Genomic effects of once-weekly, intramuscular interferon-β1a treatment after the first dose and on chronic dosing: Relationships to 5-year clinical outcomes in multiple sclerosis patients

Purpose: To characterize gene expression in multiple sclerosis (MS) patients after the first dose and chronic dosing of 30 μg, once weekly, intramuscular interferon-β1a (IFN-β) and to delineate the pharmacogenomic differences between Good Responders and Partial Responders to IFN-β therapy. Methods: The treatment responses after the first IFN-β dose and chronic IFN-β dosing were assessed in 22 relapsing MS patients (17 females, 5 males; average age: 41.5 ± SD 10.4 years). Gene expression profiles in peripheral blood mononuclear cells were obtained prior to treatment and at 1, 2, 4, 8, 24, 48, 120, 168 h after the first IFN-β dose and at 1, 6 and 12 months after chronic dosing with once-weekly 30 μg IFN-β-1a intramuscularly. Repeated measures statistics with false discovery rate control were used. The functional characteristics, biological pathways and transcription factor sites were analyzed. Results: Of the 1000 genes modulated following the first dose and upon chronic dosing of IFN-β in MS patients, approximately 35% were up-regulated and 65% were down- regulated; the percentage of modulated genes in common was approximately 50%. The expression of the pharmacodynamic mRNA markers of IFN-β effect showed differences in time profiles for the Good Responder and Partial Responders to IFN-β therapy and the Jak-STAT, TNFRSF10B, IL6, TGFβ, retinoic acid and CDC42 pathways were differentially modulated. The patients with side effects to therapy showed differences in the TGFβ1, IFNG/STAT3 and TNF pathways. Conclusions: Gene expression is a valuable tool for understanding the molecular mechanisms of IFN-β action in MS patients.