1
|
Choi D, Kim J, Yang JW, Kim JH, Park S, Shin JI. Dysregulated MicroRNAs in the Pathogenesis of Systemic Lupus Erythematosus: A Comprehensive Review. Int J Biol Sci 2023; 19:2495-2514. [PMID: 37215992 PMCID: PMC10197884 DOI: 10.7150/ijbs.74315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 12/11/2022] [Indexed: 05/24/2023] Open
Abstract
Systemic lupus erythematosus is a chronic autoimmune disease of which clinical presentation is vastly heterogeneous, ranging from mild skin rashes to severe renal diseases. Treatment goal of this illness is to minimize disease activity and prevent further organ damage. In recent years, much research has been done on the epigenetic aspects of SLE pathogenesis, for among the various factors known to contribute to the pathogenic process, epigenetic factors, especially microRNAs, bear the most therapeutic potential that can be altered unlike congenital genetic factors. This article reviews and updates what has been discovered so far about the pathogenesis of lupus, while focusing on the dysregulation of microRNAs in lupus patients in comparison to healthy controls along with the potentially pathogenic roles of the microRNAs commonly reported to be either upregulated or downregulated. Furthermore, this review includes microRNAs of which results are controversial, suggesting possible explanations for such discrepancies and directions for future research. Moreover, we aimed to emphasize the point that had been overlooked so far in studies regarding microRNA expression levels; that is, which specimen was used to assess the dysregulation of microRNAs. To our surprise, a vast number of studies have not considered this factor and have analyzed the potential role of microRNAs in general. Despite extensive investigations done on microRNA levels, their significance and potential role remain a mystery, which calls for further studies on this particular subject in regard of which specimen is used for assessment.
Collapse
Affiliation(s)
- Daeun Choi
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jimin Kim
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Won Yang
- Department of Nephrology, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Ji Hong Kim
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seoyeon Park
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
2
|
Carter LM, Alase A, Wigston Z, Psarras A, Burska A, Sutton E, Yusof MYM, Reynolds JA, McHugh N, Emery P, Wittmann M, Bruce IN, Vital EM. Gene Expression and Autoantibody Analysis Revealing Distinct Ancestry-Specific Profiles Associated With Response to Rituximab in Refractory Systemic Lupus Erythematosus. Arthritis Rheumatol 2023; 75:697-710. [PMID: 36409591 PMCID: PMC10953047 DOI: 10.1002/art.42404] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/26/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Gene expression profiles are associated with the clinical heterogeneity of systemic lupus erythematosus (SLE) but are not well studied as biomarkers for therapy. We studied gene expression and response to rituximab in a multiethnic UK cohort who were refractory to standard therapy. METHODS We evaluated baseline expression levels of transcripts known to associate with clinical features of SLE using a 96-probe TaqMan array and whole blood samples from 213 patients with active SLE who had been prospectively enrolled in the British Isles Lupus Assessment Group (BILAG) Biologics Register. We measured autoantibodies using immunoprecipitation and enzyme-linked immunosorbent assays. We determined responses to first-cycle rituximab at 6 months from treatment start in 110 SLE patients by assessing BILAG 2004 disease activity. RESULTS Interferon gene expression scores were lower in patients of European ancestry than in all other ancestry groups. The relationship between blood interferon gene expression scores and scores annotated to plasmablasts, neutrophils, myeloid lineage, inflammation, and erythropoiesis differed between patients of European and non-European ancestries. Hierarchical clustering revealed 3 distinct non-European ancestry patient subsets with stratified responses to rituximab that were not explained by sociodemographic and clinical variables, with responses lowest in an interferon-low, neutrophil-high cluster and highest in a cluster with high expression levels across all signatures (P < 0.001). Clusters in European ancestry patients did not predict response to rituximab but segregated patients by global disease activity and renal involvement. In both ancestral groups, interferon-high clusters were associated with U1 RNP/Sm antibodies. CONCLUSION Ancestry appears central to the immunologic and clinical heterogeneity in SLE. These results suggest that ancestry, disease activity, and transcriptional signatures could each assist in predicting the effectiveness of B cell depletion therapies.
Collapse
Affiliation(s)
- Lucy M. Carter
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS TrustLeedsUK
| | - Adewonuola Alase
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of LeedsLeedsUK
| | - Zoe Wigston
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of LeedsLeedsUK
| | - Antonios Psarras
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of LeedsLeedsUK
| | - Agata Burska
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of LeedsLeedsUK
| | - Emily Sutton
- Centre for Epidemiology Versus Arthritis, Division of Musculoskeletal and Dermatological SciencesUniversity of ManchesterManchesterUK
| | - Md Yuzaiful Md Yusof
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS TrustLeedsUK
| | - John A. Reynolds
- Institute of Inflammation and Ageing, University of Birmingham, and Sandwell and West Birmingham NHS TrustBirminghamUK
| | | | - Neil McHugh
- Department of Pharmacy and PharmacologyUniversity of Bath, ClavertonBathUK
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS TrustLeedsUK
| | - Miriam Wittmann
- Department of DermatologyUniversity Medical Centre, Johannes Gutenberg‐UniversityMainzGermany
| | - Ian N. Bruce
- Centre for Epidemiology Versus Arthritis, Division of Musculoskeletal and Dermatological SciencesUniversity of ManchesterManchesterUK
| | - Edward M. Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS TrustLeedsUK
| |
Collapse
|
3
|
Kim ST, Muñoz-Grajales C, Dunn SE, Schneider R, Johnson SR, Touma Z, Ahmad Z, Bonilla D, Atenafu EG, Hiraki LT, Bookman A, Wither J. Interferon and interferon-induced cytokines as markers of impending clinical progression in ANA + individuals without a systemic autoimmune rheumatic disease diagnosis. Arthritis Res Ther 2023; 25:21. [PMID: 36765391 PMCID: PMC9912609 DOI: 10.1186/s13075-023-02997-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 01/26/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Elevated levels of interferons (IFNs) are a characteristic feature of systemic autoimmune rheumatic diseases (SARDs) and may be useful in predicting impending symptomatic progression in anti-nuclear antibody-positive (ANA+) individuals lacking a SARD diagnosis. Typically, these are measured by their effect on gene expression in the blood, which has limited their utility in clinical settings. Here, we assessed whether the measurement of serum IFN-α or selected IFN-induced cytokines accurately mirrors IFN-induced gene expression in ANA+ individuals and investigated their utility as biomarkers of clinical progression. METHODS A total of 280 subjects were studied, including 50 ANA- healthy controls, 160 ANA+ individuals without a SARD diagnosis (96 asymptomatic, 64 with undifferentiated connective tissue disease), and 70 SARD patients. IFN-induced gene expression was measured by nanoString and cytokine levels by ELISA or Simoa. ANA+ individuals lacking a SARD diagnosis who had the new onset of SARD criteria over the subsequent 2 years were defined as progressors. RESULTS Measurement of IFN-α levels by high-sensitivity ELISA or Simoa correlated much better with IFN-induced gene expression than measurement of CXCL-10 or Galectin-9 levels. Despite this, high CXCL-10 and Galectin-9 levels were better predictors of subsequent progression in ANA+ individuals than measures of IFN-α or IFN-induced gene expression with the optimal combination of predictive cytokines (CXCL-10 and IFN-α as measured by ELISA), resulting in a specificity and positive predictive value of 100%. CONCLUSION Easily performed ELISA assays for CXCL-10 and IFN-α can be used to predict ANA+ individuals at high risk of imminent symptomatic progression.
Collapse
Affiliation(s)
- Sonya T. Kim
- grid.231844.80000 0004 0474 0428Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 0S8 Canada
| | - Carolina Muñoz-Grajales
- grid.231844.80000 0004 0474 0428Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 0S8 Canada ,grid.17063.330000 0001 2157 2938Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, ON Canada
| | - Shannon E. Dunn
- grid.17063.330000 0001 2157 2938Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, ON Canada ,grid.415502.7Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON Canada
| | - Raphael Schneider
- grid.415502.7Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON Canada ,grid.415502.7Division of Neurology, St. Michael’s Hospital Unity Health, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, ON Canada
| | - Sindhu R. Johnson
- grid.17063.330000 0001 2157 2938Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, ON Canada ,Toronto Scleroderma Program, Division of Rheumatology, Toronto Western and Mount Sinai Hospitals, Toronto, ON Canada
| | - Zahi Touma
- grid.17063.330000 0001 2157 2938Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, ON Canada ,grid.231844.80000 0004 0474 0428University of Toronto Lupus Clinic, Centre for Prognosis Studies in Rheumatic Diseases, Schroeder Arthritis Institute, University Health Network, Toronto, ON Canada
| | - Zareen Ahmad
- grid.17063.330000 0001 2157 2938Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, ON Canada ,Toronto Scleroderma Program, Division of Rheumatology, Toronto Western and Mount Sinai Hospitals, Toronto, ON Canada
| | - Dennisse Bonilla
- grid.231844.80000 0004 0474 0428Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 0S8 Canada
| | - Eshetu G. Atenafu
- grid.231844.80000 0004 0474 0428Biostatistics Department, Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Linda T. Hiraki
- grid.17063.330000 0001 2157 2938Division of Rheumatology, The Hospital for Sick Children, and Department of Paediatrics, University of Toronto, Toronto, ON Canada
| | - Arthur Bookman
- grid.17063.330000 0001 2157 2938Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, ON Canada ,grid.231844.80000 0004 0474 0428Division of Rheumatology, Schroeder Arthritis Institute, University Health Network, Toronto, ON Canada
| | - Joan Wither
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada. .,Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada. .,Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, ON, Canada. .,Division of Rheumatology, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.
| |
Collapse
|
4
|
Gao M, Liu S, Chatham WW, Mountz JD, Hsu HC. IL-4-Induced Quiescence of Resting Naive B Cells Is Disrupted in Systemic Lupus Erythematosus. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1513-1522. [PMID: 36165181 PMCID: PMC9741951 DOI: 10.4049/jimmunol.2200409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/11/2022] [Indexed: 12/13/2022]
Abstract
Activated naive (aNAV) B cells have been shown to be the precursor of the CD11c+T-bet+ IgD-CD27- double-negative (DN)2 or atypical memory (aMEM) B cells in systemic lupus erythematosus (SLE). To determine factors that maintain resting naive (rNAV) B cells, the transcriptomic program in naive (IGHD+IGHM +) B cells in human healthy control subjects (HC) and subjects with SLE was analyzed by single-cell RNA-sequencing analysis. In HC, naive B cells expressed IL-4 pathway genes, whereas in SLE, naive B cells expressed type I IFN-stimulated genes (ISGs). In HC, aNAV B cells exhibited upregulation of the gene signature of germinal center and classical memory (cMEM) B cells. In contrast, in SLE, aNAV B cells expressed signature genes of aMEM. In vitro exposure of SLE B cells to IL-4 promoted B cell development into CD27+CD38+ plasmablasts/plasma and IgD-CD27+ cMEM B cells. The same treatment blocked the development of CD11c+Tbet+ aNAV and DN2 B cells and preserved DN B cells as CD11c-Tbet- DN1 B cells. Lower expression of IL-4R and increased intracellular IFN-β in naive B cells was correlated with the accumulation of CD21-IgD- B cells and the development of anti-Smith and anti-DNA autoantibodies in patients with SLE (n = 47). Our results show that IL-4R and type I IFN signaling in naive B cells induce the development of distinct lineages of cMEM versus aMEM B cells, respectively. Furthermore, diminished IL-4R signaling shifted activated B cell development from the DN1 to the DN2 trajectory in patients with SLE. Therapies that enhance IL-4R signaling may be beneficial for ISGhi SLE patients.
Collapse
Affiliation(s)
- Min Gao
- University of Alabama at Birmingham, Birmingham, AL; and
| | - Shanrun Liu
- University of Alabama at Birmingham, Birmingham, AL; and
| | - W Winn Chatham
- University of Alabama at Birmingham, Birmingham, AL; and
| | - John D Mountz
- University of Alabama at Birmingham, Birmingham, AL; and
- Birmingham Veterans Affairs Medical Center, Birmingham, AL
| | - Hui-Chen Hsu
- University of Alabama at Birmingham, Birmingham, AL; and
- Birmingham Veterans Affairs Medical Center, Birmingham, AL
| |
Collapse
|
5
|
Vital EM, Merrill JT, Morand EF, Furie RA, Bruce IN, Tanaka Y, Manzi S, Kalunian KC, Kalyani RN, Streicher K, Abreu G, Tummala R. Anifrolumab efficacy and safety by type I interferon gene signature and clinical subgroups in patients with SLE: post hoc analysis of pooled data from two phase III trials. Ann Rheum Dis 2022; 81:951-961. [PMID: 35338035 PMCID: PMC9213795 DOI: 10.1136/annrheumdis-2021-221425] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/26/2022] [Indexed: 12/21/2022]
Abstract
Objectives To characterise the efficacy and safety of anifrolumab in patients with systemic lupus erythematosus (SLE) according to interferon gene signature (IFNGS), demographic and clinical subgroups. Methods We performed post hoc analyses of pooled data from the 52-week phase III TULIP-1/TULIP-2 placebo-controlled trials of intravenous anifrolumab in moderate-to-severe SLE. Outcomes were assessed in predefined subgroups: IFNGS (high/low), age, sex, body mass index, race, geographic region, age of onset, glucocorticoid use, disease activity and serological markers. Results In pooled data, patients received anifrolumab 300 mg (360/726) or placebo (366/726); 82.6% were IFNGS-high. IFNGS-high patients had greater baseline disease activity and were more likely to have abnormal serological markers versus IFNGS-low patients. In the total population, a greater proportion of patients treated with anifrolumab versus placebo achieved British Isles Lupus Assessment Group-based Composite Lupus Assessment (BICLA) response at week 52 (difference 16.6%; nominal p<0.001). BICLA response treatment differences with anifrolumab versus placebo were comparable to the total population across most predefined subgroups, including subgroups for baseline glucocorticoid dosage (<10/≥10 mg/day prednisone/equivalent) and for clinical disease activity (SLE Disease Activity Index 2000 score <10/≥10). Subgroups with larger treatment differences included IFNGS-high patients (18.2%), patients with abnormal baseline serological markers (23.1%) and Asian patients (29.2%). The safety profile of anifrolumab was similar across subgroups. Conclusions Overall, this study supports the consistent efficacy and safety of anifrolumab across a range of patients with moderate-to-severe SLE. In a few subgroups, small sample sizes limited conclusions from being drawn regarding the treatment benefit with anifrolumab. Trial registration number NCT02446912, NCT02446899.
Collapse
Affiliation(s)
- Edward M Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds, UK.,NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Joan T Merrill
- Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Eric F Morand
- Centre for Inflammatory Disease Monash Health, Monash University, Melbourne, Victoria, Australia
| | - Richard A Furie
- Division of Rheumatology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Great Neck, New York, USA
| | - Ian N Bruce
- Centre for Epidemiology Versus Arthritis, The University of Manchester, NIHR Manchester Biomedical Research Centre, Manchester, UK.,Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Japan
| | - Susan Manzi
- Lupus Center of Excellence, Autoimmunity Institute, Allegheny Health Network, Pittsburgh, Pennsylvania, USA
| | - Kenneth C Kalunian
- Division of Rheumatology, Allergy and Immunology, University of California San Diego, La Jolla, California, USA
| | - Rubana N Kalyani
- BioPharmaceuticals R&D, AstraZeneca US, Gaithersburg, Maryland, USA
| | - Katie Streicher
- BioPharmaceuticals R&D, AstraZeneca US, Gaithersburg, Maryland, USA
| | - Gabriel Abreu
- BioPharmaceuticals R&D, AstraZeneca R&D, Gothenburg, Sweden
| | - Raj Tummala
- BioPharmaceuticals R&D, AstraZeneca US, Gaithersburg, Maryland, USA
| |
Collapse
|
6
|
Hubbard EL, Pisetsky DS, Lipsky PE. Anti-RNP antibodies are associated with the interferon gene signature but not decreased complement levels in SLE. Ann Rheum Dis 2022; 81:632-643. [PMID: 35115332 DOI: 10.1136/annrheumdis-2021-221662] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/19/2022] [Indexed: 01/01/2023]
Abstract
OBJECTIVES The goals of these studies were to elucidate the inter-relationships of specific anti-nuclear antibody (ANA), complement, and the interferon gene signature (IGS) in the pathogenesis of systemic lupus erythematosus (SLE). METHODS Data from the Illuminate trials were analysed for antibodies to dsDNA as well as RNA-binding proteins (RBP), levels of C3, C4 and various IGS. Statistical hypothesis testing, linear regression analyses and classification and regression trees analysis were employed to assess relationships between the laboratory features of SLE. RESULTS Inter-relationships of ANAs, complement and the IGS differed between patients of African Ancestry (AA) and European Ancestry (EA); anti-RNP and multiple autoantibodies were more common in AA patients and, although both related to the presence of the IGS, relationships between autoantibodies and complement differed. Whereas, anti-dsDNA had an inverse relationship to C3 and C4, levels of anti-RNP were not related to these markers. The IGS was only correlated with anti-dsDNA in EA SLE and complement was more correlated to the IGS in AA SLE. Finally, autoantibodies occurred in the presence and absence of the IGS, whereas the IGS was infrequent in anti-dsDNA/anti-RBP-negative SLE patients. CONCLUSION There is a complex relationship between autoantibodies and the IGS, with anti-RNP associated in AA and both anti-dsDNA and RNP associated in EA. Moreover, there was a difference in the relationship between anti-dsDNA, but not anti-RBP, with complement levels. The lack of a relationship of anti-RNP with C3 and C4 suggests that anti-RNP immune complexes (ICs) may drive the IGS without complement fixation, whereas anti-dsDNA ICs involve complement consumption.
Collapse
Affiliation(s)
- Erika L Hubbard
- AMPEL BioSolutions LLC, Charlottesville, Virginia, USA.,RILITE Foundation, Charlottesville, Virginia, USA
| | - David S Pisetsky
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA.,Rheumatology, Durham VA Medical Center, Durham, North Carolina, USA
| | - Peter E Lipsky
- AMPEL BioSolutions LLC, Charlottesville, Virginia, USA .,RILITE Foundation, Charlottesville, Virginia, USA
| |
Collapse
|
7
|
Fu Q, He Q, Dong Q, Xie J, Geng Y, Han H, Huang Y, Lu J, Zeng Z, Wang W, Chen K, Zhan X. The role of cyclic GMP-AMP synthase and Interferon-I-inducible protein 16 as candidatebiomarkers of systemic lupus erythematosus. Clin Chim Acta 2022; 524:69-77. [PMID: 34742679 DOI: 10.1016/j.cca.2021.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 10/24/2021] [Accepted: 11/01/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Diverse clinical and serological manifestations of systemic lupus erythematosus (SLE) compromise its diagnosis and treatment. A more reliable biomarker for SLE, which can play a critical role in either diagnosis, monitoring the disease progress or evaluating the response to treatment for individualized therapeutic, is necessary. DNA sensor is an important mediator of inflammation in systemic autoimmune diseases. However, the potential role for DNA sensor as disease activity biomarkers for SLE remained obscure. We detected the aberrant activation of DNA sensors and the corresponding IFN-β response in SLE patients, and to evaluate their potential role as disease biomarkers for SLE. METHODS We quantified the expressions of IFN-I and DNA sensor, such as cGAS, IFI16, DDX41, DAI and their down-stream adaptor STING in PBMC derived from patients with SLE (n = 100), healthy controls (HCs) (n = 62) by real-time PCR. The relationships between the expression of cGAS or IFI16 and clinical features in SLE patients were investigated. ROC curve analysis was performed to examine the predictive value of cGAS and IFI16 in SLE diagnosis, disease activity monitoring, specific organ manifestation and therapeutic response. RNA interference-mediated depletion of IFI16 or cGAS was conducted to evaluate their impact on IFN-I response. RESULTS The expressions of cGAS and IFI16 were significantly higher in PBMC from SLE patients, closely correlated with the SLEDAI scores and high anti-dsDNA antibody titers. While the AUC for cGAS (0.767) was less than that of IFI16 and IFN-β, the AUC for IFI16 (0.856) and IFN-β (0.856) were similar. Expression of cGAS and IFI16 combine with IFN-β in PBMC showed high sensitivity (89.2%) and specificity (89.1%) for discrimination between mild and moderate/severe disease activity in SLE. Higher expression of IFI16 was association with ocular disorder in SLE patients. Neither IFI16 nor cGAS was a reliable indicator of therapeutic response. RNA interference-mediated depletion of IFI16 or cGAS prevented active SLE serum-induced upregulating in both IFN-α and IFN-β. CONCLUSIONS High expression levels of cGAS and IFI16 in PBMC from SLE patients correlated strongly with disease activity. Both cGAS and IFI16 mediated signaling pathway were account for the robust production of IFN-β. Expression of cGAS and IFI16 combined with IFN-β in PBMC might serve as potential biomarkers for early diagnosis and monitoring disease activity in SLE.
Collapse
Affiliation(s)
- Qiang Fu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, 2 Zhongshan Road, Guangzhou 510080, Guangdong, China
| | - Qiuying He
- Department of Laboratory Medicine, Zhongshan Hospital of Sun Yat-sen University, 2 Sunwendong Road, Zhongshan 528403, Guangdong, China
| | - Qian Dong
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, 2 Zhongshan Road, Guangzhou 510080, Guangdong, China
| | - Jinye Xie
- Department of Laboratory Medicine, Zhongshan Hospital of Sun Yat-sen University, 2 Sunwendong Road, Zhongshan 528403, Guangdong, China
| | - Yiyun Geng
- Department of Laboratory Medicine, Zhongshan Hospital of Sun Yat-sen University, 2 Sunwendong Road, Zhongshan 528403, Guangdong, China
| | - Hui Han
- Department of Laboratory Medicine, Zhongshan Hospital of Sun Yat-sen University, 2 Sunwendong Road, Zhongshan 528403, Guangdong, China
| | - Yanhua Huang
- Department of Laboratory Medicine, Zhongshan Hospital of Sun Yat-sen University, 2 Sunwendong Road, Zhongshan 528403, Guangdong, China
| | - Jianqiang Lu
- Department of Laboratory Medicine, Zhongshan Hospital of Sun Yat-sen University, 2 Sunwendong Road, Zhongshan 528403, Guangdong, China
| | - Zhijie Zeng
- Department of Laboratory Medicine, Zhongshan Hospital of Sun Yat-sen University, 2 Sunwendong Road, Zhongshan 528403, Guangdong, China
| | - Weijia Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, 2 Zhongshan Road, Guangzhou 510080, Guangdong, China.
| | - Kang Chen
- Department of Laboratory Medicine, Zhongshan Hospital of Sun Yat-sen University, 2 Sunwendong Road, Zhongshan 528403, Guangdong, China.
| | - Xiaoxia Zhan
- Department of Laboratory Medicine, Zhongshan Hospital of Sun Yat-sen University, 2 Sunwendong Road, Zhongshan 528403, Guangdong, China.
| |
Collapse
|
8
|
The Pathogenesis, Molecular Mechanisms, and Therapeutic Potential of the Interferon Pathway in Systemic Lupus Erythematosus and Other Autoimmune Diseases. Int J Mol Sci 2021; 22:ijms222011286. [PMID: 34681945 PMCID: PMC8540355 DOI: 10.3390/ijms222011286] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 12/11/2022] Open
Abstract
Therapeutic success in treating patients with systemic lupus erythematosus (SLE) is limited by the multivariate disease etiology, multi-organ presentation, systemic involvement, and complex immunopathogenesis. Agents targeting B-cell differentiation and survival are not efficacious for all patients, indicating a need to target other inflammatory mediators. One such target is the type I interferon pathway. Type I interferons upregulate interferon gene signatures and mediate critical antiviral responses. Dysregulated type I interferon signaling is detectable in many patients with SLE and other autoimmune diseases, and the extent of this dysregulation is associated with disease severity, making type I interferons therapeutically tangible targets. The recent approval of the type I interferon-blocking antibody, anifrolumab, by the US Food and Drug Administration for the treatment of patients with SLE demonstrates the value of targeting this pathway. Nevertheless, the interferon pathway has pleiotropic biology, with multiple cellular targets and signaling components that are incompletely understood. Deconvoluting the complexity of the type I interferon pathway and its intersection with lupus disease pathology will be valuable for further development of targeted SLE therapeutics. This review summarizes the immune mediators of the interferon pathway, its association with disease pathogenesis, and therapeutic modalities targeting the dysregulated interferon pathway.
Collapse
|
9
|
Abstract
Skewing of type I interferon (IFN) production and responses is a hallmark of systemic lupus erythematosus (SLE). Genetic and environmental contributions to IFN production lead to aberrant innate and adaptive immune activation even before clinical development of disease. Basic and translational research in this arena continues to identify contributions of IFNs to disease pathogenesis, and several promising therapeutic options for targeting of type I IFNs and their signaling pathways are in development for treatment of SLE patients.
Collapse
Affiliation(s)
- Sirisha Sirobhushanam
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, 5568 MSRB 2, 1150 West Medical Center Drive, Ann Arbor, MI 49109, USA
| | - Stephanie Lazar
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, 5568 MSRB 2, 1150 West Medical Center Drive, Ann Arbor, MI 49109, USA
| | - J Michelle Kahlenberg
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, 5570A MSRB 2, 1150 West Medical Center Drive, Ann Arbor, MI 49109, USA; Department of Dermatology, University of Michigan, 5570A MSRB 2, 1150 West Medical Center Drive, Ann Arbor, MI 49109, USA.
| |
Collapse
|
10
|
Wang X, Ma R, Shi W, Wu Z, Shi Y. Emerging roles of circular RNAs in systemic lupus erythematosus. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:212-222. [PMID: 33767917 PMCID: PMC7973136 DOI: 10.1016/j.omtn.2021.02.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs with covalently closed single-stranded structures lacking 5'-3' polarity and a polyadenine tail. Over recent years, a growing body of studies have been conducted to explore the roles of circRNAs in human diseases. Systemic lupus erythematosus (SLE) is a severe autoimmune disorder characterized by the presence of autoantibodies and excessive inflammation, which impact multiple organs. Recent advances have begun to shed light on the roles of circRNAs in SLE, providing fresh insights into the pathogenesis of SLE and the latent capacity for translation into clinical applications. Here, we briefly introduce these "star molecules" and summarize their roles in SLE. In addition, we outline the limitations of the current studies and raise prospects for future research.
Collapse
Affiliation(s)
- Xin Wang
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China
| | - Rui Ma
- Ministry of Education, Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weimin Shi
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhouwei Wu
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuling Shi
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
11
|
Thanou A, Jupe E, Purushothaman M, Niewold TB, Munroe ME. Clinical disease activity and flare in SLE: Current concepts and novel biomarkers. J Autoimmun 2021; 119:102615. [PMID: 33631651 DOI: 10.1016/j.jaut.2021.102615] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/19/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex and heterogeneous systemic autoimmune disease associated with innate and adaptive immune dysregulation. SLE occurs primarily in females of childbearing age, with increased prevalence and severity in minority populations. Despite improvements in treatment modalities, SLE patients frequently experience periods of heightened disease activity and flare that can lead to permanent organ damage, increased morbidity, and early mortality. Such outcomes impair quality of life and inflict a significant socioeconomic burden. Predicting changes in SLE disease activity could allow for closer monitoring and preemptive treatment, but existing clinical, demographic and serologic markers have been only modestly predictive. Novel, proactive approaches to clinical disease management are thus critically needed. Panels of blood biomarkers can detect a breadth of immune pathway dysregulation that captures SLE heterogeneity and disease activity. Alterations in the balance of pro-inflammatory and regulatory soluble mediators have been associated with changes in clinical disease activity and are detectable several weeks prior to clinical flare occurrence. A soluble mediator score has been highly predictive of impending flare in both European American and African American SLE patients, and this score does not require a priori knowledge of specific pathway activation in the patient. We review current concepts of disease activity and flare in SLE, focusing on the potential of novel blood biomarkers to characterize and predict changes in disease activity. Measuring the disordered immune response in SLE in this way promises to improve disease management and prevent organ damage in SLE.
Collapse
Affiliation(s)
| | - Eldon Jupe
- Progentec Diagnostics, Inc., Oklahoma City, OK, USA
| | | | - Timothy B Niewold
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA
| | | |
Collapse
|
12
|
Seifert S, Gundlach S, Junge O, Szymczak S. Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study. Bioinformatics 2021; 36:4301-4308. [PMID: 32399562 PMCID: PMC7520048 DOI: 10.1093/bioinformatics/btaa483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/13/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION High-throughput technologies allow comprehensive characterization of individuals on many molecular levels. However, training computational models to predict disease status based on omics data is challenging. A promising solution is the integration of external knowledge about structural and functional relationships into the modeling process. We compared four published random forest-based approaches using two simulation studies and nine experimental datasets. RESULTS The self-sufficient prediction error approach should be applied when large numbers of relevant pathways are expected. The competing methods hunting and learner of functional enrichment should be used when low numbers of relevant pathways are expected or the most strongly associated pathways are of interest. The hybrid approach synthetic features is not recommended because of its high false discovery rate. AVAILABILITY AND IMPLEMENTATION An R package providing functions for data analysis and simulation is available at GitHub (https://github.com/szymczak-lab/PathwayGuidedRF). An accompanying R data package (https://github.com/szymczak-lab/DataPathwayGuidedRF) stores the processed and quality controlled experimental datasets downloaded from Gene Expression Omnibus (GEO). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Stephan Seifert
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Sven Gundlach
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Olaf Junge
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| |
Collapse
|
13
|
Gelaye B, Foster S, Bhasin M, Tawakol A, Fricchione G. SARS-CoV-2 morbidity and mortality in racial/ethnic minority populations: A window into the stress related inflammatory basis of health disparities? Brain Behav Immun Health 2020; 9:100158. [PMID: 33052326 PMCID: PMC7543984 DOI: 10.1016/j.bbih.2020.100158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
Health disparity related to race/ethnicity has been cited as “the most serious and shameful health care issue of our time”(Peterson et al., 2018). A portion of the now recognized disproportionate impact of the COVID-19 pandemic among Black, Indigenous and People of Color (BIPOC) communities is attributable to social determinants such as socioeconomic status (SES), physical living situation, health care access, and the psychosocial factors associated with socioenvironmental circumstances such as bias, victimization, trauma and toxic stress as well as structural factors that reduce the capacity to practice physical distancing (Agurs-Collins et al., 2019). In this paper, we hypothesize that, prior to the COVID-19 pandemic, disproportionate socio-economic and environmental stressors in the BIPOC population promoted heightened stress-associated neurobiological activity (Stress-NbA). This chronic elevation in Stress-NbA results in down-stream complications of chronic stress including underactivation of anti-viral type I IFN pathway genes. This results in an increase in susceptibility to viral diseases, including coronavirus illnesses. Additionally, Stress-NbA chronically potentiates systemic inflammation (from hematopoietic system activation with myelopoiesis) increasing the prevalence of metabolic syndrome (MetS) and setting the stage for stress-related chronic non-communicable diseases (NCDs). This process was propelled by overactivation of immune cell gene expression in the nuclear factor κ-light-chain-enhancer of activated B cells (NF-kB) activation pathway and underactivation of gene expression in the anti-viral type I interferon (IFN) pathway. The higher prevalence of MetS and NCDs in minority populations turned out to be predictive of the elevated risk they would face in the presence of a highly contagious viral pandemic. The stress-related generation of a chronic non-pathogen associated molecular pattern (non-PAMP) immunoactivation state led to decreased viral immune defense and increased susceptibility to SARS-CoV-2 infection with increased risk of severe illness induced by cytokine storm syndrome (CSS). There is a disproportionate impact of the COVID-19 pandemic among Black, Indigenous and People of Color (BIPOC) communities. Prior to the COVID-19 pandemic and during the pandemic, existing disproportionate structural, socio-economic and environmental stressors in the BIPOC communities may have resulted in heightened stress-associated neurobiological activity (Stress-NbA). In this paper, we hypothesize that a combination of chronic elevation of stress-NbA, systemic inflammation, stress response and immune response related factors aligned against BIPIC communities are potential drivers of excess morbidity and mortality.
Collapse
Affiliation(s)
- Bizu Gelaye
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Simmie Foster
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Manoj Bhasin
- Department of Pediatrics and Department of Biomedical Bioinformatics, Emory University School of Medicine, Atlanta, GA, United States
| | - Ahmed Tawakol
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Gregory Fricchione
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Benson-Henry Institute for Mind Body Medicine at Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
14
|
Zervou MI, Andreou A, Matalliotakis M, Spandidos DA, Goulielmos GN, Eliopoulos EE. Association of the DNASE1L3 rs35677470 polymorphism with systemic lupus erythematosus, rheumatoid arthritis and systemic sclerosis: Structural biological insights. Mol Med Rep 2020; 22:4492-4498. [PMID: 33173951 PMCID: PMC7646740 DOI: 10.3892/mmr.2020.11547] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/30/2020] [Indexed: 01/29/2023] Open
Abstract
Although genome-wide association studies (GWAS) have identified hundreds of autoimmune disease-associated loci, much of the genetics underlying these diseases remains unknown. In an attempt to identify potential causal variants, previous studies have determined that the rs35677470 missense variant of the Deoxyribonuclease I-like 3 (DNASE1L3) gene was associated with the development of systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and systemic sclerosis (SSc). DNase1L3 is a member of the human DNase I family, representing a nuclease that cleaves double-stranded DNA during apoptosis and serving a role in the development of autoimmune diseases. The present study aimed to determine the role of the rs35677470 variant at the DNASE1L3 gene leading to the R206C mutation in SLE, RA and SSc. The underlying mechanism potentially affecting protein structure loss of function was also assessed. DNASE1L3 evolution was investigated to define conservation elements in the protein sequence. Additionally, 3D homology modeling and in silico mutagenesis was performed to localize the polymorphism under investigation. Evolutionary analysis revealed heavily conserved sequence elements among species, indicating structural/functional importance. In silico mutagenesis and 3D protein structural analysis also demonstrated the potentially varied impact of the DNASE1L3 (rs35677470) single nucleotide polymorphism (SNP), providing an explanation for its effect on the R206C variant. Structural analysis demonstrated that the rs35677470 SNP encodes a non-conservative amino acid variation, R206C, which disrupted the conserved electrostatic network holding secondary protein structure elements in position. Specifically, the R206 to E170 interaction forming part of a salt bridge network stabilizing two α-helices was interrupted, thereby affecting the molecular architecture. Previous studies on the effect of this SNP in Caucasian populations demonstrated lower DNAse1L3 activity levels, which is consistent with the current results. The present study comprehensively evaluated the shared autoimmune locus of DNASE1L3 (rs35677470), which produced an inactive form of DNaseIL3. Furthermore, structural analysis explained the potential role of the produced mutation by modifying the placement of structural elements and consequently introducing disorder in protein folding, affecting biological function.
Collapse
Affiliation(s)
- Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Athena Andreou
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Michail Matalliotakis
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Elias E Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| |
Collapse
|
15
|
Pisetsky DS, Lipsky PE. New insights into the role of antinuclear antibodies in systemic lupus erythematosus. Nat Rev Rheumatol 2020; 16:565-579. [PMID: 32884126 DOI: 10.1038/s41584-020-0480-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 01/05/2023]
Abstract
Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterized by antinuclear antibodies (ANAs) that form immune complexes that mediate pathogenesis by tissue deposition or cytokine induction. Some ANAs bind DNA or associated nucleosome proteins, whereas other ANAs bind protein components of complexes of RNA and RNA-binding proteins (RBPs). Levels of anti-DNA antibodies can fluctuate widely, unlike those of anti-RBP antibodies, which tend to be stable. Because anti-DNA antibody levels can reflect disease activity, repeat testing is common; by contrast, a single anti-RBP antibody determination is thought to suffice for clinical purposes. Experience from clinical trials of novel therapies has provided a new perspective on ANA expression during disease, as many patients with SLE are ANA negative at screening despite previously testing positive. Because trial results suggest that patients who are ANA negative might not respond to certain agents, screening strategies now involve ANA and anti-DNA antibody testing to identify patients with so-called 'active, autoantibody-positive SLE'. Evidence suggests that ANA responses can decrease over time because of the natural history of disease or the effects of therapy. Together, these findings suggest that, during established disease, more regular serological testing could illuminate changes relevant to pathogenesis and disease status.
Collapse
Affiliation(s)
- David S Pisetsky
- Departments of Medicine and Immunology, Duke University Medical Center and Medical Research Service, Veterans Administration Medical Center, Durham, NC, USA.
| | | |
Collapse
|
16
|
Catalina MD, Bachali P, Yeo AE, Geraci NS, Petri MA, Grammer AC, Lipsky PE. Patient ancestry significantly contributes to molecular heterogeneity of systemic lupus erythematosus. JCI Insight 2020; 5:140380. [PMID: 32759501 PMCID: PMC7455079 DOI: 10.1172/jci.insight.140380] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Gene expression signatures can stratify patients with heterogeneous diseases, such as systemic lupus erythematosus (SLE), yet understanding the contributions of ancestral background to this heterogeneity is not well understood. We hypothesized that ancestry would significantly influence gene expression signatures and measured 34 gene modules in 1566 SLE patients of African ancestry (AA), European ancestry (EA), or Native American ancestry (NAA). Healthy subject ancestry-specific gene expression provided the transcriptomic background upon which the SLE patient signatures were built. Although standard therapy affected every gene signature and significantly increased myeloid cell signatures, logistic regression analysis determined that ancestral background significantly changed 23 of 34 gene signatures. Additionally, the strongest association to gene expression changes was found with autoantibodies, and this also had etiology in ancestry: the AA predisposition to have both RNP and dsDNA autoantibodies compared with EA predisposition to have only anti-dsDNA. A machine learning approach was used to determine a gene signature characteristic to distinguish AA SLE and was most influenced by genes characteristic of the perturbed B cell axis in AA SLE patients. Transcriptional profiling of lupus patients and healthy controls reveals ancestry-related differences and transcriptional heterogeneity among lupus patients.
Collapse
Affiliation(s)
- Michelle D Catalina
- AMPEL BioSolutions LLC & RILITE Research Institute, Charlottesville, Virginia, USA.,EMD Serono Research & Development Institute, Billerica, Massachusetts, USA
| | - Prathyusha Bachali
- AMPEL BioSolutions LLC & RILITE Research Institute, Charlottesville, Virginia, USA
| | | | - Nicholas S Geraci
- AMPEL BioSolutions LLC & RILITE Research Institute, Charlottesville, Virginia, USA
| | - Michelle A Petri
- Division of Rheumatology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Amrie C Grammer
- AMPEL BioSolutions LLC & RILITE Research Institute, Charlottesville, Virginia, USA
| | - Peter E Lipsky
- AMPEL BioSolutions LLC & RILITE Research Institute, Charlottesville, Virginia, USA
| |
Collapse
|
17
|
Guo G, Chen A, Ye L, Wang H, Chen Z, Yan K, Shi X, Li B, Lin Q, You X, Jiang C, Zhang Q, Ding X, Xue X, Zhang H. TCONS_00483150 as a novel diagnostic biomarker of systemic lupus erythematosus. Epigenomics 2020; 12:973-988. [PMID: 32677847 DOI: 10.2217/epi-2019-0265] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We aimed to identify differentially expressed Long noncoding RNAs (lncRNAs) and explore their functional roles in systemic lupus erythematosus (SLE). Materials & methods: We identified dysregulated lncRNAs and investigated their prognostic values and potential functions using MiRTarget2, catRAPID omics and Bedtools/blast/Pearson analyses. Results: Among the 143 differentially expressed lncRNAs, TCONS_00483150 could be used to distinguish patients with SLE from healthy controls and those with rheumatoid arthritis and patients with active/stable SLE from healthy controls. TCONS_00483150 was significantly correlated with anti-Rib-P antibody positivity and low C3 levels; TCONS_00483150 dysregulation might contribute to the metabolism of RNA and proteins in SLE patients. Conclusion: Overall, our findings offer a transcriptome-wide overview of aberrantly expressed lncRNAs in patients with SLE and highlight TCONS_00483150 as a potential novel diagnostic biomarker.
Collapse
Affiliation(s)
- Gangqiang Guo
- School of Life Sciences and Technology, Tongji University, Shanghai, PR China.,Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, PR China
| | - Aqiong Chen
- Department of Rheumatology, Ningbo Medical Center Lihuili Hospital, Ningbo, PR China
| | - Lele Ye
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, PR China.,Department of Gynecologic Oncology, Wenzhou Central Hospital, Wenzhou, PR China
| | - Huijing Wang
- Kidney Disease Center, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China.,Department of Rheumatology, South Campus, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, PR China
| | - Zhiyuan Chen
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, PR China
| | - Kejing Yan
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, PR China
| | - Xinyu Shi
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, PR China
| | - Baoqing Li
- Department of Laboratory Medicine, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, PR China
| | - Qiaoai Lin
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, PR China
| | - Xiaohan You
- Department of Nephrology, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, PR China
| | - Cizhong Jiang
- School of Life Sciences and Technology, Tongji University, Shanghai, PR China
| | - Qingfeng Zhang
- Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Xiaokai Ding
- Department of Nephrology, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, PR China
| | - Xiangyang Xue
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, PR China
| | - Huidi Zhang
- Department of Nephrology, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, PR China
| |
Collapse
|
18
|
Slight-Webb S, Smith M, Bylinska A, Macwana S, Guthridge C, Lu R, Merrill JT, Chakravarty E, Arriens C, Munroe ME, Maecker HT, Utz PJ, Guthridge JM, James JA. Autoantibody-positive healthy individuals with lower lupus risk display a unique immune endotype. J Allergy Clin Immunol 2020; 146:1419-1433. [PMID: 32446964 DOI: 10.1016/j.jaci.2020.04.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/01/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Autoimmune diseases comprise a spectrum of illnesses and are on the rise worldwide. Although antinuclear antibodies (ANAs) are detected in many autoimmune diseases, up to 20% of healthy women are ANA-positive (ANA+) and most will never develop clinical symptoms. Furthermore, disease transition is higher among ANA+ African Americans compared with ANA+ European Americans. OBJECTIVE We sought to determine the immune features that might define and prevent transition to clinical autoimmunity in ANA+ healthy individuals. METHODS We comprehensively phenotyped immune profiles of African Americans and European Americans who are ANA-negative (ANA-) healthy, ANA+ healthy, or have SLE using single cell mass cytometry, next-generation RNA-sequencing, multiplex cytokine profiling, and phospho-signaling analyses. RESULTS We found that, compared with both ANA- and ANA+ healthy individuals, patients with SLE of both races displayed T-cell expansion and elevated expression of type I and II interferon pathways. We discovered a unique immune signature that suggests a suppressive immune phenotype and reduced CD11C+ autoimmunity-associated B cells in healthy ANA+ European Americans that is absent in their SLE or even healthy ANA- counterparts, or among African American cohorts. In contrast, ANA+ healthy African Americans exhibited elevated expression of T-cell activation markers and higher plasma levels of IL-6 than did healthy ANA+ European Americans. CONCLUSIONS We propose that this novel immune signature identified in ANA+ healthy European Americans may protect them from T-cell expansion, heightened activation of interferon pathways, and disease transition.
Collapse
Affiliation(s)
- Samantha Slight-Webb
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla
| | - Miles Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla
| | - Aleksandra Bylinska
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla
| | - Susan Macwana
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla
| | - Carla Guthridge
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla
| | - Rufei Lu
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Okla
| | - Joan T Merrill
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla
| | - Eliza Chakravarty
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla
| | - Cristina Arriens
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla; Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Okla; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Okla
| | - Melissa E Munroe
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla
| | - Holden T Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Paul J Utz
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, Calif
| | - Joel M Guthridge
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Okla
| | - Judith A James
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Okla; Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Okla; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Okla.
| |
Collapse
|
19
|
Anderson E, Furie R. Anifrolumab in systemic lupus erythematosus: current knowledge and future considerations. Immunotherapy 2020; 12:275-286. [PMID: 32237942 DOI: 10.2217/imt-2020-0017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that is potentially life-threatening and can affect any organ. The complex pathogenesis and heterogeneity of the disease, among other factors, present significant challenges in developing new therapies. Knowledge gained over many years has implicated type I interferon (IFN) in the pathogenesis of SLE and anti-IFN therapies hold promise as a much-needed future treatment for SLE. Anifrolumab, a human monoclonal antibody against the type I IFN receptor, has recently been evaluated in two Phase III clinical trials for the treatment of moderate-to-severe SLE. Here, we review the clinical efficacy and safety of anifrolumab and discuss the potential challenges in determining the optimal SLE patient subgroup for treatment.
Collapse
Affiliation(s)
- Erik Anderson
- Elmezzi Graduate School of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY 11030, USA
| | - Richard Furie
- Division of Rheumatology, Zucker School of Medicine at Hofstra/Northwell, 865 Northern Boulevard, Great Neck, NY 11021, USA
| |
Collapse
|
20
|
Wang TY, Wang YF, Zhang Y, Shen JJ, Guo M, Yang J, Lau YL, Yang W. Identification of Regulatory Modules That Stratify Lupus Disease Mechanism through Integrating Multi-Omics Data. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 19:318-329. [PMID: 31877408 PMCID: PMC6938958 DOI: 10.1016/j.omtn.2019.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 11/05/2022]
Abstract
Although recent advances in genetic studies have shed light on systemic lupus erythematosus (SLE), its detailed mechanisms remain elusive. In this study, using datasets on SLE transcriptomic profiles, we identified 750 differentially expressed genes (DEGs) in T and B lymphocytes and peripheral blood cells. Using transcription factor (TF) binding data derived from chromatin immunoprecipitation sequencing (ChIP-seq) experiments from the Encyclopedia of DNA Elements (ENCODE) project, we inferred networks of co-regulated genes (NcRGs) based on binding profiles of the upregulated DEGs by significantly enriched TFs. Modularization analysis of NcRGs identified co-regulatory modules among the DEGs and master TFs vital for each module. Remarkably, the co-regulatory modules stratified the common SLE interferon (IFN) signature and revealed SLE pathogenesis pathways, including the complement cascade, cell cycle regulation, NETosis, and epigenetic regulation. By integrative analyses of disease-associated genes (DAGs), DEGs, and enriched TFs, as well as proteins interacting with them, we identified a hierarchical regulatory cascade with TFs regulated by DAGs, which in turn regulates gene expression. Integrative analysis of multi-omics data provided valuable molecular insights into the molecular mechanisms of SLE.
Collapse
Affiliation(s)
- Ting-You Wang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yan Zhang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Jiangshan Jane Shen
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China; Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, China
| | - Mengbiao Guo
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Jing Yang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
| |
Collapse
|
21
|
Kwon YC, Chun S, Kim K, Mak A. Update on the Genetics of Systemic Lupus Erythematosus: Genome-Wide Association Studies and Beyond. Cells 2019; 8:cells8101180. [PMID: 31575058 PMCID: PMC6829439 DOI: 10.3390/cells8101180] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/20/2019] [Accepted: 09/28/2019] [Indexed: 12/11/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease of complex etiology that primarily affects women of childbearing age. The development of SLE is attributed to the breach of immunological tolerance and the interaction between SLE-susceptibility genes and various environmental factors, resulting in the production of pathogenic autoantibodies. Working in concert with the innate and adaptive arms of the immune system, lupus-related autoantibodies mediate immune-complex deposition in various tissues and organs, leading to acute and chronic inflammation and consequent end-organ damage. Over the past two decades or so, the impact of genetic susceptibility on the development of SLE has been well demonstrated in a number of large-scale genetic association studies which have uncovered a large fraction of genetic heritability of SLE by recognizing about a hundred SLE-susceptibility loci. Integration of genetic variant data with various omics data such as transcriptomic and epigenomic data potentially provides a unique opportunity to further understand the roles of SLE risk variants in regulating the molecular phenotypes by various disease-relevant cell types and in shaping the immune systems with high inter-individual variances in disease susceptibility. In this review, the catalogue of SLE susceptibility loci will be updated, and biological signatures implicated by the SLE-risk variants will be critically discussed. It is optimistically hoped that identification of SLE risk variants will enable the prognostic and therapeutic biomarker armamentarium of SLE to be strengthened, a major leap towards precision medicine in the management of the condition.
Collapse
Affiliation(s)
- Young-Chang Kwon
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, 222–1 Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea;
| | - Sehwan Chun
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
- Correspondence: (K.K.); (A.M.); Tel.: +82-29610604 (K.K.); +65-82338216 (A.M.)
| | - Anselm Mak
- Division of Rheumatology, University Medicine Cluster, National University Health System, Singapore 119228, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Correspondence: (K.K.); (A.M.); Tel.: +82-29610604 (K.K.); +65-82338216 (A.M.)
| |
Collapse
|
22
|
Mathian A, Mouries-Martin S, Dorgham K, Devilliers H, Yssel H, Garrido Castillo L, Cohen-Aubart F, Haroche J, Hié M, Pineton de Chambrun M, Miyara M, Pha M, Rozenberg F, Gorochov G, Amoura Z. Ultrasensitive serum interferon-α quantification during SLE remission identifies patients at risk for relapse. Ann Rheum Dis 2019; 78:1669-1676. [PMID: 31570366 DOI: 10.1136/annrheumdis-2019-215571] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Maintenance of remission has become central in the management of systemic lupus erythematosus (SLE). The importance of interferon-alpha (IFN-α) in the pathogenesis of SLE notwithstanding, its expression in remission has been poorly studied as yet. To study its expression in remission and its prognostic value in the prediction of a disease relapse, serum IFN-α levels were determined using an ultrasensitive single-molecule array digital immunoassay which enables the measurement of cytokines at physiological concentrations. METHODS A total of 254 SLE patients in remission, according to the Definition of Remission in SLE classification, were included in the study. Serum IFN-α concentrations were determined at baseline and patients were followed up for 1 year. Lupus flares were defined according to the Safety of Estrogens in Lupus Erythematosus: National Assessment version of the Systemic Lupus Erythematosus Disease Activity Index Flare Index, whereas the Kaplan-Meier analysis and Cox regression analysis were used to estimate the time to relapse and to identify baseline factors associated with time to relapse, respectively. RESULTS Of all patients in remission, 26% displayed abnormally high IFN-α serum levels that were associated with the presence of antibodies specific for ribonucleoprotein (RNP), double stranded (ds)DNA and Ro/SSA60, as well as young age. Importantly, elevated-baseline IFN-α serum levels and remission duration were associated in an independent fashion, with shorter time to relapse, while low serum levels of complement component 3 and anti-dsDNA Abs were not. CONCLUSION Direct serum IFN-α assessment with highly sensitive digital immunoassay permits clinicians to identify a subgroup of SLE patients, clinically in remission, but at higher risk of relapse.
Collapse
Affiliation(s)
- Alexis Mathian
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Suzanne Mouries-Martin
- Centre Hospitalier Universitaire de Dijon, Hôpital François-Mitterrand, service de médecine interne et maladies systémiques (médecine interne 2), Dijon, France
| | - Karim Dorgham
- Sorbonne Université, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Hervé Devilliers
- Centre Hospitalier Universitaire de Dijon, Hôpital François-Mitterrand, service de médecine interne et maladies systémiques (médecine interne 2) et Centre d'Investigation Clinique, Inserm CIC 1432, Dijon, France
| | - Hans Yssel
- Sorbonne Université, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Laura Garrido Castillo
- Sorbonne Université, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Fleur Cohen-Aubart
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Julien Haroche
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Miguel Hié
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Marc Pineton de Chambrun
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Makoto Miyara
- Sorbonne Université, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Micheline Pha
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Flore Rozenberg
- Université de Paris, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Service de Virologie, Paris, France
| | - Guy Gorochov
- Sorbonne Université, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Zahir Amoura
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| |
Collapse
|
23
|
Thanarajasingam U, Muppirala AN, Jensen MA, Ghodke-Puranik Y, Dorschner JM, Vsetecka DM, Amin S, Makol A, Ernste F, Osborn T, Moder K, Chowdhary V, Niewold TB. Type I Interferon Predicts an Alternate Immune System Phenotype in Systemic Lupus Erythematosus. ACR Open Rheumatol 2019; 1:499-506. [PMID: 31777831 PMCID: PMC6858011 DOI: 10.1002/acr2.11073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/30/2019] [Indexed: 01/05/2023] Open
Abstract
Objective Type I interferon (IFN) is important to systemic lupus erythematosus (SLE) pathogenesis, but it is not clear how chronic elevations in IFN alter immune function. We compared cytokine responses after whole blood stimulation with Toll‐like receptor (TLR) agonists in high‐ and low‐IFN SLE patient subgroups. Methods SLE patients and nonautoimmune controls were recruited, and SLE patients were categorized as either high or low IFN. Whole blood was dispensed into tubes coated with lipopolysaccharide (LPS), oligonucleotides with cytosine‐guanine repeats, Resiquimod, IFN‐α, and IFN‐α + LPS. Cytokine production in patient sera and after whole blood TLR stimulation was measured by multiplex assay, and type I IFN was assessed using a functional assay. Results Circulating plasmacytoid dendritic cell numbers were specifically reduced in high‐IFN SLE patients and not in low‐IFN SLE patients. In serum, we observed that the correlations between cytokines in serum differed to a much greater degree between the high‐ and low‐IFN groups (P < 0.0001) than the absolute cytokine levels differed between these same groups. In stimulated conditions, the high‐IFN patients had less cytokine production in response to TLR ligation than the low‐IFN SLE patients. LPS produced the most diverse response, and a number of interactions between type I IFN and LPS were observed. Conclusion We find striking differences in resting and stimulated cytokine patterns in high‐ vs. low‐IFN SLE patients, which supports the biological importance of these patient subsets. These data could inform personalized treatment approaches and the pathogenesis of SLE flare following infection.
Collapse
|
24
|
Abstract
Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease whose pathogenesis can be conceptualized by a model based on a central role for immune complexes (ICs) between antinuclear antibodies and nucleic acids. According to this model, ICs can promote pathogenesis by two main mechanisms: deposition in the tissue to incite local inflammation and interaction with cells of the innate immune system to stimulate the production of cytokines, most prominently type 1 interferon. The latter stimulation results from the uptake of DNA and RNA in the form of ICs into cells and subsequent signaling by internal nucleic acid sensors for DNA and RNA. These sensors are likely important for the response to intracellular infection, although they may also be triggered during cell stress or injury by DNA or RNA aberrantly present in the cytoplasm. For IC formation, a source of extracellular DNA and RNA is essential. The current model of SLE posits that cell death is the origin of the nucleic acids in the ICs and that impairment of clearance mechanisms increases the amount of nuclear material in the extracellular space. This model of SLE is important since it points to new approaches to therapy; agents targeting interferon or the interferon receptor are examples of therapeutic approaches derived from this model. Future studies will explore novel biomarkers to monitor the operation of these mechanisms and to elucidate other steps in pathogenesis that can be targeted for therapy.
Collapse
Affiliation(s)
- David S Pisetsky
- Department of Medicine and Immunology, Duke University Medical Center and Medical Research Service, VA Medical Center, Durham, NC, USA
| |
Collapse
|
25
|
Bermea RS, Adegunsoye A, Oldham J, Ventura I, Lee C, Chung JH, Montner S, Noth I, Strek ME, Vij R. Anti-RNA binding protein positivity in idiopathic interstitial pneumonia. Respir Med 2018; 146:23-27. [PMID: 30665514 DOI: 10.1016/j.rmed.2018.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/24/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Idiopathic interstitial pneumonias (IIP) are diffuse lung diseases whose cause is unknown and often present with features of autoimmunity despite not meeting criteria for a connective tissue disease (CTD). Recent studies suggest that anti-RNA binding protein (anti-RBP) antibodies, which include anti-SSA, anti-SSB, anti-Sm, and anti-RNP, play a role in the loss of immune tolerance and severity of pulmonary hypertension (PH) in CTDs. We hypothesized that anti-RBP positive (RBP+) subjects would have worse measures of lung function, radiographic findings, PH, and survival than anti-RBP negative (RBP-) subjects. METHODS Subjects with both IIP and serologies for review were identified retrospectively and stratified based on anti-RBP antibody seropositivity. Baseline cohort characteristics, pulmonary function tests (PFT), ambulatory oxygen requirement, radiographic characteristics, markers of PH, and transplant-free survival were compared between anti-RBP positive and negative groups. RESULTS Five hundred twenty patients with IIP were identified, of which ten percent (n = 53) were anti-RBP positive. RBP+ as compared to RBP- subjects had significantly worse PFTs as indicated by FEV1 (59.6 vs. 64.9, p = 0.046) and FVC (71.6 vs. 78.8, p = 0.018). There was a higher prevalence of radiographic honeycombing (49.1% vs. 38.3%, p = 0.006) and emphysema (22.6% vs. 5.1%, p < 0.001) in the RBP+ group despite no difference in smoking history. The Pulmonary Artery-Aorta ratio was also larger in the RBP+ group (0.93 vs. 0.88, p = 0.040). There was no difference in transplant-free survival between groups (log rank = 0.912). CONCLUSION Anti-RBP+ IIP patients may have worse lung function, increased chest radiographic abnormalities, and PH compared with those without these antibodies.
Collapse
Affiliation(s)
- Rene S Bermea
- Department of Medicine, The University of Chicago, Chicago, IL, USA.
| | - Ayodeji Adegunsoye
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Justin Oldham
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of California at Davis, Davis, CA, USA
| | - Iazsmin Ventura
- Section of Rheumatology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Cathryn Lee
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Jonathan H Chung
- Department of Radiology, The University of Chicago, Chicago, IL, USA
| | - Steven Montner
- Department of Radiology, The University of Chicago, Chicago, IL, USA
| | - Imre Noth
- Division of Pulmonary & Critical Care, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Mary E Strek
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Rekha Vij
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| |
Collapse
|
26
|
Hamilton JA, Wu Q, Yang P, Luo B, Liu S, Li J, L Mattheyses A, Sanz I, Chatham WW, Hsu HC, Mountz JD. Cutting Edge: Intracellular IFN-β and Distinct Type I IFN Expression Patterns in Circulating Systemic Lupus Erythematosus B Cells. THE JOURNAL OF IMMUNOLOGY 2018; 201:2203-2208. [PMID: 30201809 DOI: 10.4049/jimmunol.1800791] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/14/2018] [Indexed: 11/19/2022]
Abstract
In systemic lupus erythematosus (SLE), type I IFNs promote induction of type I IFN-stimulated genes (ISG) and can drive B cells to produce autoantibodies. Little is known about the expression of distinct type I IFNs in lupus, particularly high-affinity IFN-β. Single-cell analyses of transitional B cells isolated from SLE patients revealed distinct B cell subpopulations, including type I IFN producers, IFN responders, and mixed IFN producer/responder clusters. Anti-Ig plus TLR3 stimulation of SLE B cells induced release of bioactive type I IFNs that could stimulate HEK-Blue cells. Increased levels of IFN-β were detected in circulating B cells from SLE patients compared with controls and were significantly higher in African American patients with renal disease and in patients with autoantibodies. Together, the results identify type I IFN-producing and -responding subpopulations within the SLE B cell compartment and suggest that some patients may benefit from specific targeting of IFN-β.
Collapse
Affiliation(s)
- Jennie A Hamilton
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Qi Wu
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - PingAr Yang
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Bao Luo
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Shanrun Liu
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Jun Li
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Alexa L Mattheyses
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Ignacio Sanz
- Division of Rheumatology, Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, GA 30322; and
| | - W Winn Chatham
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Hui-Chen Hsu
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - John D Mountz
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294; .,Birmingham VA Medical Center, Birmingham, AL 35233
| |
Collapse
|
27
|
The genetics and molecular pathogenesis of systemic lupus erythematosus (SLE) in populations of different ancestry. Gene 2018; 668:59-72. [DOI: 10.1016/j.gene.2018.05.041] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/13/2018] [Indexed: 01/21/2023]
|
28
|
Wang YF, Zhang Y, Zhu Z, Wang TY, Morris DL, Shen JJ, Zhang H, Pan HF, Yang J, Yang S, Ye DQ, Vyse TJ, Cui Y, Zhang X, Sheng Y, Lau YL, Yang W. Identification of ST3AGL4, MFHAS1, CSNK2A2 and CD226 as loci associated with systemic lupus erythematosus (SLE) and evaluation of SLE genetics in drug repositioning. Ann Rheum Dis 2018; 77:1078-1084. [PMID: 29625966 DOI: 10.1136/annrheumdis-2018-213093] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 01/13/2023]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is a prototype autoimmune disease with a strong genetic component in its pathogenesis. Through genome-wide association studies (GWAS), we recently identified 10 novel loci associated with SLE and uncovered a number of suggestive loci requiring further validation. This study aimed to validate those loci in independent cohorts and evaluate the role of SLE genetics in drug repositioning. METHODS We conducted GWAS and replication studies involving 12 280 SLE cases and 18 828 controls, and performed fine-mapping analyses to identify likely causal variants within the newly identified loci. We further scanned drug target databases to evaluate the role of SLE genetics in drug repositioning. RESULTS We identified three novel loci that surpassed genome-wide significance, including ST3AGL4 (rs13238909, pmeta=4.40E-08), MFHAS1 (rs2428, pmeta=1.17E-08) and CSNK2A2 (rs2731783, pmeta=1.08E-09). We also confirmed the association of CD226 locus with SLE (rs763361, pmeta=2.45E-08). Fine-mapping and functional analyses indicated that the putative causal variants in CSNK2A2 locus reside in an enhancer and are associated with expression of CSNK2A2 in B-lymphocytes, suggesting a potential mechanism of association. In addition, we demonstrated that SLE risk genes were more likely to be interacting proteins with targets of approved SLE drugs (OR=2.41, p=1.50E-03) which supports the role of genetic studies to repurpose drugs approved for other diseases for the treatment of SLE. CONCLUSION This study identified three novel loci associated with SLE and demonstrated the role of SLE GWAS findings in drug repositioning.
Collapse
Affiliation(s)
- Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Yan Zhang
- Guangzhou Institute of Paediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zhengwei Zhu
- Institute/Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, China
| | - Ting-You Wang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - David L Morris
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Jiangshan Jane Shen
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Huoru Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Jing Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Sen Yang
- Institute/Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, China
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Timothy J Vyse
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Yong Cui
- Departmentof Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Xuejun Zhang
- Institute/Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, China
| | - Yujun Sheng
- Institute/Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| |
Collapse
|
29
|
Abstract
The type I interferon pathway has been implicated in the pathogenesis of a number of rheumatic diseases, including systemic lupus erythematosus, Sjögren syndrome, myositis, systemic sclerosis, and rheumatoid arthritis. In normal immune responses, type I interferons have a critical role in the defence against viruses, yet in many rheumatic diseases, large subgroups of patients demonstrate persistent activation of the type I interferon pathway. Genetic variations in type I interferon-related genes are risk factors for some rheumatic diseases, and can explain some of the heterogeneity in type I interferon responses seen between patients within a given disease. Inappropriate activation of the immune response via Toll-like receptors and other nucleic acid sensors also contributes to the dysregulation of the type I interferon pathway in a number of rheumatic diseases. Theoretically, differences in type I interferon activity between patients might predict response to immune-based therapies, as has been demonstrated for rheumatoid arthritis. A number of type I interferon and type I interferon pathway blocking therapies are currently in clinical trials, the results of which are promising thus far. This Review provides an overview of the many ways in which the type I interferon system affects rheumatic diseases.
Collapse
Affiliation(s)
- Theresa L. Wampler Muskardin
- Colton Center for Autoimmunity, Department of Medicine, New York University School of Medicine, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Timothy B. Niewold
- Colton Center for Autoimmunity, Department of Medicine, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine and Pediatrics, New York University School of Medicine, New York, NY, USA
| |
Collapse
|
30
|
Zhuang H, Han S, Li Y, Kienhöfer D, Lee P, Shumyak S, Meyerholz R, Rosadzinski K, Rosner D, Chan A, Xu Y, Segal M, Sobel E, Yang LJ, Hoffmann MH, Reeves WH. A Novel Mechanism for Generating the Interferon Signature in Lupus: Opsonization of Dead Cells by Complement and IgM. Arthritis Rheumatol 2017; 68:2917-2928. [PMID: 27274010 DOI: 10.1002/art.39781] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 06/01/2016] [Indexed: 01/05/2023]
Abstract
OBJECTIVE In vitro studies suggest that the type I interferon (IFN) signature seen in most lupus patients results from Fcγ receptor-mediated uptake of nucleic acid-containing immune complexes by plasmacytoid dendritic cells and engagement of endosomal Toll-like receptors. The aim of this study was to reexamine the pathogenesis of the IFN signature in vivo. METHODS Lupus was induced in mice by injecting pristane. Some mice were treated with normal immunoglobulin or with cobra venom factor to deplete complement. The IFN signature was evaluated by polymerase chain reaction. The IFN signature also was determined in C4-deficient patients and control subjects. RESULTS Wild-type C57BL/6 mice with pristane-induced lupus developed a strong IFN signature, which was absent in immunoglobulin-deficient (μMT), C3-/- , and CD18-/- mice. Intravenous infusion of normal IgM, but not IgG, restored the IFN signature in μMT mice, and the IFN signature in wild-type mice was inhibited by depleting complement, suggesting that opsonization by IgM and complement is involved in IFN production. Consistent with that possibility, the levels of "natural" IgM antibodies reactive with dead cells were increased in pristane-treated wild-type mice compared with untreated controls, and in vivo phagocytosis of dead cells was impaired in C3-deficient mice. To examine the clinical relevance of these findings, we identified 10 C4-deficient patients with lupus-like disease and compared them with 152 C4-intact patients and 21 healthy controls. In comparison with C4-intact patients, C4-deficient patients had a different clinical/serologic phenotype and lacked the IFN signature. CONCLUSION These studies define previously unrecognized roles of natural IgM, complement, and complement receptors in generating the IFN signature in lupus.
Collapse
Affiliation(s)
| | | | - Yi Li
- University of Florida, Gainesville
| | | | - Pui Lee
- Boston Children's Hospital, Boston, Massachusetts
| | | | | | | | | | | | - Yuan Xu
- University of Florida, Gainesville
| | | | | | | | | | | |
Collapse
|
31
|
Arriens C, Wren JD, Munroe ME, Mohan C. Systemic lupus erythematosus biomarkers: the challenging quest. Rheumatology (Oxford) 2017; 56:i32-i45. [PMID: 28013203 DOI: 10.1093/rheumatology/kew407] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Indexed: 01/01/2023] Open
Abstract
SLE, a multisystem heterogeneous disease, is characterized by production of antibodies to cellular components, with activation of both the innate and the adaptive immune system. Decades of investigation of blood biomarkers has resulted in incremental improvements in the understanding of SLE. Owing to the heterogeneity of immune dysregulation, no single biomarker has emerged as a surrogate for disease activity or prediction of disease. Beyond identification of surrogate biomarkers, a multitude of clinical trials have sought to inhibit elevated SLE biomarkers for therapeutic benefit. Armed with new -omics technologies, the necessary yet daunting quest to identify better surrogate biomarkers and successful therapeutics for SLE continues with tenacity.
Collapse
Affiliation(s)
- Cristina Arriens
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation.,Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Jonathan D Wren
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation
| | - Melissa E Munroe
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, Houston, TX, USA
| |
Collapse
|
32
|
Munroe ME, Vista ES, Merrill JT, Guthridge JM, Roberts VC, James JA. Pathways of impending disease flare in African-American systemic lupus erythematosus patients. J Autoimmun 2017; 78:70-78. [PMID: 28162788 PMCID: PMC5340190 DOI: 10.1016/j.jaut.2016.12.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/21/2016] [Accepted: 12/24/2016] [Indexed: 02/09/2023]
Abstract
Immune dysregulation in systemic lupus erythematosus (SLE) contributes to increased disease activity. African-American (AA) SLE patients have an increased prevalence of complications from disease flares and end-organ damage that leads to increased morbidity and early mortality. We previously reported alterations in inflammatory and regulatory immune mediator levels prior to disease flare in European American (EA) SLE patients. In the current study, we assessed baseline and follow-up plasma levels of 52 soluble mediators, including innate, adaptive, chemokine, and TNF superfamily members, in AA SLE patients who developed SELENA-SLEDAI defined flare 6 or 12 weeks after baseline assessment. These patients were compared to themselves during a comparable, clinically stable period (SNF, n = 18), or to demographically matched SLE patients without impending disease flare (NF, n = 13 per group). We observed significant (q < 0.05) alterations in 34 soluble mediators at baseline, with increased levels of both innate (IL-1α and type I interferons [IFN]) and adaptive cytokines (Th1-, Th2-, and Th17-type), as well as IFN-associated chemokines and soluble TNF superfamily members weeks before clinical disease flare. In contrast, stable SLE patients exhibited increased levels of the regulatory mediators IL-10 (q ≤ 0.0045) and TGF-β (q ≤ 0.0004). Because heterogeneous immune pathways were altered prior to clinical disease flare, we developed a soluble mediator score that encapsulates all mediators tested. This score is the sum of all log transformed, standardized soluble mediator levels assessed at baseline (pre-flare), weighted by their Spearman correlation coefficients for association with the SELENA-SLEDAI score at time of concurrent flare. While baseline SELENA-SLEDAI scores were similar between flare vs. NF (p = 0.7214) and SNF (p = 0.5387), the SMS was significantly higher in pre-flare SLE patients (Flare vs NF or SNF, p < 0.0001). By capturing alterations in the balance between inflammatory and regulatory mediators associated with SLE pathogenesis, the soluble mediator score approximates the immune status of SLE patients and provides a robust, predictive gauge of impending disease flare.
Collapse
Affiliation(s)
- Melissa E Munroe
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Evan S Vista
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA; St. Luke's Medical Center, Taguig, 1112, Philippines
| | - Joan T Merrill
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Joel M Guthridge
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Virginia C Roberts
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Judith A James
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA; Departments of Medicine and Pathology, Oklahoma Clinical and Translational Science Institute, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, BMSB 451, Oklahoma City, OK, 73104, USA.
| |
Collapse
|
33
|
Wither J, Johnson SR, Liu T, Noamani B, Bonilla D, Lisnevskaia L, Silverman E, Bookman A, Landolt-Marticorena C. Presence of an interferon signature in individuals who are anti-nuclear antibody positive lacking a systemic autoimmune rheumatic disease diagnosis. Arthritis Res Ther 2017; 19:41. [PMID: 28245862 PMCID: PMC5331647 DOI: 10.1186/s13075-017-1243-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/23/2017] [Indexed: 01/08/2023] Open
Abstract
Background Elevated levels of type I interferons (IFNs) are a characteristic feature of the systemic autoimmune rheumatic diseases (SARDs) and are thought to play an important pathogenic role. However, it is unknown whether these elevations are seen in anti-nuclear antibody–positive (ANA+) individuals who lack sufficient criteria for a SARD diagnosis. We examined IFN-induced gene expression in asymptomatic ANA+ individuals and patients with undifferentiated connective tissue disease (UCTD) to address this question. Methods Healthy ANA− control subjects and ANA+ titre (≥1:160 by immunofluorescence) participants meeting no criteria, meeting at least one criterion (UCTD) or meeting SARD classification criteria were recruited. Whole peripheral blood IFN-induced and BAFF gene expression were quantified using NanoString technology. The normalized levels of five IFN-induced genes were summed to produce an IFN5 score. Results The mean IFN5 scores were increased in all ANA+ participant subsets as compared with healthy control subjects. We found that 36.8% of asymptomatic ANA+ and 50% of UCTD participants had IFN5 scores >2 SD above the mean for healthy control subjects. In all ANA+ subsets, the IFN5 score correlated with the presence of anti-Ro/La antibodies. In the asymptomatic ANA+ subset, this score also correlated with the ANA titre, whereas in the other ANA+ subsets, it correlated with the number of different ANA specificities. Development of new SARD criteria was seen in individuals with normal and high IFN5 scores. Conclusions An IFN signature is seen in a significant proportion of ANA+ individuals and appears to be associated with ANA titre and type of autoantibodies, rather than with the presence or development of clinical SARD symptoms.
Collapse
Affiliation(s)
- Joan Wither
- Krembil Research Institute, University Health Network, Toronto, ON, Canada. .,Division of Rheumatology, University Health Network, Toronto, ON, Canada. .,Department of Medicine, University of Toronto, Toronto, ON, Canada. .,Department of Immunology, University of Toronto, Toronto, ON, Canada. .,Toronto Western Hospital, 1E-420, 399 Bathurst Street, Toronto, ON, M5T 2S8, Canada.
| | - Sindhu R Johnson
- Division of Rheumatology, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada.,Division of Rheumatology, Mount Sinai Hospital, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Tony Liu
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Babak Noamani
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Dennisse Bonilla
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | | | - Earl Silverman
- Division of Rheumatology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Arthur Bookman
- Division of Rheumatology, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | | |
Collapse
|
34
|
Defining biological subsets in systemic lupus erythematosus: progress toward personalized therapy. Pharmaceut Med 2017; 31:81-88. [PMID: 28827978 DOI: 10.1007/s40290-017-0178-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Systemic lupus erythematosus (SLE) is a heterogeneous disease with respect to disease severity, response to treatment, and organ damage. The pathogenesis of SLE includes immunological mechanisms which are driven by both genetic and environmental factors. There are clear differences in the pathogenesis of SLE between patients of different ancestral backgrounds, including differences in genetic risk factors, immunological parameters, and clinical manifestations. Patients with high vs. low levels of type I interferon (IFN) in circulation represents one major biological subset within SLE, and these two groups of patients are present in all ancestral backgrounds. Genetic factors, autoantibodies, and levels of other cytokines all differ between high and low IFN patients. This distinction has also been important in predicting response to treatment with anti-type I IFN therapies, providing a precedent in SLE for biological subsets predicting treatment response. This review will highlight some recent developments in defining biological subsets of SLE based on disease pathophysiology, and the idea that improved knowledge of disease heterogeneity will inform our efforts to personalize therapy in this disease.
Collapse
|
35
|
Abstract
Finding better treatments for lupus nephritis requires an understanding of the pathogenesis of the causative systemic disease, how this leads to kidney disease, and how lupus nephritis progresses to end-stage kidney disease. Here, we provide a brief conceptual overview on the related pathomechanisms. As a main focus we discuss in detail the roles of neutrophils, dendritic cells, Toll-like receptors, and interferon-α in the pathogenesis of lupus nephritis by separately reviewing their roles in extrarenal systemic autoimmunity and in intrarenal inflammation and immunopathology.
Collapse
|
36
|
Abstract
PURPOSE OF REVIEW The field of systemic lupus erythematosus (SLE) genetics has been advancing rapidly in recent years. This review will summarize recent advances in SLE genetics. RECENT FINDINGS Genome-wide-association and follow-up studies have greatly expanded the list of associated polymorphisms, and much current work strives to integrate these polymorphisms into immune system biology and the pathogenic mediators involved in the disease. This review covers some current areas of interest, including genetic studies in non-European SLE patient populations, studies of pathogenic immune system subphenotypes such as type I interferon and autoantibodies, and a rapidly growing body of work investigating the functional consequences of the genetic polymorphisms associated with SLE. SUMMARY These studies provide a fascinating window into human SLE disease biology. As the work proceeds from genetic association signal to altered human biology, we move closer to tailoring interventions based upon an individual's genetic substrate.
Collapse
|
37
|
Long H, Yin H, Wang L, Gershwin ME, Lu Q. The critical role of epigenetics in systemic lupus erythematosus and autoimmunity. J Autoimmun 2016; 74:118-138. [PMID: 27396525 DOI: 10.1016/j.jaut.2016.06.020] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 06/29/2016] [Indexed: 02/09/2023]
Abstract
One of the major disappointments in human autoimmunity has been the relative failure on genome-wide association studies to provide "smoking genetic guns" that would explain the critical role of genetic susceptibility to loss of tolerance. It is well known that autoimmunity refers to the abnormal state that the dysregulated immune system attacks the healthy cells and tissues due to the loss of immunological tolerance to self-antigens. Its clinical outcomes are generally characterized by the presence of autoreactive immune cells and (or) the development of autoantibodies, leading to various types of autoimmune disorders. The etiology and pathogenesis of autoimmune diseases are highly complex. Both genetic predisposition and environmental factors such as nutrition, infection, and chemicals are implicated in the pathogenic process of autoimmunity, however, how much and by what mechanisms each of these factors contribute to the development of autoimmunity remain unclear. Epigenetics, which refers to potentially heritable changes in gene expression and function that do not involve alterations of the DNA sequence, has provided us with a brand new key to answer these questions. In the recent decades, increasing evidence have demonstrated the roles of epigenetic dysregulation, including DNA methylation, histone modification, and noncoding RNA, in the pathogenesis of autoimmune diseases, especially systemic lupus erythematosus (SLE), which have shed light on a new era for autoimmunity research. Notably, DNA hypomethylation and reactivation of the inactive X chromosome are two epigenetic hallmarks of SLE. We will herein discuss briefly how genetic studies fail to completely elucidate the pathogenesis of autoimmune diseases and present a comprehensive review on landmark epigenetic findings in autoimmune diseases, taking SLE as an extensively studied example. The epigenetics of other autoimmune diseases such as rheumatic arthritis, systemic sclerosis and primary biliary cirrhosis will also be summarized. Importantly we emphasize that the stochastic processes that lead to DNA modification may be the lynch pins that drive the initial break in tolerance.
Collapse
Affiliation(s)
- Hai Long
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, China
| | - Heng Yin
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, China
| | - Ling Wang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - M Eric Gershwin
- Division of Rheumatology, Allergy, and Clinical Immunology, University of California at Davis, Davis, CA, USA
| | - Qianjin Lu
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, China.
| |
Collapse
|
38
|
Postal M, Sinicato NA, Appenzeller S, Niewold TB. Drugs in early clinical development for Systemic Lupus Erythematosus. Expert Opin Investig Drugs 2016; 25:573-83. [PMID: 26950689 DOI: 10.1517/13543784.2016.1162291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
INTRODUCTION While immunosuppressive therapy has positively impacted the prognosis of systemic lupus erythematosus (SLE), many patients still do not respond to traditional therapy. Thus, active SLE disease remains a significant problem. Furthermore, conventional immunosuppressive treatments for SLE are associated a high risk of side effects. These issues call for improvement in our current therapeutic armamentarium. AREAS COVERED In this review, the authors highlight the recent developments in therapies for SLE, and present an overview of drugs which are in early clinical development for SLE. There are many new therapeutic approaches being developed, including those focused on B-cell targets, T-cell downregulation, co-stimulatory blockade, anti-cytokine agents, and kinase inhibition, and Toll-like receptor inhibition. They also discuss peptide therapy as a potential method to re-establish immune tolerance, and some of the challenges ahead in developing and testing novel agents for SLE. EXPERT OPINION Many novel agents are currently in development for SLE, but this encouraging news is tempered by several disappointments in clinical trials and provides a timely moment to reflect on the future of therapeutic development in SLE. It seems likely that biological heterogeneity between patients is a major contributor to difficulty in drug design in SLE.
Collapse
Affiliation(s)
- Mariana Postal
- a Rheumatology Unit, Department of Medicine, Faculty of Medical Science , State University of Campinas , Campinas , Brazil
| | - Nailú Angélica Sinicato
- a Rheumatology Unit, Department of Medicine, Faculty of Medical Science , State University of Campinas , Campinas , Brazil
| | - Simone Appenzeller
- a Rheumatology Unit, Department of Medicine, Faculty of Medical Science , State University of Campinas , Campinas , Brazil
| | - Timothy B Niewold
- b Division of Rheumatology, Department of Immunology , Mayo Clinic , Rochester , MN , USA
| |
Collapse
|
39
|
Btk inhibition treats TLR7/IFN driven murine lupus. Clin Immunol 2016; 164:65-77. [PMID: 26821304 DOI: 10.1016/j.clim.2016.01.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 11/23/2022]
Abstract
Bruton's tyrosine kinase (Btk) is expressed in a variety of immune cells and previous work has demonstrated that blocking Btk is a promising strategy for treating autoimmune diseases. Herein, we utilized a tool Btk inhibitor, M7583, to determine the therapeutic efficacy of Btk inhibition in two mouse lupus models driven by TLR7 activation and type I interferon. In BXSB-Yaa lupus mice, Btk inhibition reduced autoantibodies, nephritis, and mortality. In the pristane-induced DBA/1 lupus model, Btk inhibition suppressed arthritis, but autoantibodies and the IFN gene signature were not significantly affected; suggesting efficacy was mediated through inhibition of Fc receptors. In vitro studies using primary human macrophages revealed that Btk inhibition can block activation by immune complexes and TLR7 which contributes to tissue damage in SLE. Overall, our results provide translational insight into how Btk inhibition may provide benefit to a variety of SLE patients by affecting both BCR and FcR signaling.
Collapse
|
40
|
López de Padilla CM, Niewold TB. The type I interferons: Basic concepts and clinical relevance in immune-mediated inflammatory diseases. Gene 2015; 576:14-21. [PMID: 26410416 DOI: 10.1016/j.gene.2015.09.058] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 09/04/2015] [Accepted: 09/22/2015] [Indexed: 02/08/2023]
Abstract
There is increasing scientific and clinical interest in elucidating the biology of type I Interferons, which began approximately 60 years ago with the concept of "viral interference", a property that reduces the ability of a virus to infect cells. Although our understanding of the multiple cellular and molecular functions of interferons has advanced significantly, much remains to be learned and type I Interferons remain an active and fascinating area of inquiry. In this review, we cover some general aspects of type I interferon genes, with emphasis on interferon-alpha, and various aspects of molecular mechanisms triggered by type I interferons and toll-like receptor signaling by the Janus activated kinase/signal transducer activation of transcription (JAK-STAT) pathway and interferon regulatory factor pathway. We will also describe the role of type I interferons in autoimmune and inflammatory diseases, and its potential use as therapeutic agent.
Collapse
Affiliation(s)
| | - Timothy B Niewold
- Division of Rheumatology and Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA.
| |
Collapse
|
41
|
Ghodke-Puranik Y, Niewold TB. Immunogenetics of systemic lupus erythematosus: A comprehensive review. J Autoimmun 2015; 64:125-36. [PMID: 26324017 DOI: 10.1016/j.jaut.2015.08.004] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 08/12/2015] [Indexed: 12/24/2022]
Abstract
Our understanding of the genetic basis of systemic lupus erythematosus has progressed rapidly in recent years. While many genetic polymorphisms have been associated with disease susceptibility, the next major step involves integrating these genetic polymorphisms into the molecular mechanisms and cellular immunology of the human disease. In this review, we summarize some recent work in this area, including the genetics of the type I IFN response in SLE, including polygenic and monogenic factors, as well as epigenetic influences. Contributions of both HLA and non-HLA polymorphisms to the complex genetics of SLE are reviewed. We also review recent reports of specific gene deficits leading to monogenic SLE-like syndromes. The molecular functions of common SLE-risk variants are reviewed in depth, including regulatory variations in promoter and enhancer elements and coding-change polymorphisms, and studies which are beginning to define the molecular and cellular functions of these polymorphisms in the immune system. We discuss epigenetic influences on lupus, with an emphasis on micro-RNA expression and binding, as well as epigenetic modifications that regulate the expression levels of various genes involved in SLE pathogenesis and the ways epigenetic marks modify SLE susceptibility genes. The work summarized in this review provides a fascinating window into the biology and molecular mechanisms of human SLE. Understanding the functional mechanisms of causal genetic variants underlying the human disease greatly facilitates our ability to translate genetic associations toward personalized care, and may identify new therapeutic targets relevant to human SLE disease mechanisms.
Collapse
Affiliation(s)
| | - Timothy B Niewold
- Division of Rheumatology, Department of Immunology, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
42
|
Kalunian KC, Merrill JT, Maciuca R, McBride JM, Townsend MJ, Wei X, Davis JC, Kennedy WP. A Phase II study of the efficacy and safety of rontalizumab (rhuMAb interferon-α) in patients with systemic lupus erythematosus (ROSE). Ann Rheum Dis 2015; 75:196-202. [PMID: 26038091 DOI: 10.1136/annrheumdis-2014-206090] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 03/22/2015] [Indexed: 01/01/2023]
Abstract
OBJECTIVES To examine the safety and efficacy of rontalizumab, a humanised IgG1 anti-interferon α (anti-IFN-α) monoclonal antibody, in patients with moderate-to-severe systemic lupus erythematosus (SLE). METHODS Patients with active SLE were randomised (2:1) to 750 mg intravenous rontalizumab every 4 weeks or placebo (Part 1), and 300 mg subcutaneous rontalizumab every 2 weeks or placebo (Part 2). BACKGROUND Hydroxychloroquine and corticosteroids were allowed. Patients taking immunosuppressants at baseline were required per protocol to discontinue. Efficacy end points included reduction in disease activity by British Isles Lupus Disease Activity Group (BILAG)-2004 (primary), and SLE response index (SRI, secondary) at Week 24. Efficacy was also examined by an exploratory measure of IFN-regulated gene expression (interferon signature metric, ISM). RESULTS Patients (n=238) received rontalizumab (n=159) or placebo (n=79). At baseline, the mean Safety of Estrogens in Lupus Erythematosus National Assessment version of the SLE Disease Activity Index (SELENA-SLEDAI) score in all cohorts was ~10, and 75.6% of patients had a high ISM (ISM-High). Efficacy response rates by BILAG and SRI were similar between rontalizumab and placebo groups. However, in the exploratory subgroup of ISM-Low patients, SRI response was higher and steroid use was lower in the rontalizumab-treated patients. There was also a reduction in SELENA-SLEDAI flare index rates (HR 0.61, 0.46 to 0.81, p=0.004) in this subgroup. Adverse events were similar between placebo and rontalizumab groups. CONCLUSIONS The primary and secondary end points of this trial were not met in all patients or in patients with high ISM scores. In an exploratory analysis, rontalizumab treatment was associated with improvements in disease activity, reduced flares and decreased steroid use in patients with SLE with low ISM scores. TRIAL REGISTRATION NUMBER NCT00962832.
Collapse
Affiliation(s)
- Kenneth C Kalunian
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Joan T Merrill
- Clinical Pharmacology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | | | | | | | - Xiaohui Wei
- Genentech, South San Francisco, California, USA
| | | | | |
Collapse
|
43
|
Tang Q, Danila MI, Cui X, Parks L, Baker BJ, Reynolds RJ, Raman C, Wanseck KC, Redden DT, Johnson MR, Bridges SL. Expression of Interferon-γ Receptor Genes in Peripheral Blood Mononuclear Cells Is Associated With Rheumatoid Arthritis and Its Radiographic Severity in African Americans. Arthritis Rheumatol 2015; 67:1165-70. [PMID: 25708927 PMCID: PMC4414815 DOI: 10.1002/art.39056] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 01/27/2015] [Indexed: 12/29/2022]
Abstract
OBJECTIVE The factors responsible for radiographic severity in African American patients with rheumatoid arthritis (RA) are poorly understood. We sought to identify genes whose expression in peripheral blood mononuclear cells is associated with radiographic severity in RA. METHODS In the first phase of the study, we performed real-time quantitative polymerase chain reaction to analyze the expression of 182 candidate genes in 40 African American RA patients with extremes of radiographic damage (low versus high radiographic scores) and disease duration (≤2 years versus >2 years) and 20 healthy African American control subjects; the genes were selected based on plausible immune pathways. In the second phase, we analyzed the expression of the genes that were shown to be significantly associated with radiographic scores in 576 African American patients with RA and 51 African American control subjects who had not been studied previously, accounting for autoantibody status and disease duration. RESULTS We observed significant differences in IFNGR1 expression between patients with RA and control subjects (adjusted P [P(adj)] = 6 × 10(-14)) and in IFNGR2 expression between RA patients with erosions and those with no erosions (P(adj) = 0.01 by Wilcoxon's rank sum test). We also observed significant correlations between IFNGR2 expression and radiographic scores (P(adj) = 0.03 for erosions, P(adj) = 0.04 for joint space narrowing, and P(adj) = 0.03 for total radiographic score [zero-inflated negative binomial regression model]) and annualized progression rate (P(adj) = 0.0024 by Spearman's correlation analysis). CONCLUSION These findings have important implications with respect to the role of interferon-γ (IFNγ) in the pathogenesis of RA and may lead to identification of a biomarker for radiographic damage. Additional studies are needed to define the cell subsets responsible for the association of IFNγ receptor gene expression with radiographic findings, which downstream mechanisms are involved, and generalizability to other RA populations.
Collapse
Affiliation(s)
- Qi Tang
- University of Alabama at Birmingham and Second Xiangya Hospital of Central South University, Changsha, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Sharma S, Jin Z, Rosenzweig E, Rao S, Ko K, Niewold TB. Widely divergent transcriptional patterns between SLE patients of different ancestral backgrounds in sorted immune cell populations. J Autoimmun 2015; 60:51-58. [PMID: 25921064 DOI: 10.1016/j.jaut.2015.04.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 04/04/2015] [Accepted: 04/06/2015] [Indexed: 12/25/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease of uncertain etiology. Patients from different ancestral backgrounds demonstrate differences in clinical manifestations and autoantibody profiles. We examined genome-wide transcriptional patterns in major immune cell subsets across different ancestral backgrounds. Peripheral blood was collected from African-American (AA) and European-American (EA) SLE patients and controls. CD4 T-cells, CD8 T-cells, monocytes, and B cells were purified by flow sorting, and each cell subset from each subject was run on a genome-wide expression array. Cases were compared to controls of the same ancestral background. The overlap in differentially expressed gene (DEG) lists between different cell types from the same ancestral background was modest (<10%), and only 5-8% overlap in DEG lists was observed when comparing the same cell type between different ancestral backgrounds. IFN-stimulated gene (ISG) expression was not up-regulated synchronously in all cell types from a given patient, for example a given subject could have high ISG expression in T and B cells, but not in monocytes. AA subjects demonstrated more concordance in ISG expression between cell types from the same individual, and AA patients demonstrated significant down-regulation of metabolic gene expression which was not observed in EA patients. ISG expression was significantly decreased in B cells in patients taking immunosuppressants, while ISGs in other cell types did not differ with medication use. In conclusion, gene expression was strikingly different between immune cell subsets and between ancestral backgrounds in SLE patients. These findings emphasize the critical importance of studying multiple ancestral backgrounds and multiple cell types in gene expression studies. Ancestral backgrounds which are not studied will not benefit from personalized medicine strategies in SLE.
Collapse
Affiliation(s)
- Shruti Sharma
- University of Chicago, Gwen Knapp Center for Lupus Research
| | - Zhongbo Jin
- Mayo Clinic, Division of Rheumatology and Department of Immunology
| | | | - Swapna Rao
- University of Chicago, Gwen Knapp Center for Lupus Research
| | - Kichul Ko
- University of Chicago, Gwen Knapp Center for Lupus Research
| | | |
Collapse
|
45
|
Kariuki SN, Ghodke-Puranik Y, Dorschner JM, Chrabot BS, Kelly JA, Tsao BP, Kimberly RP, Alarcón-Riquelme ME, Jacob CO, Criswell LA, Sivils KL, Langefeld CD, Harley JB, Skol AD, Niewold TB. Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus. Genes Immun 2015; 16:15-23. [PMID: 25338677 PMCID: PMC4305028 DOI: 10.1038/gene.2014.57] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 12/13/2022]
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disorder characterized by inflammation of multiple organ systems and dysregulated interferon responses. SLE is both genetically and phenotypically heterogeneous, greatly reducing the power of case-control studies in SLE. Elevated circulating interferon-alpha (IFN-α) is a stable, heritable trait in SLE, which has been implicated in primary disease pathogenesis. About 40-50% of patients have high IFN-α, and high levels correspond with clinical differences. To study genetic heterogeneity in SLE, we performed a case-case study comparing patients with high vs low IFN-α in over 1550 SLE cases, including genome-wide association study and replication cohorts. In meta-analysis, the top associations in European ancestry were protein kinase, cyclic GMP-dependent, type I (PRKG1) rs7897633 (P(Meta) = 2.75 × 10(-8)) and purine nucleoside phosphorylase (PNP) rs1049564 (P(Meta) = 1.24 × 10(-7)). We also found evidence for cross-ancestral background associations with the ankyrin repeat domain 44 (ANKRD44) and pleckstrin homology domain containing, family F member 2 gene (PLEKHF2) loci. These loci have not been previously identified in case-control SLE genetic studies. Bioinformatic analyses implicated these loci functionally in dendritic cells and natural killer cells, both of which are involved in IFN-α production in SLE. As case-control studies of heterogeneous diseases reach a limit of feasibility with respect to subject number and detectable effect size, the study of informative pathogenic sub-phenotypes becomes an attractive strategy for genetic discovery in complex disease.
Collapse
Affiliation(s)
| | | | - Jessica M. Dorschner
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN
| | - Beverly S. Chrabot
- Gwen Knapp Center for Lupus Research, University of Chicago, Chicago, IL
| | - Jennifer A. Kelly
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Betty P. Tsao
- Department of Medicine, University of California, Los Angeles, CA
| | | | - Marta E. Alarcón-Riquelme
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government
| | - Chaim O. Jacob
- Department of Medicine, University of Southern California, Los Angeles, CA
| | - Lindsey A. Criswell
- Rosalind Russell / Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA
| | - Kathy L. Sivils
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Carl D. Langefeld
- Department of Biostatistical Sciences, Wake Forest University, Winston-Salem, NC
| | - John B. Harley
- Cincinnati Children’s Hospital Medical Center and Cincinnati VA Medical Center, Cincinnati, OH
| | - Andrew D. Skol
- Department of Human Genetics, University of Chicago, Chicago, IL
| | - Timothy B. Niewold
- Department of Immunology and Division of Rheumatology, Mayo Clinic, Rochester, MN
| |
Collapse
|
46
|
Oliveira L, Sinicato NA, Postal M, Appenzeller S, Niewold TB. Dysregulation of antiviral helicase pathways in systemic lupus erythematosus. Front Genet 2014; 5:418. [PMID: 25505487 PMCID: PMC4243696 DOI: 10.3389/fgene.2014.00418] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/10/2014] [Indexed: 11/13/2022] Open
Abstract
In the autoimmune disease systemic lupus erythematosus (SLE), our normal antiviral defenses are inappropriately activated, resulting in over-activity of the type I interferon (IFN) pathway. This increased activity of the type I IFN pathway is an important primary pathogenic factor in the disease. Emerging evidence has implicated the antiviral helicases in this process. The antiviral helicases normally function as nucleic acid receptors in viral immunity. Genetic variations in antiviral helicase genes have been associated with SLE, supporting the idea that helicase pathways are involved in the primary pathogenesis of SLE. Studies have documented functional consequences of these genetic variations within the type I IFN pathway in human cell lines and SLE patients. In this review, we summarize the function of helicases in the anti-viral immune response, and how this response is dysregulated in SLE patients. In particular, we will focus on known functional genetic polymorphisms in the IFIH1 (MDA5) and mitochondrial antiviral signaling protein genes which have been implicated in human SLE. These data provide fascinating evidence for dysregulation of helicase-mediated innate immunity in SLE, and may support novel therapeutic strategies in the disease.
Collapse
Affiliation(s)
- Luciana Oliveira
- Rheumatology Unit, Department of Medicine, Faculty of Medical Science, State University of Campinas Campinas, Brazil
| | - Nailú A Sinicato
- Rheumatology Unit, Department of Medicine, Faculty of Medical Science, State University of Campinas Campinas, Brazil
| | - Mariana Postal
- Rheumatology Unit, Department of Medicine, Faculty of Medical Science, State University of Campinas Campinas, Brazil
| | - Simone Appenzeller
- Rheumatology Unit, Department of Medicine, Faculty of Medical Science, State University of Campinas Campinas, Brazil
| | - Timothy B Niewold
- Mayo Clinic, Division of Rheumatology, Department of Immunology Rochester, MN, USA
| |
Collapse
|
47
|
Dey-Rao R, Sinha AA. Genome-wide transcriptional profiling of chronic cutaneous lupus erythematosus (CCLE) peripheral blood identifies systemic alterations relevant to the skin manifestation. Genomics 2014; 105:90-100. [PMID: 25451738 DOI: 10.1016/j.ygeno.2014.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/24/2014] [Accepted: 11/11/2014] [Indexed: 12/15/2022]
Abstract
Major gaps remain regarding pathogenetic mechanisms underlying clinical heterogeneity in lupus erythematosus (LE). As systemic changes are likely to underlie skin specific manifestation, we analyzed global gene expression in peripheral blood of a small cohort of chronic cutaneous LE (CCLE) patients and healthy individuals. Unbiased hierarchical clustering distinguished patients from controls revealing a "disease" based signature. Functional annotation of the differentially expressed genes (DEGs) highlight enrichment of interferon related immune response and apoptosis signatures, along with other key pathways. There is a 26% overlap of the blood and lesional skin transcriptional profile from a previous analysis by our group. We identified four transcriptional "hot spots" at chromosomal regions harboring statistically increased numbers of DEGs which offer prioritized potential loci for downstream fine mapping studies in the search for CCLE specific susceptibility loci. Additionally, we uncover evidence to support both shared and distinct mechanisms for cutaneous and systemic manifestations of lupus.
Collapse
Affiliation(s)
- R Dey-Rao
- Department of Dermatology, University at Buffalo, Buffalo, NY, USA
| | - A A Sinha
- Department of Dermatology, University at Buffalo, Buffalo, NY, USA.
| |
Collapse
|
48
|
Autoimmune disease genetics 2013. J Immunol Res 2014; 2014:487643. [PMID: 25165727 PMCID: PMC4140134 DOI: 10.1155/2014/487643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 06/19/2014] [Indexed: 11/17/2022] Open
|
49
|
Niewold TB. Type I interferon in human autoimmunity. Front Immunol 2014; 5:306. [PMID: 25071767 PMCID: PMC4074699 DOI: 10.3389/fimmu.2014.00306] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 06/16/2014] [Indexed: 12/17/2022] Open
Affiliation(s)
- Timothy B Niewold
- Division of Rheumatology and Department of Immunology, Mayo Clinic , Rochester, MN , USA
| |
Collapse
|