An antisense oligomer conjugate with unpredicted bactericidal activity against Fusobacterium nucleatum

Fusobacteria are commensal members of the oral microbiome that can spread from their primary niche and colonize distal sites in the human body. Their enrichment in colorectal and breast cancer tissue has been associated with tumor growth, metastasis, and chemotherapeutic resistance. The use of non-selective antibiotics to remove fusobacteria impairs tumor progression, but prolonged application risks side effects such as gastrointestinal problems and dysbiosis. Species-specific antisense antibiotics based on peptide nucleic acid (PNA) have shown efficacy in many Gram-negative species, suggesting that antisense PNAs may also enable a tailored depletion of fusobacteria. Here, we have investigated the antibacterial potential of cell-penetrating peptide (CPP)-PNA conjugates targeting the mRNA of putative essential genes in Fusobacterium nucleatum . Unexpectedly, we observed no growth inhibition with any of the target-specific PNAs, but identified a non-targeting control CPP-PNA (FUS79, (RXR) ₄ XB-GACATAATTGT) as a potent growth inhibitor of F. nucleatum . Our data suggest that the CPP and specific sequence features of FUS79 are responsible for its activity, rather than an antisense effect. Interestingly, FUS79 also inhibits the growth of five additional fusobacterial strains but not of F. nucleatum ssp. vincentii (FNV). RNA-seq analysis indicates that FUS79 induces a membrane stress response in a vulnerable F. nucleatum strain but not in FNV. Collectively, our attempt at developing antisense antibiotics for fusobacteria discovers a potent growth inhibitor, whose bactericidal effect appears independent of target-specific mRNA inhibition.