Fusobacterium nucleatum infection modulates the transcriptome and epigenome of colon cancer cells in an oxygen-dependent manner [RNA-seq]

We studied how Fusobacterium nucleatum infection under hypoxia regulated the epigenome and transcriptome of colon cancer cells. The six datasets that are described in this study are labeled as follows: (a) Normoxia - No Bacteria (NN), (b) Normoxia - infection with Fnn (NF), (c) Normoxia - infection with E. coli (NE), (d) Hypoxia - No Bacteria (HN), (e) Hypoxia - infection with Fnn (HF), and (f) Hypoxia - infection with E. coli (HE). Overall design: We split HCT116 cells into two sets of flasks and conditioned them to hypoxic and normoxic environments. One set of cells continued to proliferate in normoxia (18% oxygen) while the other half was exposed to hypoxia (1% oxygen) for 24 hours. After the initial exposure to the oxygen environment, the conditioned cells were infected with Fnn for 4 hours in their respective oxygen environments in pre-equilibrated media. Infection with non-invasive E. coli with otherwise identical conditions was used as a control to validate host cell response. The cells were further incubated for 24 hours in their respective oxygen environments with pre-equilibrated media before they were extracted for analysis.