Epigenetic reader SP140 loss of function drives Crohn’s disease due to uncontrolled macrophage topoisomerases

How mis-regulated chromatin directly impacts human immune disorders is poorly understood. Speckled Protein 140 (SP140) is an immune-restricted PHD and bromodomain-containing epigenetic “reader,” and SP140 loss-of-function mutations associate with Crohn’s disease (CD), multiple sclerosis (MS), and chronic lymphocytic leukemia (CLL). However, the relevance of these mutations and mechanisms underlying SP140-driven pathogenicity remains unexplored. Using a global proteomic strategy, we identified SP140 as a repressor of topoisomerases (TOPs) that maintains heterochromatin and macrophage fate. In humans and mice, SP140 loss resulted in unleashed TOP activity, de-repression of developmentally silenced genes, and ultimately defective microbe-inducible macrophage transcriptional programs and bacterial killing that drive intestinal pathology. Pharmacological inhibition of TOP1/2 rescued these defects. Furthermore, exacerbated colitis was restored with TOP1/2 inhibitors in Sp140−/− mice, but not wild-type mice, in vivo. Collectively, we identify SP140 as a TOP repressor and reveal repurposing of TOP inhibition to reverse immune diseases driven by SP140 loss. [Display omitted] •Mutations within immune epigenetic reader SP140 associate with Crohn’s disease (CD)•Proteomics-revealed SP140 represses topoisomerases (TOP1/2) at heterochromatin•Mice and CD patients with loss of SP140 have uncontrolled macrophage TOP1/2•TOP inhibitors rescued defective macrophage function and colitis due to SP140 loss SP140 acts as a repressor of topoisomerases and maintains macrophage cytokine and bacterial killing functions, preventing inflammatory conditions such as Crohn’s disease.