190 Highly efficient, massively-parallel single-cell RNA-seq analysis of leprosy skin lesions identifies IL-1β as a key regulator of an antimicrobial gene network linked to host defense

Reversal reactions (RR) in leprosy provide an opportunity to investigate mechanisms of host defense against bacterial infections in skin, as patients upgrade from the disseminated lepromatous (L-lep) form to the self-limiting tuberculoid (T-lep) form, often associated with significant tissue injury. Here we performed single-cell RNA-seq to study gene networks associated with host defense comparing lesions from RR vs. L-lep patients (n=10). We detected 43,363 genes in 21,318 cells, with an average of 741 genes and 3,556 transcripts per cell. The 11 subclusters of T cells, myeloid cells, keratinocytes (KC), endothelial cells (EC) and fibroblasts (FB) that were enriched in RR lesions contained 567 genes that encoded programs known to be involved in antimicrobial responses. In addition, pseudotime analysis identified differentiation of macrophages (MF) and KC in the progression from L-lep to RR. We identified IL-1β as a key upstream regulator of the antimicrobial gene network as well as the differentiation programs of both MF and KC. In addition to the direct regulation of genes involved in the vitamin D antimicrobial pathway (IFNG, CD40LG, CD40, IL32, VDR), IL-1β induced the antimicrobial chemokines (CCL2, CCL4, CCL8, CCL20; CXCL1, CXCL2, CXCL3, CXCL8, CXCL11; CX3CL1) and antimicrobial proteins (GBP2; MMP9, MMP14; S100A6, S100A10) in different cell types. IL-1β regulated Th17 cell responses including the antimicrobial protein IL-26. IL-1β coordinates the antimicrobial response from diverse cell types in leprosy as well as inducing differentiation of MF, KC and T cells, such that blockade of the IL-1 receptor could provide an opportunity to mitigate concomitant tissue damage that leads to permanent nerve injury in RR patients.