. 2016 Nov;75(11):2007-2013.

doi: 10.1136/annrheumdis-2015-208441. Epub 2016 Jan 18.

Decreased SMG7 expression associates with lupus-risk variants and elevated antinuclear antibody production

Yun Deng¹, Jian Zhao¹, Daisuke Sakurai¹, Andrea L Sestak², Vadim Osadchiy¹, Carl D Langefeld³, Kenneth M Kaufman⁴, Jennifer A Kelly⁵, Judith A James⁶, Michelle A Petri⁷, Sang-Cheol Bae⁸, Marta E Alarcón-Riquelme⁹, Graciela S Alarcón¹⁰, Juan-Manuel Anaya¹¹, Lindsey A Criswell¹², Barry I Freedman¹³, Diane L Kamen¹⁴, Gary S Gilkeson¹⁴, Chaim O Jacob¹⁵, Joan T Merrill¹⁶, Patrick M Gaffney⁵, Kathy Moser Sivils¹⁷, Timothy B Niewold¹⁸, Rosalind Ramsey-Goldman¹⁹, John D Reveille²⁰, R Hal Scofield²¹, Anne M Stevens²², Susan A Boackle²³, Luis M Vilá²⁴, I I Woong Sohn⁸, Seung Lee⁸, Deh-Ming Chang²⁵, Yeong Wook Song²⁶, Timothy J Vyse²⁷, John B Harley⁴, Elizabeth E Brown²⁸, Jeffrey C Edberg¹⁰, Robert P Kimberly¹⁰, Rita M Cantor²⁹, Bevra H Hahn¹, Jennifer M Grossman¹, Betty P Tsao¹

Affiliations

¹ Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.
² Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.
³ Department of Biostatistical Sciences, Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
⁴ Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA.
⁵ Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.
⁶ Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.
⁷ Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
⁸ Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea.
⁹ Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Pfizer-Universidad de Granada-Junta de Andalucía Center for Genomics and Oncological Research, Granada, Spain.
¹⁰ Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA.
¹¹ Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogotá, Colombia.
¹² Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California, USA.
¹³ Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
¹⁴ Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA.
¹⁵ Department of Medicine, University of Southern California, Los Angeles, California, USA.
¹⁶ Department of Clinical Pharmacology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.
¹⁷ Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.
¹⁸ Division of Rheumatology and Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA.
¹⁹ Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
²⁰ Department of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA.
²¹ Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA US Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma, USA.
²² Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, Washington, USA Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA.
²³ Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA US Department of Veterans Affairs Medical Center, Denver, Colorado, USA.
²⁴ Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico.
²⁵ Taipei Veterans General Hospital, Taipei City, Taiwan.
²⁶ Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Medical Research Center, Seoul National University, Seoul, Korea.
²⁷ Division of Genetics and Molecular Medicine and Immunology, King's College London, London, UK.
²⁸ Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
²⁹ Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA.

PMID: 26783109
PMCID: PMC4949149
DOI: 10.1136/annrheumdis-2015-208441

Decreased SMG7 expression associates with lupus-risk variants and elevated antinuclear antibody production

Yun Deng et al. Ann Rheum Dis. 2016 Nov.

. 2016 Nov;75(11):2007-2013.

doi: 10.1136/annrheumdis-2015-208441. Epub 2016 Jan 18.

Authors

Affiliations

¹ Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.
² Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.
³ Department of Biostatistical Sciences, Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
⁴ Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA.
⁵ Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.
⁶ Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.
⁷ Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
⁸ Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea.
⁹ Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Pfizer-Universidad de Granada-Junta de Andalucía Center for Genomics and Oncological Research, Granada, Spain.
¹⁰ Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA.
¹¹ Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogotá, Colombia.
¹² Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California, USA.
¹³ Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
¹⁴ Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA.
¹⁵ Department of Medicine, University of Southern California, Los Angeles, California, USA.
¹⁶ Department of Clinical Pharmacology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.
¹⁷ Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.
¹⁸ Division of Rheumatology and Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA.
¹⁹ Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
²⁰ Department of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA.
²¹ Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA US Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma, USA.
²² Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, Washington, USA Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA.
²³ Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA US Department of Veterans Affairs Medical Center, Denver, Colorado, USA.
²⁴ Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico.
²⁵ Taipei Veterans General Hospital, Taipei City, Taiwan.
²⁶ Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Medical Research Center, Seoul National University, Seoul, Korea.
²⁷ Division of Genetics and Molecular Medicine and Immunology, King's College London, London, UK.
²⁸ Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
²⁹ Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA.

PMID: 26783109
PMCID: PMC4949149
DOI: 10.1136/annrheumdis-2015-208441

Abstract

Objectives: Following up the systemic lupus erythematosus (SLE) genome-wide association studies (GWAS) identification of NMNAT2 at rs2022013, we fine-mapped its 150 kb flanking regions containing NMNAT2 and SMG7 in a 15 292 case-control multi-ancestry population and tested functions of identified variants.

Methods: We performed genotyping using custom array, imputation by IMPUTE 2.1.2 and allele specific functions using quantitative real-time PCR and luciferase reporter transfections. SLE peripheral blood mononuclear cells (PBMCs) were cultured with small interfering RNAs to measure antinuclear antibody (ANA) and cyto/chemokine levels in supernatants using ELISA.

Results: We confirmed association at NMNAT2 in European American (EA) and Amerindian/Hispanic ancestries, and identified independent signal at SMG7 tagged by rs2702178 in EA only (p=2.4×10^-8, OR=1.23 (95% CI 1.14 to 1.32)). In complete linkage disequilibrium with rs2702178, rs2275675 in the promoter region robustly associated with SMG7 mRNA levels in multiple expression quantitative trait locus (eQTL) datasets. Its risk allele was dose-dependently associated with decreased SMG7 mRNA levels in PBMCs of 86 patients with SLE and 119 controls (p=1.1×10^-3 and 6.8×10^-8, respectively) and conferred reduced transcription activity in transfected HEK-293 (human embryonic kidney cell line) and Raji cells (p=0.0035 and 0.0037, respectively). As a critical component in the nonsense-mediated mRNA decay pathway, SMG7 could regulate autoantigens including ribonucleoprotein (RNP) and Smith (Sm). We showed SMG7 mRNA levels in PBMCs correlated inversely with ANA titres of patients with SLE (r=-0.31, p=0.01), and SMG7 knockdown increased levels of ANA IgG and chemokine (C-C motif) ligand 19 in SLE PBMCs (p=2.0×10^-5 and 2.0×10^-4, respectively).

Conclusion: We confirmed NMNAT2 and identified independent SMG7 association with SLE. The inverse relationship between levels of the risk allele-associated SMG7 mRNAs and ANA suggested the novel contribution of mRNA surveillance pathway to SLE pathogenesis.

Keywords: Autoantibodies; Gene Polymorphism; Systemic Lupus Erythematosus.

Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

PubMed Disclaimer

Conflict of interest statement

Conflicts of Interest: None declared.

Figures

**Figure 1. Association of SNPs in the *NMNAT2/SMG7* region with SLE**
(A) The genomic structure of the *NMNAT2/SMG7* region and positions of genetic variants are indicated. (B) The allelic P value (−log₁₀P value) of each genetic variant with SLE is plotted against its position as a circle (genotyped) or a triangle (imputed) for European American (EA), Amerindian/Hispanic (HS), African American (AA) and Asian (AS), respectively. Genetic variants are highlighted using different colors according to their strength of linkage disequilibrium (r²) with rs2022013 (shown as a blue diamond) in each ancestry. The dashed line represents a Bonferroni corrected P<1×10⁻³. Arrows identify rs2022013 and SNPs demonstrating the most significant association signals in each ancestry. Black rectangle identifies group 3 SNPs at *SMG7* strongly associated with SLE in EA and the best-associated SNP rs2702178 is indicated. (C) Trans-ancestral meta-analysis is conducted on 8 SNPs that remain significant associations after Bonferroni correction in both EA and HS. Black rectangle identifies group 1&2 SNPs at *NMNAT2* intron 1 showing *P_meta* values exceeding the GWAS significance level. The dashed line represents the significance level of 5×10⁻⁸.

**Figure 2. The SLE-risk C allele of rs2275675 associated with decreased *SMG7* expression**
(A) Association of rs2275675 genotypes with *SMG7* mRNA levels in PBMCs from European-derived SLE patients and healthy controls, respectively. Each symbol represents an individual and horizontal lines indicate mean ± SEM values. (B&C) Allelic differences of rs2275675 and rs10911339 in luciferase activity. Data show the mean ± SEM results of three independent experiments.

**Figure 3. Decreased *SMG7* levels associated with increased ANA**
(A) *SMG7* mRNA levels in PBMCs correlated inversely with ANA titers of SLE patients. Among 68 patients, 56 were recruited at UCLA and 12 were recruited at OMRF, and their ANA titers were measured in Clinical Laboratory at each site. (B&C) Increased ANA IgG and CCL19 levels after *SMG7* silencing in SLE PBMCs. PBMCs from ANA positive SLE patients (n=13) were incubated for 5 days in the presence or absence of siRNA targeting *SMG7*, *GAPDH* or siRNA with a non-targeting sequence (NC), respectively. ANA IgG (B) and CCL19 (C) levels in culture supernatants were measured by ELISA, and plotted as fold change with respect to mock (culture medium only). Results are presented as mean ± SEM.

See this image and copyright information in PMC

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Decreased SMG7 expression associates with lupus-risk variants and elevated antinuclear antibody production

Affiliations

Decreased SMG7 expression associates with lupus-risk variants and elevated antinuclear antibody production

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical

Research Materials

Miscellaneous