Transcriptomic analysis of naïve B cells and plasma cells as well as in vitro stimulated B cells from Blimp1-GFP reporter mice [Blimp1_reporter_PC_stim]

Though it is known that plasma cells utilize the unfolded protein response to remodel their ER it is generally believed that this follows Blimp1-mediated transcriptional and translational increases in immunoglobulin protein. In this study we utilize Blimp1 reporter mice to examine the earliest activation of UPR-affiliated gene expression in plasma cell inductive stimulation of B cells. We combine in-vivo gene expression of follicular B cells, marginal zone B cells from spleen and short and long lived plasma cells from bone marrow with in-vivo generated activated B cells and plasma cells from the same mice to examine gene expression before and after Blimp1-upregulation. Using a novel in-vitro stimulation approach we separate those UPR-affiliated genes activated by B cell activation and those requiring a plasma cell inductive stimulus. We report here that these plasma cell specific UPR-affiliated genes are activated in absence of ER-stress prior to upregulation of Blimp1. Overall design: Samples are biological replicates from five mice across 4 in-vivo cell types and 7 ex-vivo stimulated cell cultures. cDNA was prepared from RNA with 3' polyA capture method. Transcript abundance was measured by Kallisto psuedo-alignment and normalized (voom) and differential expression was assessed using limma.