Transcriptional profilling of pathogen-specific T helper cells

Introduction: We reported a in vitro pathogen-specific priming system to using pathogen lysate stimulated splenic CD11c+ DCs to differentiate pathogen-specific murine T helper cells. This method allowed us to compare side-by-side transcriptional profiles of bulk T helper cells that are specific to distinct pathogens and to study their composition and functionality. Method: We stimulated mouse splenic CD11c+ DCs with 10ug/ml Lm or Cr lysate for 5hours. The DCs were subsequently washed and co-cultured at 1:5 ratio to purified, CFSE-labeled CD62L+CD44- mouse naïve CD4 T cells. At day-7, CD90+CFSE- (Pathogen-specific Th cells) or CD90+CFSE+ (naive T cells) were sorted from the same culture and were subjected to RNA isolation, library prep and subsequent sequencing. Conclusion: We found that Lm- and Cr-specific Th cells have distinct transcriptomes and contained distinct Th subtypes. Lm-specific Th cells contained higher expressions of Th1-associated cytokines, while Cr-specific Th cells contained higher levels of Th17 associate cytokines and transcription factors. In addition, we have identified heterogeneity within the pathogen-specific Th cells, as they express various cytokines from multiple Th lineages. Lastly, we found a vast variety of genes differentially expressed between Lm- and Cr-specific Th cells, indicating that different pathogen-stimulated DCs denote distinct function and developmental cues to T cells during differentiation. mRNA profiles of Lm- or Cr-specific Th cells were generated by Illumina sequencing in duplicate. CFSE+CD90+ naïve T cell from Lm and Cr condition cultures served as control.