A gene expression module that identifies low-density granulocytes in the blood of patients with systemic lupus erythematosus is associated with low complement, elevated anti-dsDNA titer and both the interferon and TNF signatures

Abstract SLE is an autoimmune disease characterized by the presence of abnormal low-density granulocytes (LDG) with a heightened capacity for spontaneous NETosis. To characterize LDGs in SLE, gene expression profiles derived from isolated LDGs were characterized by Weighted Gene Co-expression Network Analysis, and a 92 gene module was identified. This module contains 30 genes with the Neutrophil Degranulation GO designation and many genes associated with DNA synthesis and proliferation. Comparison with gene expression by bone marrow neutrophil precursors demonstrated that the module of genes was most similar to that expressed by promyelocytes/myelocytes. The LDG gene signature was assessed in gene expression data sets from SLE whole blood (WB), PBMC, kidney, synovium, and skin. The LDG module was enriched consistently in blood but inconsistently in tissues. Lack of granule protein transcripts in tissues suggests that LDGs are not enriched in SLE affected organs. The LDG gene signature was also analyzed in WB and PBMC of 1,417 SLE patients by Gene Set Variation Analysis (GSVA). 35% of inactive patients and 50% of active patients expressed an LDG signature, which showed a significant but modest correlation with disease activity as measured by the SLE Disease Activity Index (r = 0.16, p = 4.1E-9). The LDG signature was also associated with the presence of anti-dsDNA (p < 1E-6), decreased levels of C3 and C4 (p < 1E-6), the type 1 interferon signature (p < 1E-11) and a module of genes induced by TNF (p < 1E-15, all by Fisher’s exact test). These findings suggest that LDGs are a population of immature neutrophils over-represented in the blood of SLE patients in association with cytokine stimulation, the presence of autoantibodies, and complement consumption.