Integrated transcriptomic and quantitative proteomic analysis identifies potential RNA sensors that respond to the Ag85A DNA vaccine.

OBJECTIVE: DNA vaccine has emerged as a promising approach with potential for Tuberculosis (TB) prevention in adults. However, the mechanism behind DNA vaccines is still largely unknown. MATERIALS AND METHODS: Utilizing the CRISPR/Cas9 technique, we engineered Ag85A mutated dendritic cells (Ag85A-M-DCs) in which the Ag85A mRNA derived from Mycobacterium tuberculosis was expressed but not the corresponding protein. Control cells (Ag85A-DCs) expressed both Ag85A mRNA and protein. To better understand the mechanism of antigen presentation following DNA vaccination, integrated transcriptomic and proteomic analysis of dendritic cells (DCs), Ag85A-DCs, and Ag85A-M-DCs were performed. RESULTS: A total of 723, 278, and 933 differentially expressed genes (DEGs), and 209, 134, and 509 differentially expressed proteins (DEPs) were identified between Ag85A-M-DCs and DCs, Ag85A-DCs and DCs, and Ag85A-M-DCs and Ag85A-DCs, respectively. Integration analysis detected 59, 15, and 64 associated DEGs/DEPs with the same expression trend between Ag85A-M-DCs and DCs, Ag85A-DCs and DCs, and Ag85A-M-DCs and Ag85A-DCs, respectively. KEGG pathway analysis showed that chemokine signaling pathway and MAPK signaling pathway were enriched in all three pairs of comparisons. The protein and protein interaction network revealed that ANXA1 was in the top 10 high-degree hub genes closely related to other genes in all three pairs of comparisons. CONCLUSION: The results indicated that Ag85A DNA vaccine might transmit immunogenicity information and induce immune responses by activating chemokine signaling pathway and MAPK signaling pathway. ANXA1 may serve as a key target molecule of the Ag85A vaccine with additional potential for TB prevention.