CD4+CD28+KIR+CD11ahi T cells correlate with disease activity and are characterized by a pro-inflammatory epigenetic and transcriptional profile in lupus patients
Introduction
Systemic lupus erythematosus is a chronic multisystem autoimmune disease characterized by periods of disease flares and remission. Genetic susceptibility might explain at least in part familial aggregation of the disease, and plays a role in determining age of disease onset, severity, and disease heterogeneity [1], [2], [3]. Epigenetic aberrancies also play a role in the pathogenesis of lupus [4]. Lupus T cells are characterized by reduced expression and activity of the maintenance DNA methyltransferase DNMT1, resulting in T cell hypomethylation. Several factors might be mechanistically involved in reduced DNMT1 expression and the methylation defect in lupus T cells [5]. These include defective ERK pathway signaling, and increased expression and activity of PP2A, mTOR, and GADD45a [6], [7].
CD4+ T cells from lupus patients are characterized by robust demethylation in interferon-regulated genes [8]. In addition, CD4+ T cells in lupus are characterized by overexpression of several methylation sensitive genes, including CD11a, CD70, Perforin, CD40L, and the KIR gene cluster [9]. Normal CD4+ T cells treated with DNA demethylating agents overexpress these same genes similar to lupus T cells, and become autoreactive in vitro [10]. Further, demethylated T cells or T cells with induced defect in DNMT1 expression can cause autoimmunity in animal models [11], [12], [13].
Using multi-color flow cytometry, a novel CD4+CD28+ T cell subset characterized by cell surface CD11ahi and KIR expression was recently identified in patients with active lupus [14]. This T cell subset also expresses other methylation sensitive genes known to be overexpressed on lupus T cells, including CD70 and CD40L. Indeed, treating T cells from normal healthy individuals with DNA demethylating agents results in expansion of this T cell subset [14]. The goal of this study was to characterize this novel T cell subset to reveal the complete repertoire of genes that identify this subset and therefore understand its functional role upon disease pathogenesis. In addition, we aimed to determine if expansion of this T cell subset interacts with genetic risk to predict disease activity in lupus patients.
Section snippets
Lupus patients
Female participants previously diagnosed with lupus were included in this study. All patients fulfilled the American College of Rheumatology classification criteria for SLE [15]. A Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) score was calculated at the clinical visit concurrently with enrollment in the study and blood sampling draw. Patients who had received cyclophosphamide within the past 6 months or who were on methotrexate were excluded from this study, as cyclophosphamide
In vitro generated CD4+CD28+KIR+CD11ahi T cells are demethylated and characterized by a pro-inflammatory transcriptional profile
We previously demonstrated that CD4+CD28+KIR+CD11ahi T cells express proteins of other methylation sensitive genes known to be hypomethylated in lupus T cells, such as CD70 and CD40L, and that treating CD4+ T cells with the DNA methylation inhibitor 5-azacytidine results in the generation of CD4+CD28+KIR+CD11ahi T cells [14]. To assess the extent of DNA demethylation in this T cell subset, we evaluated genome-wide DNA methylation changes in experimentally derived CD4+CD28+KIR+CD11ahi T cells
Discussion
The role of CD4+ T cell DNA hypomethylation in the pathogenesis of lupus has been thoroughly investigated [4]. We described a demethylated T cell subset characterized by KIR and CD11a overexpression in lupus patients. The KIR locus is comprised of 15 KIR genes, which are most commonly expressed on natural killer cells. However, because regulation of the KIR locus is methylation sensitive, KIR genes have previously been shown to be expressed in the context of lupus [14], [34]. Furthermore, KIR
Conclusion
Our findings indicate that the novel CD4+CD28+KIR+CD11ahi T cell subset is demethylated and characterized by pro-inflammatory chromatin accessibility and transcriptional profiles in lupus patients. We identified a number of pathways and specific genes overexpressed in this T cell subset. These data suggest that eliminating CD4+CD28+KIR+CD11ahi T cells or blocking some of the specific pro-inflammatory characteristics we identified might provide novel therapeutic options for lupus.
Conflict of interest
None of the authors has any financial conflict of interest to disclose.
Competing interest
None declared.
Acknowledgements
This work was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health grants number U19AI110502 and R01AI097134.
References (40)
- et al.
The critical role of epigenetics in systemic lupus erythematosus and autoimmunity
J. Autoimmun.
(2016) - et al.
Genome-wide DNA methylation study suggests epigenetic accessibility and transcriptional poising of interferon-regulated genes in naive CD4+ T cells from lupus patients
J. Autoimmun.
(2013) - et al.
DNA hypomethylation in inflammatory arthritis: reversal with methotrexate
J. Lab. Clin. Med.
(1996) - et al.
Sex-specific differences in the relationship between genetic susceptibility, T cell DNA demethylation and lupus flare severity
J. Autoimmun.
(2012) - et al.
CD4(+) T cells epigenetically modified by oxidative stress cause lupus-like autoimmunity in mice
J. Autoimmun.
(2015) - et al.
Genetic advances in systemic lupus erythematosus: an update
Curr. Opin. Rheumatol.
(2017) - et al.
Early disease onset is predicted by a higher genetic risk for lupus and is associated with a more severe phenotype in lupus patients
Ann. Rheum. Dis.
(2011) - et al.
Phenotypic associations of genetic susceptibility loci in systemic lupus erythematosus
Ann. Rheum. Dis.
(2011) - et al.
Epigenetic variability in systemic lupus erythematosus: what we learned from genome-wide DNA methylation studies
Curr. Rheumatol. Rep.
(2017) - et al.
Decreased Ras-mitogen-activated protein kinase signaling may cause DNA hypomethylation in T lymphocytes from lupus patients
Arthritis Rheum.
(2001)
Metabolic control of the epigenome in systemic Lupus erythematosus
Autoimmunity
Dissecting complex epigenetic alterations in human lupus
Arthritis Res. Ther.
Phenotypic and functional similarities between 5-azacytidine-treated T cells and a T cell subset in patients with active systemic lupus erythematosus
Arthritis Rheum.
Treating activated CD4+ T cells with either of two distinct DNA methyltransferase inhibitors, 5-azacytidine or procainamide, is sufficient to cause a lupus-like disease in syngeneic mice
J. Clin. Investig.
Mechanism of drug-induced lupus. I. Cloned Th2 cells modified with DNA methylation inhibitors in vitro cause autoimmunity in vivo
J. Immunol.
Defective T-cell ERK signaling induces interferon-regulated gene expression and overexpression of methylation-sensitive genes similar to lupus patients
Genes Immun.
Characterisation of an epigenetically altered CD4(+) CD28(+) Kir(+) T cell subset in autoimmune rheumatic diseases by multiparameter flow cytometry
Lupus Sci. Med.
Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus
Arthritis Rheum.
Clinical and immunologic effects of monthly administration of intravenous cyclophosphamide in severe systemic lupus erythematosus
N. Engl. J. Med.
Trimmomatic: a flexible trimmer for Illumina sequence data
Bioinformatics
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These two authors equally contributed to this work.