MMP1 and Granuloma: To confirm the presence of the MMP1+CXCL5+ phenotype via an orthogonal method, we stained sections of human lung from the same surgical cohort that contained distinct TB granuloma (5 μm sections from two patients) for associated gene products of the MMP1+CXCL5+ subcluster: COL1, TDO2, MMP1, MMP3, and CA12, together with PI-15 and CTHRC-1, which were also significantly upregulated in this subcluster (Fig. S4 B and Data S8).