Abstract

Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease with a strong genetic component characterized by autoantibody production and a type I interferon signature1. Here we report a missense variant (g.74779296G>A; p.Arg90His) in NCF1, encoding the p47phox subunit of the phagocyte NADPH oxidase (NOX2), as the putative underlying causal variant that drives a strong SLE-associated signal detected by the Immunochip in the GTF2IRD1GTF2I region at 7q11.23 with a complex genomic structure. We show that the p.Arg90His substitution, which is reported to cause reduced reactive oxygen species (ROS) production2, predisposes to SLE (odds ratio (OR) = 3.47 in Asians (Pmeta = 3.1 × 10−104), OR = 2.61 in European Americans, OR = 2.02 in African Americans) and other autoimmune diseases, including primary Sjögren's syndrome (OR = 2.45 in Chinese, OR = 2.35 in European Americans) and rheumatoid arthritis (OR = 1.65 in Koreans). Additionally, decreased and increased copy numbers of NCF1 predispose to and protect against SLE, respectively. Our data highlight the pathogenic role of reduced NOX2-derived ROS levels in autoimmune diseases.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    Systemic lupus erythematosus. N. Engl. J. Med. 365, 2110–2121 (2011).

  2. 2.

    et al. Copy number variation of the gene NCF1 is associated with rheumatoid arthritis. Antioxid. Redox Signal. 16, 71–78 (2012).

  3. 3.

    & Advances in lupus genetics and epigenetics. Curr. Opin. Rheumatol. 26, 482–492 (2014).

  4. 4.

    & Promise and pitfalls of the Immunochip. Arthritis Res. Ther. 13, 101 (2011).

  5. 5.

    et al. High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry. Nat. Genet. 48, 323–330 (2016).

  6. 6.

    , & NADPH oxidase inhibits the pathogenesis of systemic lupus erythematosus. Sci. Transl. Med. 4, 157ra141 (2012).

  7. 7.

    et al. Reactive oxygen species deficiency induces autoimmunity with type 1 interferon signature. Antioxid. Redox Signal. 21, 2231–2245 (2014).

  8. 8.

    et al. Lupus-associated causal mutation in neutrophil cytosolic factor 2 (NCF2) brings unique insights to the structure and function of NADPH oxidase. Proc. Natl. Acad. Sci. USA 109, E59–E67 (2012).

  9. 9.

    et al. A physical map, including a BAC/PAC clone contig, of the Williams–Beuren syndrome–deletion region at 7q11.23. Am. J. Hum. Genet. 66, 47–68 (2000).

  10. 10.

    et al. A p47-phox pseudogene carries the most common mutation causing p47-phox-deficient chronic granulomatous disease. J. Clin. Invest. 100, 1907–1918 (1997).

  11. 11.

    et al. Autosomal recessive chronic granulomatous disease caused by deletion at a dinucleotide repeat. Proc. Natl. Acad. Sci. USA 88, 2753–2757 (1991).

  12. 12.

    , & Identification of a novel NCF-1 (p47-phox) pseudogene not containing the signature GT deletion: significance for A47 degrees chronic granulomatous disease carrier detection. Blood 100, 1845–1851 (2002).

  13. 13.

    et al. A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren's syndrome at 7q11.23. Nat. Genet. 45, 1361–1365 (2013).

  14. 14.

    et al. Phosphorylation of p47phox directs phox homology domain from SH3 domain toward phosphoinositides, leading to phagocyte NADPH oxidase activation. Proc. Natl. Acad. Sci. USA 100, 4474–4479 (2003).

  15. 15.

    et al. The PX domains of p47phox and p40phox bind to lipid products of PI(3)K. Nat. Cell Biol. 3, 675–678 (2001).

  16. 16.

    , , , & p47phox Phox homology domain regulates plasma membrane but not phagosome neutrophil NADPH oxidase activation. J. Biol. Chem. 285, 35169–35179 (2010).

  17. 17.

    et al. Neutrophil extracellular traps enriched in oxidized mitochondrial DNA are interferogenic and contribute to lupus-like disease. Nat. Med. 22, 146–153 (2016).

  18. 18.

    , , & Phagocyte NADPH oxidase and specific immunity. Clin. Sci. (Lond.) 128, 635–648 (2015).

  19. 19.

    et al. Molecular characterization of LC3-associated phagocytosis reveals distinct roles for Rubicon, NOX2 and autophagy proteins. Nat. Cell Biol. 17, 893–906 (2015).

  20. 20.

    et al. Noncanonical autophagy inhibits the autoinflammatory, lupus-like response to dying cells. Nature 533, 115–119 (2016).

  21. 21.

    et al. Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus. Nat. Genet. 48, 940–946 (2016).

  22. 22.

    Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum. 40, 1725 (1997).

  23. 23.

    et al. The American Rheumatism Association 1987 revised criteria for the classification of rheumatoid arthritis. Arthritis Rheum. 31, 315–324 (1988).

  24. 24.

    et al. Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome. Nat. Genet. 45, 1284–1292 (2013).

  25. 25.

    et al. Classification criteria for Sjögren's syndrome: a revised version of the European criteria proposed by the American-European Consensus Group. Ann. Rheum. Dis. 61, 554–558 (2002).

  26. 26.

    et al. High-density genotyping of immune loci in Koreans and Europeans identifies eight new rheumatoid arthritis risk loci. Ann. Rheum. Dis. 74, e13 (2015).

Download references

Acknowledgements

We thank all subjects for their participation in this study. We thank E. Magdangal and Y. Shi for help with DNA preparation and organization. We also thank A. Lusis for valuable discussion and comments. This work was supported by US National Institutes of Health grants R01AR043814 (B.P.T.), R21AR065626 (B.P.T.), R01AR056360 (P.M.G.), R01AR063124 (P.M.G.), U19AI082714 (P.M.G.), R01AR043274 (K.L.S.), R01DE015223 (K.L.S.), R01DE018209 (K.L.S.), R01AR050782 (K.L.S.), R01AR065953 (C.J.L. and K.L.S.), P50AR0608040 (K.L.S. and C.J.L.), U19AI082714 (K.L.S. and C.J.L.) and P60AR062755 (D.L.K. and G.S.G.), the Lupus Foundation of America (B.P.T.), the Alliance for Lupus Research (B.P.T.), the Sjögren's Syndrome Foundation (K.L.S. and C.J.L.), Korea Healthcare Technology R&D Project of the Ministry for Health and Welfare in the Republic of Korea grants HI13C2124 (S.-C.B.) and HI15C3182 (K.K.), National Basic Research Program of China (973 program) grant 2014CB541902 (N.S.), Key Research Program of Bureau of Frontier Sciences and Education Chinese Academy of Sciences grant QYZDJ-SSW-SMC006 (N.S.), Key Research Program of the Chinese Academy of Sciences grant KJZD-EW-L01-3 (N.S.), State Key Laboratory of Oncogenes and Related Genes grant 91-14-05 (N.S.), National Natural Science Foundation of China grant 31630021 (N.S.), Strategic Priority Research Program of the Chinese Academy of Sciences grant XDA12020107 (N.S.). Clinical and Translational Science Institute (CTSI) grants UL1RR033176 (UCLA), UL1TR000124 (UCLA) and UL1TR001450 (MUSC), and funds from the Spaulding-Paolozzi Autoimmunity Center of Excellence (MUSC), the Richard M. Silver, MD, Endowment for Inflammation Research (B.P.T.) and the SmartState® Center of Economic Excellence in Inflammation and Fibrosis Research (B.P.T.). The funders had no role in study design, data collection, analysis and interpretation, writing of the report, or decision to submit the paper for publication.

Author information

Author notes

    • Jian Zhao
    •  & Jianyang Ma

    These authors contributed equally to this work.

Affiliations

  1. Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA.

    • Jian Zhao
    • , Yun Deng
    • , Diane L Kamen
    • , Gary S Gilkeson
    •  & Betty P Tsao
  2. Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.

    • Jian Zhao
    • , Yun Deng
    • , Bevra H Hahn
    • , Jennifer M Grossman
    •  & Betty P Tsao
  3. Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.

    • Jianyang Ma
    •  & Nan Shen
  4. Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.

    • Jennifer A Kelly
    • , Astrid Rasmussen
    • , Christopher J Lessard
    • , Kathy L Sivils
    •  & Patrick M Gaffney
  5. Department of Biology, Kyung Hee University, Seoul, Republic of Korea.

    • Kwangwoo Kim
  6. Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea.

    • So-Young Bang
    • , Hye-Soon Lee
    •  & Sang-Cheol Bae
  7. Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

    • Quan-Zhen Li
    •  & Edward K Wakeland
  8. Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Shanghai, China.

    • Rong Qiu
    •  & Nan Shen
  9. Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing, China.

    • Mengru Liu
    • , Jianping Guo
    •  & Zhanguo Li
  10. Department of Rheumatology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China.

    • Wenfeng Tan
  11. Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.

    • Christopher J Lessard
    •  & Kathy L Sivils
  12. State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

    • Nan Shen
  13. Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.

    • Nan Shen
  14. Collaborative Innovation Center for Translational Medicine at Shanghai Jiao Tong University School of Medicine, Shanghai, China.

    • Nan Shen

Authors

  1. Search for Jian Zhao in:

  2. Search for Jianyang Ma in:

  3. Search for Yun Deng in:

  4. Search for Jennifer A Kelly in:

  5. Search for Kwangwoo Kim in:

  6. Search for So-Young Bang in:

  7. Search for Hye-Soon Lee in:

  8. Search for Quan-Zhen Li in:

  9. Search for Edward K Wakeland in:

  10. Search for Rong Qiu in:

  11. Search for Mengru Liu in:

  12. Search for Jianping Guo in:

  13. Search for Zhanguo Li in:

  14. Search for Wenfeng Tan in:

  15. Search for Astrid Rasmussen in:

  16. Search for Christopher J Lessard in:

  17. Search for Kathy L Sivils in:

  18. Search for Bevra H Hahn in:

  19. Search for Jennifer M Grossman in:

  20. Search for Diane L Kamen in:

  21. Search for Gary S Gilkeson in:

  22. Search for Sang-Cheol Bae in:

  23. Search for Patrick M Gaffney in:

  24. Search for Nan Shen in:

  25. Search for Betty P Tsao in:

Contributions

J.Z., B.P.T. and N.S. led the study. J.Z., Y.D. and B.P.T. wrote the manuscript. J.Z., J.M., Y.D. and R.Q. performed the experiments. J.Z., J.M., Y.D., J.A.K. and K.K. analyzed the data and performed statistical analysis. S.-Y.B., H.-S.L., Q.-Z.L., E.K.W., M.L., J.G., Z.L., W.T., A.R., C.J.L., K.L.S., B.H.H., J.M.G., D.L.K., G.S.G., S.-C.B. and P.M.G. contributed primarily to sample collection and/or genotyping. All authors reviewed the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Jian Zhao or Nan Shen or Betty P Tsao.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–7 and Supplementary Tables 1–11

  2. 2.

    Supplementary Data

    Raw TaqMan data for the R90H variant in NCF1.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/ng.3782

Further reading