Use of type I interferon-inducible mRNAs as pharmacodynamic markers and potential diagnostic markers in trials with sifalimumab, an anti-IFNα antibody, in systemic lupus erythematosus

Abstract

Type I interferons are implicated in the pathogenesis of systemic lupus erythematosus (SLE). Type I interferon-inducible mRNAs are widely and concordantly overexpressed in the periphery and involved tissues of a subset of SLE patients, and provide utility as pharmacodynamic biomarkers to aid dose selection, as well as potential indicators of patients who might respond favorably to anti-IFNα therapy in SLE. We implemented a three-tiered approach to identify a panel of type I interferon-inducible mRNAs to be used as potential pharmacodynamic biomarkers to aid dose selection in clinical trials of sifalimumab, an anti-IFNα monoclonal antibody under development for the treatment of SLE. In a single-dose escalation phase 1 trial, we observed a sifalimumab-specific and dose-dependent inhibition of the overexpression of type I interferon-inducible mRNAs in the blood of treated subjects. Inhibition of expression of type I interferon-inducible mRNAs and proteins was also observed in skin lesions of SLE subjects from the same trial. Inhibiting IFNα resulted in a profound downstream effect in these SLE subjects that included suppression of mRNAs of B-cell activating factor belonging to the TNF family and the signaling pathways of TNFα, IL-10, IL-1β, and granulocyte-macrophage colony-stimulating factor in both the periphery and skin lesions. A scoring method based on the expression of type I interferon-inducible mRNAs partitioned SLE patients into two distinct subpopulations, which suggests the possibility of using these type I interferon-inducible genes as predictive biomarkers to identify SLE patients who might respond more favorably to anti-type I interferon therapy.

Figure 1

Relative expression of type I interferon-inducible mRNAs in the whole blood of rheumatic disease patients. Representative heatmap visualizing the relative expression of 807 type I interferon-inducible mRNAs in whole blood from 106 systemic lupus erythematosus (SLE) subjects (red), 20 polymyositis (PM) subjects (green), 22 dermatomyositis (DM) subjects (blue), and 66 rheumatoid arthritis (RA) subjects (pink) compared with whole blood from 24 healthy subjects (black). Fold change values are graphed for each subject and are grouped by disease.

Figure 2

Distribution and density of type I interferon signature scores in systemic lupus erythematosus patients. (a) Distribution of the type I interferon signature scores in 202 systemic lupus erythematosus (SLE) patients measured at baseline. The type I interferon signature score is calculated as the median fold change (relative to a pooled normal healthy donor sample) of the 21-member type I interferon-inducible transcript pharmacodynamic (PD) marker panel for each patient. The cut-off point for an SLE patient scored as type I interferon signature positive was identified at a value of at least 2 (1 on a log₂ scale), as represented by both the red points in (a) and the rightmost density in (b). Patients scored as type I interferon signature negative are represented by the blue points in and the leftmost density in (b). y axis, type I interferon signature score calculated for the 21-member mRNA PD marker panel on a log2 scale. x axis, type I interferon signature score calculated for the 21-member transcript PD marker panel on a log₂ scale. (b) Density plot of the type I interferon signature scores for these 202 SLE patients. Two distributional modes are illustrated, indicating a clear partitioning between the SLE populations of type I interferon signature positive and negative.

Figure 3

Sifalimumab inhibition of overexpression of the type I interferon signature in systemic lupus erythematosus patients. Dose responses of sifalimumab therapy in whole blood of systemic lupus erythematosus (SLE) patients with an overexpressed type I interferon-inducible gene signature as measured by the type I interferon-inducible gene signature score. Neutralization of the 21 type I interferon-inducible mRNAs by treatment averaged for each dose cohort observed from day 0 (pretreatment) to day 7 (posttreatment). y axis, values calculated as the fraction of neutralization of certain days post-treatment/pretreatment (day 0 predosing), subtracted from 1 for each patient separately. Those values that exceed 1 from this formula are a result of an increase in transcript levels of type I interferon-inducible mRNAs in whole blood following treatment (mostly in placebo-treated SLE patients). Significance for the difference between dose levels and placebo treatment using Hotelling's T² test: 0.3 mg/kg, P = 0.09; 1 mg/kg, P = 0.04; 3 mg/kg, P = 0.01; 10 mg/kg, P = 0.007; 30 mg/kg, P = 0.004. From top to bottom: red line, placebo; blue line, 0.3 mg/kg sifalimumab; green line, 1 mg/kg sifalimumab; orange line, 3 mg/kg sifalimumab; black line, 10 mg/kg sifalimumab; pink line, 30 mg/kg sifalimumab.

Figure 4

Sifalimumab treatment in a responding systemic lupus erythematosus patient. Effect of sifalimumab treatment in a single systemic lupus erythematosus patient who responded to 10 mg/kg drug treatment. (a) Immunohistochemical analyses of paired biopsies (days 0 predosing and day 14 postdosing) from lesional skin obtained from this patient. BDCA2 is a specific marker for plasmacytoid dendritic cells, and CD83 is a marker for myeloid dendritic cells. IP10 is a type I interferon-inducible protein whose overexpression that was observed in lesional skin at day 0 was decreased at day 14. There is a concordant reduction of IP10 protein expression and mRNA expression in the lesional skin of this patient with sifalimumab treatment. (b) Skin lesion clearance in this patient following sifalimumab treatment (day 0 predosing; days 7, 14, and 28 postdosing).