Th1 polarization in Bordetella pertussis vaccine responses is maintained through a positive feedback loop

Outbreaks of Bordetella pertussis (BP), the causative agent of whooping cough, continue despite broad vaccination coverage and have been increasing since vaccination switched from whole-BP (wP) to acellular BP (aP) vaccines. wP vaccination has been associated with more durable protective immunity and an induced Th1 polarized memory T cell response. Here, a multi-omics approach was applied to profile the immune response of 30 wP and 31 aP-primed individuals and identify correlates of T cell polarization before and after Tdap booster vaccination. We found that transcriptional changes indicating an interferon response on day 1 post-booster along with elevated plasma concentrations of IFN-γ and interferon-induced chemokines that peaked at day 1-3 post-booster correlated best with the Th1 polarization of the vaccine-induced memory T cell response on day 28. Our studies suggest that wP-primed individuals maintain their Th1 polarization through this early memory interferon response. This suggests that stimulating the interferon pathway during vaccination could be an effective strategy to elicit a predominant Th1 response in aP-primed individuals that protects better against infection. 2 million PBMC were lysed using QIAzol Lysis Reagent (Qiagen). Samples were stored at -80C until RNA extraction. RNA was extracted using the miRNeasy Mini Kit (Qiagen) including DNase treatment according to the manufacturer's instructions. The Smart-seq2 protocol was used to perform full-length bulkRNAseq. Briefly, RNA was captured using oligo-poly(dT)-30 primers and reverse transcription was performed using 50-template switching oligos (LNA technologies, Exicon). cDNA was pre-amplified using PCR and purified twice by magnetic beads (volume ratio 0.6x and 0.8x Ampure-XP magnetic beads, Beckman Coulter). cDNA was measured using capillary electrophoresis (Fragment analyzer, Advance analytical) and 0.5 ng of cDNA was used to generate indexed Illumina libraries (Nextera XT library preparation kit, Illumina). Each library's fragment size was measured by capillary electrophoresis (Fragment analyzer, Advance analytical) and was quantified (Picogreen, Thermofisher). Libraries were pooled at equal molar concentration and sequenced paired-end to a minimum depth of 15 million reads with each a length of 100 base pairs.