Systems biology mapping of rBCG-LTAK63-induced protection against tuberculosis reveals the significance of autophagy and circadian rhythm regulation by cAMP

Using systems biology and RNA sequencing data from lung cells, we investigated the immune mechanisms of protection induced by this vaccine in mice, both after immunization and following challenge. The RNA-seq data were analyzed using IPA (Ingenuity Pathways Analysis), CEMiTools (modular co-expression analysis). The RNA-seq derived results were analysed through correlation with immune response and disease outcomes, such as bacillary load, pathology score (infiltrated cell number, inflammatory area, and functional area). Bulk RNA-seq applyed to comprehensively study the impact of rBCG-LTAK63 vaccination in mice at various time points before and after Mtb exposure, aiming to understand how these alterations influence lung immune response and contribute to TB protection. Babl/c mice were immunized and lungs and lymph nodes were collected, for RNA-seq, at 7, 90 after immunization. At 90 days after immunization, animals that left were challenged with 500 CFU of Mycobacterium tuberculosis H37Rv, via intranasal instilation.At 97 and 120 days post immunization (7 days and 30 days post challenge), the lungs were collected, RNA sequencing. Eight samples were sequenced in each timepoints. Two saline controls were included (one in 7 dpi and other in 90 dpi). The infection control group, were included at 7dpc and 30 dpc.