Topoisomerase IIIb protects from immune dysregulation and tumorigenesis

Topoisomerase III-beta (Top3b) reduces nucleic acid torsional stress and intertwining generated during RNA and DNA metabolism while protecting the genome from pathological R-loops, which otherwise result in DNA breakage and genome instability. By studying Top3b knockout mice (Top3b-KO), we find that the loss of Top3b accelerates the development of spontaneous atypical lymphoid hyperplasia and lymphomas arising in spleens and lymph nodes, the organs with prominent Top3b expression. Aging Top3b-KO mice also display splenomegaly and systemic immune alterations including neutrophilia and lymphopenia consistent with chronic inflammation. At the molecular level, Top3b deficiency causes genome-wide R-loop accumulation in splenocytes as measured by CUT&Tag sequencing. Increased R-loops are associated with genomic breaks and activation of immune signaling pathways including innate and adaptive immune cell signaling, IL-4 signaling, FAK signaling and cGAS-STING. Additionally, knocking-out Top3b promotes the rapid development of syngeneic EL4 T-cell lymphomas. In conclusion, our work suggests that Top3b protects from lymphoma, tumorigenesis and immune dysregulations. To investigate the roles of topoisomerase III-beta (Top3b) in preventing tumorigenesis and immune dysregulation we performed R-loop CUT&Tag sequencing using S9.6 antibody (R-loop CUT&Tag) to map genomic locations of R-loops and genome-wide transcriptomics in WT vs Top3b-KO splenocytes. We isolated RNA from three replicates of WT and three replicates of Top3b-KO splenocytes followed by ribo-depleted total RNA-seq.