At flare, three transcripts were uniquely expressed in CR, seven transcripts in PR, and 20 transcripts in NR when compared with normal. When compared with NR flares, CR flares showed increased MME, FADD, and CD274 and decreased ITGB2 and C1S expression. Change in transcript expression from initial to repeat biopsy was compared within each group and between groups. From biopsy 1 to biopsy 2, the CR group showed increased NCAM1 and decreased ILRL1 and FKBP5 expression. The NR group showed increased IL1RAP and CD5 and decreased C7, IL28B, and IL12RB1 expression. When compared with the CR group, the NR group showed increased IL17a, NOS2, FCAR and IL1RAP and decreased NCAM1, C7, and IL28B expression. NR flares had significant activation of T-cell and B-cell receptor signaling, IL-10, STAT3, and TNF-R pathways when compared with CR flares. Compared with NR flares, CR flares showed significant activation of T-cell regulation, antigen presentation, and apoptotic pathways.