Spatial Transcriptomics of Controlled vs Uncontrolled Tuberculosis in a Mouse Model

To further characterize gene expression in controlled vs uncontrolled tuberculosis lung lesions, we performed spatial transcriptomics analysis using the NanostringGeoMX Digital Spatial Profiler (DSP) system. Based on routine hematoxyline and eosin histopathology, we selected lungs from 2 mice with paucibacillary controlled lesions and 2 mice with advanced uncontrolled multibacillary lesions with necrotic areas. Additional FFPE sections were stained with fluorescent CD45-, pan-keratin-specific antibodies and DAPI. Diseased regions of interest (ROI) were selected to focus on myeloid-rich areas avoiding necrosis and tertiary lymphoid tissue . Eight ROI each of contolled and uncontrolled lesions (respectively) were studied. The profiling used the Mouse Whole Transcriptome Atlas (WTA) panel which targets ~21,000+ transcripts for mouse protein coding genes