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

Alternative splicing (AS) has been implicated in host responses to diverse pathogens, but our understanding of its role in Mycobacterium tuberculosis infection remains incomplete. Using RNA-sequencing and splicing-aware computational pipelines, we quantified AS in Mtb-infected bone marrow-derived macrophages (BMDMs). We found that ~5% of expressed macrophage genes exhibit one or more splicing changes at 8h post-Mtb infection, highlighting AS as a key layer of regulation in the macrophage response to intracellular pathogens. 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 hnRNPA2B1 promotes the early induction of inflammatory genes while dampening several type I interferon-stimulated genes. HnRNPA2B1 also controls alternative splicing of transcripts, notably Irgm1, a critical immunity-related GTPase. We report that the abundance of Irgm1-long, the canonical isoform, and Irgm1-short, an isoform lacking a lysosomal targeting domain is differentially regulated in response to diverse inflammatory cues. Macrophages overexpressing Irgm1-short are defective in restricting Mtb replication and accumulate LC3+ bacilli. 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.