HnRNPA2B1 tunes antimycobacterial immune responses in macrophages through alternative splicing of Irgm1

The onset and progression of active tuberculosis disease result from upsetting the delicate balance between Mtb virulence and host defenses. Because it dynamically tunes the functional output of protein expression in cells, alternative splicing (AS), a process by which different mRNAs can be generated from a single gene, is positioned to play a critical role in maintaining an equilibrated Mtb-macrophage host-pathogen interface. To gain insight into how alternative splicing shapes antimycobacterial immune responses, we used RNA sequencing and splicing-aware computational pipelines to quantify alternative splicing in Mtb-infected bone marrow-derived murine macrophages. We found that ~5% of expressed macrophage genes exhibit one or more splicing changes at 8 h post-Mtb infection, highlighting alternative splicing as a key regulatory node in the macrophage response to Mtb. We next sought to identify RNA-binding proteins that play an outsized role in shaping the macrophage transcriptome during Mtb infection. We discovered that the splicing factor heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1) promotes the early induction of inflammatory genes while dampening several type I interferon-stimulated genes in response to Mtb. HnRNPA2B1 also controls alternative splicing of many genes during Mtb infection, including Irgm1, a critical immunity-related GTPase. The balance of Irgm1-long vs. -short is differentially regulated in response to diverse inflammatory cues, and macrophages overexpressing Irgm1-short are defective in autophagosomal targeting, lysosomal homeostasis, and restriction of Mtb replication. These data highlight a key role for AS in shaping the macrophage transcriptome and pinpoint hnRNPA2B1 as a novel restriction factor in the cell-intrinsic response to Mtb.