tak, P. P., Smeets, T. J., Boyle, D. L., Kraan, M. C., Shi, Y., Zhuang, S. et al. p53 overexpression in synovial tissue from patients with early and longstanding rheumatoid arthritis compared with patients with reactive arthritis and osteoarthritis. Arthritis Rheum. 42, 948–953 (1999).
Firestein, G. S., Echeverri, F., Yeo, M., Zvaifler, N. J. & Green, D. R. Somatic mutations in the p53 tumor suppressor gene in rheumatoid arthritis synovium. Proc. Natl Acad. Sci. USA 94, 10895–10900 (1997).
Bohuslav, J., Chen, L. F., Kwon, H., Mu, Y. & Greene, W. C. p53 induces NF-kappaB activation by an IkappaB kinase-independent mechanism involving phosphorylation of p65 by ribosomal S6 kinase 1. J. Biol. Chem. 279, 26115–26125 (2004).
Chen, L., Xu, B., Liu, L., Luo, Y., Zhou, H., Chen, W. et al. Cadmium induction of reactive oxygen species activates the mTOR pathway, leading to neuronal cell death. Free Radic. Biol. Med. 50, 624–632 (2011).
Cejka, D., Hayer, S., Niederreiter, B., Sieghart, W., Fuereder, T., Zwerina, J. et al. Mammalian target of rapamycin signaling is crucial for joint destruction in experimental arthritis and is activated in osteoclasts from patients with rheumatoid arthritis. Arthritis Rheum. 62, 2294–2302 (2010).
Laragione, T. & Gulko, P. S. mTOR regulates the invasive properties of synovial fibroblasts in rheumatoid arthritis. Mol. Med. 16, 352–358 (2010).
Valcárcel-Ares, M. N., Riveiro-Naveira, R. R., Vaamonde-García, C., Loureiro, J., Hermida-Carballo, L., Blanco, F. J. et al. Mitochondrial dysfunction promotes and aggravates the inflammatory response in normal human synoviocytes. Rheumatology (Oxford) 53, 1332–1343 (2014).
We thank the DNA donors and supporting medical staff for making this study possible. We thank Miyako Nakagawa and Tomomi Ito (Division of Rheumatology, Tokai University School of Medicine), Masayuki Tanaka and Hideki Hayashi (Department of Bioinformatics, Support Center for Medical Research and Education, Tokai University) for their excellent technical assistance. We also thank Dr Atsushi Toyoda (Comparative Genomics Laboratory, National Institute of Genetics), Dr Shoji Tsuji, Dr Jun Mitsui and Dr Hiroyuki Ishiura (Department of Neurology, Division of Neuroscience, Graduate School of Medicine, The University of Tokyo), Dr Shinichi Morishita and Dr Jun Yoshimura (Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo) for their supporting based on the Grant in-Aid-for Scientific Research on Innovative Areas ‘Genome Science’ (No.221S0002) from Ministry of Education, Culture, Sports, Science and Technology of Japan. This work was supported in part by, a Grant in-Aid-for Scientific Research on Innovative Areas ‘Genome Science’ (No.221S0002) from Ministry of Education, Culture, Sports, Science and Technology of Japan and a Grant-in-Aid for Scientific Research from the Japanese Ministry of Health, Labour and Welfare.
The authors declare no conflict of interest.
Supplementary Information accompanies the paper on Journal of Human Genetics website
About this article
Redox Biology (2019)
Biochemical Pharmacology (2019)
Identification of rare coding variants in TYK2 protective for rheumatoid arthritis in the Japanese population and their effects on cytokine signalling
Annals of the Rheumatic Diseases (2019)
A novel nonsense variant in SUPT20H gene associated with Rheumatoid Arthritis identified by Whole Exome Sequencing of multiplex families
PLOS ONE (2019)
Investigating oxidation state-induced toxicity of PEGylated graphene oxide in ocular tissue using gene expression profiles