Fusobacterium nucleatum (F. nucleatum) species was shown to be enriched in human CRC (Ito et al., 2015) and to correlate with poor prognosis (Yu et al., 2016). Bacteriophage (‘phage’) are viruses that specifically infect bacteria and play a critical role in regulating bacterial populations. We previously showed the isolation of 12 novel natural phages targeting all 4 sub-species of F. nucleatum: animalis, nucleatum, vincentii, polymorphum (Zelcbuch et al., AACR, 2020). The aims of the current study were to develop (1) Novel technologies and algorithms for differentiating between F. nucleatum subspecies while analyzing their abundance and prevalence in CRC samples (2) Synthetic biology tools for introducing therapeutic payloads into the F. nucleatum phage genome.
For F. nucleatum subspecies analysis, 59 pairs of frozen CRC tumor and normal adjacent tissues were subjected to species specific qPCR for calculating the absolute number of F. nucleatum cells. Targeted NGS of the NusG gene, was carried out to analyze the relative abundance of F. nucleatum subspecies. For phage engineering, plasmids containing payloads for immuno-stimulation treatment, such as IL15 and GM-CSF, were constructed and introduced into E.coli for payload bioactivity verification.
Targeted-NGS revealed that F. nucleatum animalis was the most prevalent subspecies in the tested cohort (40/57 [70.1%]) and was significantly expressed in tumors compared to adjacent tissues (p= 7.3 E-03). The prevalence of other subspecies was lower: polymorphum (23/59 [39.8%]); vincentii or nucleatum– (11/59 [18.6%]). Payloads bioactivities were validated in E.coli: IL-15 induced significant bioluminescence expression in a reporter -based assay and a high proliferation rate in primary murine NK cells, GM-CSF induced a high proliferation rate of FDC-1-P1 cell line. Next steps include inserting the payloads into the phage genome and validating their functionality in animal models.
The high prevalence and abundance of the F. nucleatum animalis in CRC samples suggests it may serve as a target for phage-based treatment. Delivery of an immune-stimulating payload to CRC by engineered phage may offer novel treatment approaches for CRC patients.
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All authors have declared no conflicts of interest.