Standing on Shoulders: Interferon Research From Viral Interference to Lupus Pathogenesis and Treatment

The discovery of interferon in the 1950s represents much more than the identification of the first cytokine and the key mediator of antiviral host defense. Defining the molecular nature and complexity of the type I interferon family, as well as its inducers and molecular mechanisms of action, was the work of investigators working at the highest level and producing insights of great consequence. Current knowledge of receptor-ligand interactions, cell signaling, and transcriptional regulation derives from studies of type I interferon. It is on the shoulders of the giants who produced that knowledge that others stand and have revealed critical mechanisms of the pathogenesis of systemic lupus erythematosus and other autoimmune diseases. The design of novel therapeutics is informed by the advances in investigation of type I interferon, with the potential for important impact on patient management.

Evaluation of Peripheral Blood Leukocyte Subsets in Systemic Lupus Erythematosus (SLE) Enabled by a Microfluidic Cell Separator

Although granulocyte signatures have been associated with SLE severity, their role in SLE has been poorly understood due to the suboptimal methods for granulocyte recovery from peripheral blood. An automated microfluidic technology (Sorterra™ prototype) was used to isolate all leukocytes with minimal platelet (PLT) or red blood cell (RBC) contamination to assess the cell subsets.

Leukocytes were isolated from peripheral blood collected from healthy donors (HD) and SLE patients (3 female, 3 male in each group) using Sorterra, RBC lysis, or Ficoll®. Viability and recovery of each leukocyte subset was evaluated by cell counter and flow cytometry.

Sorterra recovered 92±4% of leukocytes from HD and SLE samples with negligible RBC/PLT/microparticle (MP) contamination, whereas Ficoll isolated 35±15% of leukocytes, losing nearly all the granulocytes and retaining a substantial level of RBC/PLT/MP. With RBC lysis, up to 65% of neutrophils and 41% of eosinophils were lost in the process. Sorterra recovered more monocytes (~80%) than Ficoll (p<0.05). The recovery of lymphocytes by Sorterra (~90%) was not different from Ficoll or RBC lysis. The recovery of T and B cell subsets, NK, and NKT cells, was also not different among the isolation methods. The viability of Sorterra isolated leukocytes was significantly higher than the Ficoll isolated cells.

The Sorterra prototype was superior to RBC lysis and Ficoll in recovering total leukocytes with high viability and ease of use and provided a more consistent leukocyte isolate from HD and SLE patients than other methods. The ability to recover granulocytes in their native state is unmatched by existing technologies and enables future studies to better elucidate the role of granulocytes in SLE development.

Distinctions in gene-expression in PBMC from male and female SLE patients

The female predisposition for multiple autoimmune diseases is well known. The mechanisms might be related to the female reproductive system, sex hormones, incomplete X-chromosomal inactivation etc. We investigated gene expression in PBMC of quiescent SLE patients and corresponding healthy donors of both genders (10 matching samples per group) using the RNA-seq approach.

Principal component analysis differentiated the 4 donor groups, with PC1 reflecting disease and PC2 reflecting gender. Male SLE patients received the highest score on PC1 and were placed closer to females than healthy males on PC2. We identified 796 and 99 differentially expressed genes in male and female SLE patients compared to HD (p<0.05, logFC=1.5). Fewer genes (20 vs. 27) differed between genders in SLE vs. HD (p<0.05, logFC=1.5). Weighted Gene Co-expression Network Analysis (WGCNA) identified 24 clusters of co-expressed genes. The most intriguing were clusters that differed in male and female HD and were upregulated in SLE of both genders. Those clusters include genes related to EGF receptor ligands (AREG, EREG, HBEGF), transcription factors ATF3, NR4A1, NR4A2, NR4A3, cytokines and chemokines (CCL3, CXCL2, CXCL8, CCL3L3, IL1A, IL1B).

Despite being clinically similar, male SLE patients showed a higher level of affected genes and had a lower divergence from females based on gender-related genes. Male HD had the lowest basal level of pro-inflammatory genes and EGF receptor ligands. EGFR is expressed in pituitary and involved in the reproductive hypothalamic-pituitary axis, possibly providing relative protection of males. We propose that gender-specific differences in gene expression reveal immunopathogenic mechanisms in autoimmune disease.

Type I Interferons in Autoimmune Disease

Type I interferons, which make up the first cytokine family to be described and are the essential mediators of antivirus host defense, have emerged as central elements in the immunopathology of systemic autoimmune diseases, with systemic lupus erythematosus as the prototype. Lessons from investigation of interferon regulation following virus infection can be applied to lupus, with the conclusion that sustained production of type I interferon shifts nearly all components of the immune system toward pathologic functions that result in tissue damage and disease. We review recent data, mainly from studies of patients with systemic lupus erythematosus, that provide new insights into the mechanisms of induction and the immunologic consequences of chronic activation of the type I interferon pathway. Current concepts implicate endogenous nucleic acids, driving both cytosolic sensors and endosomal Toll-like receptors, in interferon pathway activation and suggest targets for development of novel therapeutics that may restore the immune system to health.

Novel molecular signatures in mononuclear cell populations from patients with systemic lupus erythematosus

To gain novel insights into the immunopathogenesis of systemic lupus erythematosus we have analyzed gene expression data from isolated CD4⁺ T cells, CD8⁺ T cells, CD19⁺ B cells, and CD56⁺ NK-cell enriched peripheral blood cell fractions from patients and healthy donors. As predicted, type I interferon-inducible gene transcripts are overexpressed in all populations. Transcripts preferentially expressed in SLE CD4⁺ and CD8⁺ T cells include those associated with Tregulatory and Th17 effector cell programs, respectively, but in each case additional transcripts predicted to limit differentiation of those effector cells are detected. Evidence for involvement of the Wnt/β-catenin pathway was observed in both B and T cell fractions, and novel transcripts were identified in each cell population. These data point to disrupted T effector cell differentiation and the Wnt/β-catenin pathway as contributors to immune dysfunction in SLE while further supporting a central role for the type I interferon pathway in lupus.

Identification of Candidate Predictors of Lupus Flare

Systemic lupus erythematosus, the prototype systemic autoimmune disease, is characterized by extensive self-reactivity, inflammation, and organ system damage. Sustained production of type I interferon is seen in many patients and contributes to immune dysregulation. Disease activity fluctuates with periods of relative quiescence or effective management by immunosuppressive drugs, followed by disease flares. Tissue damage accumulates over time, with kidneys and cardiovascular system particularly affected. Identification of the underlying molecular mechanisms that precede clinical exacerbations, allowing prediction of future flare, could lead to therapeutic interventions that prevent severe disease. We generated gene expression data from a longitudinal cohort of lupus patients, some showing at least one period of severe flare and others with relatively stable disease over the period of study. Candidate predictors of future clinical flare were identified based on analysis of differentially expressed gene transcripts between the flare and non-flare groups at a time when all patients had relatively quiescent clinical disease activity. Our results suggest the hypothesis that altered regulation of genome stability and nucleic acid fidelity may be important molecular precursors of future clinical flare, generating endogenous nucleic acid triggers that engage intracellular mechanisms that mimic a chronic host response to viral infection.

Measuring interferon alpha and other cytokines in SLE

The progression of disease in patients with systemic lupus erythematosus (SLE) is affected by production, accumulation, and actions of cytokines. Type I interferon (IFN), specifically IFN-α, is recognized as a central mediator of disease pathogenesis in SLE. We describe a functional assay to measure type I IFN activity in SLE plasma and have also measured the response of peripheral blood cells to that cytokine family. This method can be scaled to assess IFN functional activity, as well as activity and cellular response to other cytokines, in relation to cellular and serologic parameters relevant to SLE.

Transcriptional regulation of the human FCGR2B gene mediated by promoter polymorphisms associated with Systemic Lupus Erythematosus (35.38)

The inihibitory Fc gamma receptor IIb is an important negative regulator of peripheral tolerance. The [−343 G to C] SNP in the human FCGR2B promoter is associated with Systemic lupus erythematosus (SLE). The mutant promoter [−343C/C] hasdecreased transcriptional activity. Analyses by electromobility shift, chromatin immunoprecipitation and promoter pull-down assays demonstrated binding of AP1 factors to the FCGR2B promoter. The binding of AP1 factors was decreased with the mutant FCGR2B promoter compared with the common promoter. The −343 G to C substitution enabled the specific interaction of the transcription factor Yin-Yang 1 with the mutant FCGR2B promoter. Yin-Yang 1 competed with AP1 for binding at the −343 site, and contributed to the repression of the mutant FCGR2B promoter activity. The [−343 C/C] genotype was found to be in linkage disequilibrium with the [−77 T to A] SNP relative to the transcription initiation site. The [−77 A/A] promoter constructs displayed increased activity compared with [−77 T/T] promoter constructs in luciferase assays, suggesting a role for the −77 SNP in the transactivation of the FCGR2B promoter. Allelic variations at positions −343 and −77 identified in the human FCGR2B promoter differentially modulate the transcriptional activity and may play a role in the expression and progression of SLE disease.

The Role of Activating Protein 1 in the Transcriptional Regulation of the Human FCGR2B Promoter Mediated by the -343 G → C Polymorphism Associated with Systemic Lupus Erythematosus

The inhibitory receptor FcgammaRIIb is a negative regulator of antibody production and inflammatory responses. The -343 G --> C polymorphism in the human FCGR2B promoter is associated with systemic lupus erythematosus. The -343 C mutant promoter has decreased transcriptional activity. In the present study, we show that the transcriptional change correlates with quantitative differences in the interaction of the activating protein 1 complex with the mutant FCGR2B promoter. Promoter pulldown and chromatin immunoprecipitation assays demonstrated binding of c-Jun to the FCGR2B promoter. Phosphorylation of c-Jun was accompanied by transactivation of both FCGR2B promoter variants, whereas dephosphorylation of c-Jun by an inhibitor of c-Jun N-terminal kinase, markedly decreased the promoter activities. The -343 G --> C substitution enabled the specific interaction of the transcription factor Yin-Yang 1 with the mutant FCGR2B promoter. Yin-Yang 1 competed with activating protein 1 for binding at the -343 site, and contributed to the repression of the mutant FCGR2B promoter activity. This mechanism could be responsible for the decreased expression of FcgammaRIIb associated with the -343 C/C homozygous FCGR2B genotype in lupus patients. These findings provide a rationale for the transcriptional defect mediated by the -343 C/C FCGR2B promoter polymorphism associated with systemic lupus erythematosus, and add to our understanding of the complex transcriptional regulation of the human FCGR2B promoter.

Inhibitory Fc Gamma Receptors: From Gene to Disease

Multiple lines of evidence have revealed a key role for inhibitory Fc gamma receptors class IIb (FcgammaRIIb) as negative modulators of innate and adaptive immune responses. Acquired and genetic factors regulate the expression of FcgammaRIIb receptors and modify their inhibitory potential. Recent advances have highlighted the importance of FcgammaRIIb receptors in influencing the development of cancer and autoimmunity. The association of increased FcgammaRIIb expression with tumor development is believed to operate at effector cell level resulting in inhibition of antitumor cytotoxicity. In autoimmune diseases, FcgammaRIIb receptors play a major role in controlling the amplitude of antibody- and immune complex-mediated reactions. Generally, FcgammaRIIb deficiency is associated with increased susceptibility and severity to organ-specific and systemic autoimmunity. This article discusses the proposed mechanisms for FcgammaRIIb deregulation associated with malignant and autoimmune pathology in animal models and human diseases.