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The mechanisms governing neutrophil response to  Mycobacterium tuberculosis  remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific  in vivo  biotinylation in zebrafish to analyse the initial response of neutrophils to  Mycobacterium marinum , a close genetic relative of  M .  tuberculosis  used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including  caspase b ,  NLRC3  ortholog ( wu: fb15h11 ) and  il1β . Crispr/Cas9-mediated knockout of  caspase b , which acts by proteolytic processing of il1β, results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterial infection, thus impairing granuloma development. We also show that a number of immediate early response genes (IEGs) are responsible for orchestrating the initial neutrophil response to mycobacterial infection. Further perturbation of the IEGs exposes egr3 as a key transcriptional regulator controlling  il1β  transcription.

Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum