CITE-seq analysis of Mycobacterium tuberculosis infected B6 and Sp140-deficient mouse lungs

Mycobacterium tuberculosis (Mtb) causes 1.5 million deaths annually. Active tuberculosis correlates with a neutrophil-driven type I interferon (IFN) signature, but the underlying cellular mechanisms remain poorly understood. We found that interstitial macrophages (IMs) and plasmacytoid dendritic cells (pDCs) are dominant producers of type I IFN during Mtb infection in mice and non-human primates, and pDCs localize near human Mtb granulomas. Depletion of pDCs reduces Mtb burdens, implicating pDCs in tuberculosis pathogenesis. During IFN-driven disease, we observe abundant DNA-containing neutrophil extracellular traps (NETs) known to activate pDCs. Single cell RNA-seq indicates that type I IFNs act on IMs to impair their responses to IFNg, a cytokine critical for Mtb control. Cell type-specific disruption of the type I IFN receptor suggests IFNs act on IMs to inhibit Mtb control. We propose pDC-derived type I IFNs, driven by NETs, act on IMs to drive bacterial replication, further neutrophil recruitment, and active tuberculosis disease. Overall design: Lungs were harvested from C57BL/6 and Sp140-deficient naïve mice (2 animals per genotype) or mice infected with Mycobacterium tuberculosis for 25 days (3 animals per genotype). Myeloid cells were magnetically enriched based on Ly6G and CD64. After enrichment, infected cells were isolated by Fluorescence-activated cell sorting (FACS) to separate Mtb infected and bystander myeloid cells based on Wasabi expression. Naive samples where isolated by FACS into macrophages and a monocyte/neutrophil mixture, which were pooled at a 1 to 2 ratio for greater macrophage representation.