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. Overall design: 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