Background/Purpose:  Gene expression studies support a pivotal role for type I interferon (IFN) in SLE. Previous work using a modular repertoire analysis based on co-clustered gene sets, has demonstrated that the SLE IFN signature is not restricted to a type I IFN signature, but involves the gradual activation of 3 distinct IFN modules (M1.2, M3.4 and M5.12) driven by various IFN types. The aim of this study was to refine and discover novel modular interactions in adult SLE patients.

Methods: Consecutive SLE patients fulfilling the ACR criteria were enrolled (n=157 samples). Disease activity (DA) was measured according to the SELENA-SLEDAI score. Microarray data were generated using Illumina beadchips. Modular repertoire analyses were performed using the second generation of a blood modular framework comprising 260 modules. Modules with 20% transcripts differentially expressed compared to healthy matched controls were considered active. A novel graph theoretic approach, previously applied to the analysis of somatic evolution in cancer (unpublished), was used to generate an ordered, branching progression model of modular activation in which upstream module activity predisposes the activation of downstream modules. An SLE-specific graph based on module activation in our dataset was built in order to generate hypotheses regarding disease progression in SLE. Trajectories of a focused subgraph were enumerated and samples were clustered to their most likely trajectory group. Significance to clinical characteristics was evaluated using Fisher’s exact test and ANOVA, for categorical and continuous characteristics, respectively.

Results:  The graph theoretic analysis revealed two distinct patterns involving IFN and neutrophil related modules. Both patterns involved the upregulation of M1.2 followed by M3.4. At this point, the patterns split into the activation of either M5.12 or the M5.15 neutrophil module. Along the shared trajectory, we observed a monotonic increase in DA, dsDNA titers, and corticosteroid dosage. The subjects on the neutrophil (M5.15) trajectory had a marked increase in DA and corticosteroid dosage, although dsDNA levels were unchanged. Moreover, the neutrophil trajectory also had a larger (p=0.04) enrichment for renal involvement (80%) than the M5.12 IFN trajectory (40%). 

Conclusion:  Our analysis revealed a refinement within the hierarchical structure of the peripheral blood IFN modules previously described. Two subgroups, defined by progression along disjoint paths bolstered by their association to overall DA, active nephritis, dsDNA levels, and corticosteroid dosage, are identified. This suggests a dual mode of disease progression in SLE, with either the completion of IFN signature (to include IFNγ) or the activation of neutrophil path associated with renal involvement.